Starting phenix.real_space_refine on Sat Jul 4 13:12:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8emx_28268/07_2026/8emx_28268.cif Found real_map, /net/cci-nas-00/data/ceres_data/8emx_28268/07_2026/8emx_28268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8emx_28268/07_2026/8emx_28268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8emx_28268/07_2026/8emx_28268.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8emx_28268/07_2026/8emx_28268.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8emx_28268/07_2026/8emx_28268.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8emx_28268/07_2026/8emx_28268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8emx_28268/07_2026/8emx_28268.map" } resolution = 3.3 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= 0.003 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11643 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 78 5.16 5 C 7374 2.51 5 N 2039 2.21 5 O 2222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11714 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5926 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 47, 'TRANS': 695} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2521 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 414 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2513 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 339 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.72, per 1000 atoms: 0.23 Number of scatterers: 11714 At special positions: 0 Unit cell: (90.308, 128.288, 140.948, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 78 16.00 O 2222 8.00 N 2039 7.00 C 7374 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 569.9 milliseconds 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2832 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 23 sheets defined 24.7% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 removed outlier: 3.657A pdb=" N ARG A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 97 through 101 removed outlier: 4.169A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 101 " --> pdb=" O ARG A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 128 through 140 removed outlier: 3.891A pdb=" N LEU A 135 " --> pdb=" O TRP A 131 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 163 removed outlier: 3.844A pdb=" N ALA A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 179 removed outlier: 3.878A pdb=" N PHE A 179 " --> pdb=" O ILE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 192 removed outlier: 3.517A pdb=" N GLU A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 removed outlier: 3.695A pdb=" N PHE A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A 219 " --> pdb=" O ARG A 215 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 234 removed outlier: 3.865A pdb=" N ASP A 227 " --> pdb=" O ARG A 223 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 removed outlier: 3.809A pdb=" N PHE A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLN A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 280 removed outlier: 3.548A pdb=" N ALA A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.763A pdb=" N SER A 297 " --> pdb=" O MET A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 347 through 355 removed outlier: 3.914A pdb=" N ARG A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 399 Processing helix chain 'A' and resid 418 through 432 removed outlier: 3.578A pdb=" N ALA A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 426 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS A 429 " --> pdb=" O MET A 425 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 437 removed outlier: 3.859A pdb=" N LEU A 437 " --> pdb=" O GLY A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 581 removed outlier: 3.567A pdb=" N ALA A 580 " --> pdb=" O GLU A 577 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER A 581 " --> pdb=" O GLY A 578 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 577 through 581' Processing helix chain 'A' and resid 589 through 593 removed outlier: 3.773A pdb=" N THR A 592 " --> pdb=" O GLU A 589 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 593 " --> pdb=" O MET A 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 589 through 593' Processing helix chain 'A' and resid 604 through 612 removed outlier: 3.901A pdb=" N LYS A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN A 612 " --> pdb=" O ALA A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 626 Processing helix chain 'A' and resid 632 through 640 removed outlier: 3.565A pdb=" N PHE A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A 638 " --> pdb=" O MET A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 666 removed outlier: 3.915A pdb=" N ASN A 666 " --> pdb=" O GLN A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 690 removed outlier: 3.761A pdb=" N PHE A 690 " --> pdb=" O ASN A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 removed outlier: 3.528A pdb=" N ARG A 706 " --> pdb=" O GLU A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 791 removed outlier: 3.622A pdb=" N LEU A 791 " --> pdb=" O LEU A 788 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 788 through 791' Processing helix chain 'A' and resid 814 through 816 No H-bonds generated for 'chain 'A' and resid 814 through 816' Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 876 through 881 removed outlier: 3.755A pdb=" N GLY A 881 " --> pdb=" O ALA A 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 26 removed outlier: 3.725A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 9 through 24 removed outlier: 4.016A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.902A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.703A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'C' and resid 3 through 26 removed outlier: 3.836A pdb=" N LEU C 7 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 14 " --> pdb=" O GLU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'D' and resid 9 through 24 removed outlier: 4.156A pdb=" N ARG D 13 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 43 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 4.610A pdb=" N THR A 55 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR A 42 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASN A 119 " --> pdb=" O TRP A 31 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP A 71 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 171 Processing sheet with id=AA3, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 388 removed outlier: 6.375A pdb=" N LEU A 363 " --> pdb=" O GLU A 413 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 598 through 599 removed outlier: 6.691A pdb=" N GLU A 598 " --> pdb=" O MET A 617 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 619 through 621 removed outlier: 3.515A pdb=" N TYR A 648 " --> pdb=" O PHE A 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 781 through 786 removed outlier: 4.431A pdb=" N LYS A 785 " --> pdb=" O ASN A 726 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN A 726 " --> pdb=" O LYS A 785 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LEU A 728 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N SER A 845 " --> pdb=" O LEU A 728 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N VAL A 730 " --> pdb=" O GLU A 843 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLU A 843 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL A 732 " --> pdb=" O TYR A 841 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR A 841 " --> pdb=" O VAL A 732 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 745 through 752 removed outlier: 5.710A pdb=" N GLU A 800 " --> pdb=" O PHE A 805 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE A 805 " --> pdb=" O GLU A 800 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.662A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.078A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 81 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 100 through 103 removed outlier: 7.291A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 121 through 123 removed outlier: 3.546A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.793A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 189 through 191 removed outlier: 3.602A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 229 through 231 Processing sheet with id=AB7, first strand: chain 'B' and resid 250 through 253 removed outlier: 6.935A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.446A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 47 through 50 removed outlier: 6.595A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.833A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE C 80 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.859A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 167 " --> pdb=" O THR C 159 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.696A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER C 191 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 203 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.744A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE C 253 " --> pdb=" O PHE C 241 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR C 243 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG C 251 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 273 through 277 removed outlier: 3.650A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA C 287 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 936 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: 2.10 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3858 1.34 - 1.46: 1922 1.46 - 1.57: 6042 1.57 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 11939 Sorted by residual: bond pdb=" CA ASN C 268 " pdb=" C ASN C 268 " ideal model delta sigma weight residual 1.522 1.551 -0.029 1.51e-02 4.39e+03 3.72e+00 bond pdb=" C PRO A 370 " pdb=" N PRO A 371 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.67e+00 bond pdb=" CA ASN C 268 " pdb=" CB ASN C 268 " ideal model delta sigma weight residual 1.535 1.559 -0.024 1.37e-02 5.33e+03 3.11e+00 bond pdb=" CB CYS A 669 " pdb=" SG CYS A 669 " ideal model delta sigma weight residual 1.808 1.756 0.052 3.30e-02 9.18e+02 2.50e+00 bond pdb=" C LEU A 835 " pdb=" N PRO A 836 " ideal model delta sigma weight residual 1.331 1.351 -0.020 1.31e-02 5.83e+03 2.42e+00 ... (remaining 11934 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 15482 1.74 - 3.48: 587 3.48 - 5.22: 86 5.22 - 6.95: 12 6.95 - 8.69: 10 Bond angle restraints: 16177 Sorted by residual: angle pdb=" C ASP A 125 " pdb=" N ASP A 126 " pdb=" CA ASP A 126 " ideal model delta sigma weight residual 121.54 129.70 -8.16 1.91e+00 2.74e-01 1.82e+01 angle pdb=" C TYR A 279 " pdb=" N GLU A 280 " pdb=" CA GLU A 280 " ideal model delta sigma weight residual 122.70 114.54 8.16 1.98e+00 2.55e-01 1.70e+01 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 124.82 131.83 -7.01 1.78e+00 3.16e-01 1.55e+01 angle pdb=" C THR C 86 " pdb=" N THR C 87 " pdb=" CA THR C 87 " ideal model delta sigma weight residual 121.54 128.97 -7.43 1.91e+00 2.74e-01 1.51e+01 angle pdb=" N LEU A 835 " pdb=" CA LEU A 835 " pdb=" C LEU A 835 " ideal model delta sigma weight residual 109.81 118.30 -8.49 2.21e+00 2.05e-01 1.47e+01 ... (remaining 16172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6384 17.99 - 35.98: 690 35.98 - 53.98: 109 53.98 - 71.97: 25 71.97 - 89.96: 9 Dihedral angle restraints: 7217 sinusoidal: 2846 harmonic: 4371 Sorted by residual: dihedral pdb=" CA ASP A 248 " pdb=" C ASP A 248 " pdb=" N PHE A 249 " pdb=" CA PHE A 249 " ideal model delta harmonic sigma weight residual 180.00 156.66 23.34 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA TYR A 406 " pdb=" C TYR A 406 " pdb=" N PRO A 407 " pdb=" CA PRO A 407 " ideal model delta harmonic sigma weight residual 180.00 -157.27 -22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA HIS C 266 " pdb=" C HIS C 266 " pdb=" N ASP C 267 " pdb=" CA ASP C 267 " ideal model delta harmonic sigma weight residual 180.00 157.55 22.45 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 7214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1296 0.051 - 0.101: 425 0.101 - 0.152: 92 0.152 - 0.203: 11 0.203 - 0.253: 2 Chirality restraints: 1826 Sorted by residual: chirality pdb=" CB VAL A 621 " pdb=" CA VAL A 621 " pdb=" CG1 VAL A 621 " pdb=" CG2 VAL A 621 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB THR A 344 " pdb=" CA THR A 344 " pdb=" OG1 THR A 344 " pdb=" CG2 THR A 344 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB VAL A 172 " pdb=" CA VAL A 172 " pdb=" CG1 VAL A 172 " pdb=" CG2 VAL A 172 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.75e-01 ... (remaining 1823 not shown) Planarity restraints: 2097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 370 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO A 371 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 371 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 371 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 773 " -0.046 5.00e-02 4.00e+02 6.90e-02 7.63e+00 pdb=" N PRO A 774 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 774 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 774 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 268 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.54e+00 pdb=" C ASN C 268 " -0.048 2.00e-02 2.50e+03 pdb=" O ASN C 268 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE C 269 " 0.016 2.00e-02 2.50e+03 ... (remaining 2094 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2941 2.79 - 3.32: 9632 3.32 - 3.85: 18569 3.85 - 4.37: 21669 4.37 - 4.90: 39070 Nonbonded interactions: 91881 Sorted by model distance: nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.263 3.040 nonbonded pdb=" OE1 GLU A 577 " pdb=" OH TYR A 648 " model vdw 2.268 3.040 nonbonded pdb=" OG1 THR A 317 " pdb=" OD1 ASN A 693 " model vdw 2.280 3.040 nonbonded pdb=" OD1 ASP C 247 " pdb=" OG1 THR C 249 " model vdw 2.299 3.040 nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.303 3.040 ... (remaining 91876 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 'B' and (resid 4 through 34 or (resid 35 through 36 and (name N or name C \ A or name C or name O or name CB )) or resid 37 through 152 or (resid 153 and (n \ ame N or name CA or name C or name O or name CB )) or resid 154 through 174 or ( \ resid 175 and (name N or name CA or name C or name O or name CB )) or resid 176 \ through 196 or (resid 197 and (name N or name CA or name C or name O or name CB \ )) or resid 198 through 255 or (resid 256 through 257 and (name N or name CA or \ name C or name O or name CB )) or resid 258 through 289 or (resid 290 through 29 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 294 through \ 340)) selection = (chain 'C' and (resid 4 through 213 or (resid 214 through 215 and (name N or nam \ e CA or name C or name O or name CB )) or resid 216 or (resid 217 and (name N or \ name CA or name C or name O or name CB )) or resid 218 through 258 or (resid 25 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 260 through \ 340)) } 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: 4.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 12.440 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 0.063 11939 Z= 0.240 Angle : 0.809 8.692 16177 Z= 0.450 Chirality : 0.051 0.253 1826 Planarity : 0.007 0.104 2097 Dihedral : 15.136 89.961 4385 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % 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: -4.74 (0.17), residues: 1486 helix: -3.75 (0.17), residues: 349 sheet: -2.99 (0.21), residues: 399 loop : -2.85 (0.19), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 150 TYR 0.024 0.002 TYR A 746 PHE 0.024 0.002 PHE B 241 TRP 0.014 0.002 TRP A 356 HIS 0.007 0.002 HIS C 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 (11939) covalent geometry : angle 0.80867 / 0.45 (16177) hydrogen bonds : bond 0.22573 / 14.55 ( 330) hydrogen bonds : angle 8.38535 / 5.76 ( 936) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.469 Fit side-chains REVERT: A 228 LYS cc_start: 0.8261 (tmmt) cc_final: 0.8001 (tttt) REVERT: A 729 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7787 (mtp85) REVERT: B 188 MET cc_start: 0.8526 (mmt) cc_final: 0.8182 (mmt) REVERT: G 14 LYS cc_start: 0.8085 (tppp) cc_final: 0.7618 (tppp) REVERT: G 27 ARG cc_start: 0.7433 (mtp85) cc_final: 0.7151 (mtp85) REVERT: C 45 MET cc_start: 0.7567 (mtp) cc_final: 0.7171 (mtp) REVERT: C 48 ARG cc_start: 0.6597 (ttp-170) cc_final: 0.4377 (ttp-170) REVERT: C 246 ASP cc_start: 0.7772 (t0) cc_final: 0.7325 (t0) REVERT: D 17 GLU cc_start: 0.8301 (tp30) cc_final: 0.7330 (mm-30) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1296 time to fit residues: 33.7503 Evaluate side-chains 146 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.0570 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.2900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 726 ASN B 13 GLN B 17 GLN B 36 ASN B 62 HIS C 266 HIS D 44 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.124779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.094817 restraints weight = 17482.485| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.75 r_work: 0.3029 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11939 Z= 0.157 Angle : 0.585 8.826 16177 Z= 0.311 Chirality : 0.044 0.154 1826 Planarity : 0.005 0.082 2097 Dihedral : 5.198 35.311 1632 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.42 % Allowed : 13.28 % Favored : 85.30 % 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: -3.69 (0.19), residues: 1486 helix: -2.39 (0.23), residues: 352 sheet: -2.55 (0.22), residues: 380 loop : -2.36 (0.20), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 8 TYR 0.019 0.002 TYR A 746 PHE 0.015 0.001 PHE B 241 TRP 0.013 0.001 TRP C 169 HIS 0.007 0.001 HIS C 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (11939) covalent geometry : angle 0.58511 / 0.31 (16177) hydrogen bonds : bond 0.04395 / 2.92 ( 330) hydrogen bonds : angle 5.79733 / 4.03 ( 936) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.482 Fit side-chains REVERT: A 289 ASP cc_start: 0.7859 (m-30) cc_final: 0.6707 (p0) REVERT: A 383 MET cc_start: 0.8359 (ppp) cc_final: 0.7890 (mmt) REVERT: A 750 ASP cc_start: 0.8215 (m-30) cc_final: 0.7829 (m-30) REVERT: B 32 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7259 (pt0) REVERT: B 55 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7692 (tt) REVERT: B 163 ASP cc_start: 0.8310 (t70) cc_final: 0.8069 (t0) REVERT: B 188 MET cc_start: 0.9014 (mmt) cc_final: 0.8695 (mmt) REVERT: G 18 GLN cc_start: 0.8432 (mt0) cc_final: 0.8136 (mt0) REVERT: C 45 MET cc_start: 0.8118 (mtp) cc_final: 0.7849 (mtp) REVERT: C 48 ARG cc_start: 0.6505 (ttp-170) cc_final: 0.4121 (ttp-170) REVERT: C 246 ASP cc_start: 0.8130 (t0) cc_final: 0.7660 (t0) outliers start: 18 outliers final: 13 residues processed: 177 average time/residue: 0.1119 time to fit residues: 28.4782 Evaluate side-chains 166 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain D residue 37 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 9 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 52 optimal weight: 0.0570 chunk 6 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 ASN B 17 GLN C 295 ASN D 44 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.125592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.094866 restraints weight = 17552.545| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.90 r_work: 0.3051 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11939 Z= 0.109 Angle : 0.530 7.406 16177 Z= 0.277 Chirality : 0.042 0.140 1826 Planarity : 0.004 0.074 2097 Dihedral : 4.669 32.612 1632 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.50 % Allowed : 15.89 % Favored : 82.61 % 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: -3.14 (0.20), residues: 1486 helix: -1.71 (0.26), residues: 354 sheet: -2.24 (0.23), residues: 386 loop : -2.11 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 8 TYR 0.014 0.001 TYR A 746 PHE 0.010 0.001 PHE B 241 TRP 0.011 0.001 TRP C 169 HIS 0.004 0.001 HIS C 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (11939) covalent geometry : angle 0.53020 / 0.28 (16177) hydrogen bonds : bond 0.03415 / 2.30 ( 330) hydrogen bonds : angle 5.19802 / 3.59 ( 936) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.445 Fit side-chains REVERT: A 140 MET cc_start: 0.8245 (mmt) cc_final: 0.8023 (mmt) REVERT: A 199 ARG cc_start: 0.7801 (tmm160) cc_final: 0.7394 (ttm110) REVERT: A 289 ASP cc_start: 0.7900 (m-30) cc_final: 0.6782 (p0) REVERT: A 330 SER cc_start: 0.9271 (t) cc_final: 0.9039 (p) REVERT: A 383 MET cc_start: 0.8391 (ppp) cc_final: 0.7805 (mmt) REVERT: A 609 ARG cc_start: 0.8491 (ttp-170) cc_final: 0.8260 (ttp80) REVERT: A 750 ASP cc_start: 0.8112 (m-30) cc_final: 0.7710 (m-30) REVERT: B 32 GLN cc_start: 0.7709 (tm-30) cc_final: 0.7215 (pt0) REVERT: B 55 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7712 (tt) REVERT: B 138 GLU cc_start: 0.8316 (tp30) cc_final: 0.8110 (tp30) REVERT: B 163 ASP cc_start: 0.8251 (t70) cc_final: 0.8029 (t0) REVERT: B 188 MET cc_start: 0.8992 (mmt) cc_final: 0.8632 (mmt) REVERT: G 18 GLN cc_start: 0.8490 (mt0) cc_final: 0.8213 (mt0) REVERT: C 9 GLN cc_start: 0.7978 (pp30) cc_final: 0.7688 (pp30) REVERT: C 48 ARG cc_start: 0.6509 (ttp-170) cc_final: 0.4092 (ttp-170) REVERT: C 124 TYR cc_start: 0.8354 (m-10) cc_final: 0.8006 (m-10) REVERT: C 246 ASP cc_start: 0.7997 (t0) cc_final: 0.7641 (t0) outliers start: 19 outliers final: 12 residues processed: 168 average time/residue: 0.1170 time to fit residues: 27.8648 Evaluate side-chains 161 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 189 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 109 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 42 optimal weight: 0.0010 chunk 93 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 48 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 770 ASN B 17 GLN D 18 GLN D 44 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.126912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.095996 restraints weight = 17450.900| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.88 r_work: 0.3062 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11939 Z= 0.097 Angle : 0.507 6.449 16177 Z= 0.264 Chirality : 0.042 0.140 1826 Planarity : 0.004 0.067 2097 Dihedral : 4.410 29.587 1632 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.34 % Allowed : 16.92 % Favored : 81.74 % 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: -2.76 (0.20), residues: 1486 helix: -1.27 (0.27), residues: 354 sheet: -1.99 (0.24), residues: 386 loop : -1.95 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 8 TYR 0.013 0.001 TYR A 746 PHE 0.032 0.001 PHE C 199 TRP 0.010 0.001 TRP C 82 HIS 0.004 0.001 HIS D 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (11939) covalent geometry : angle 0.50710 / 0.26 (16177) hydrogen bonds : bond 0.03032 / 2.03 ( 330) hydrogen bonds : angle 4.97256 / 3.42 ( 936) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.420 Fit side-chains REVERT: A 199 ARG cc_start: 0.7829 (tmm160) cc_final: 0.7595 (tpp80) REVERT: A 289 ASP cc_start: 0.7838 (m-30) cc_final: 0.6715 (p0) REVERT: A 609 ARG cc_start: 0.8446 (ttp-170) cc_final: 0.8212 (ttp80) REVERT: A 750 ASP cc_start: 0.8082 (m-30) cc_final: 0.7687 (m-30) REVERT: B 32 GLN cc_start: 0.7685 (tm-30) cc_final: 0.7207 (pt0) REVERT: B 55 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7707 (tt) REVERT: B 138 GLU cc_start: 0.8335 (tp30) cc_final: 0.8095 (tp30) REVERT: B 188 MET cc_start: 0.8966 (mmt) cc_final: 0.8611 (mmt) REVERT: G 18 GLN cc_start: 0.8567 (mt0) cc_final: 0.8315 (mt0) REVERT: C 9 GLN cc_start: 0.7969 (pp30) cc_final: 0.7626 (pp30) REVERT: C 48 ARG cc_start: 0.6465 (ttp-170) cc_final: 0.4057 (ttp-170) REVERT: C 246 ASP cc_start: 0.8027 (t0) cc_final: 0.7632 (t0) REVERT: C 258 ASP cc_start: 0.8330 (t0) cc_final: 0.7964 (t0) outliers start: 17 outliers final: 13 residues processed: 173 average time/residue: 0.1071 time to fit residues: 26.6558 Evaluate side-chains 167 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 228 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 18 GLN D 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.124694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.094058 restraints weight = 17340.200| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.88 r_work: 0.3022 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11939 Z= 0.148 Angle : 0.536 6.868 16177 Z= 0.278 Chirality : 0.043 0.153 1826 Planarity : 0.004 0.065 2097 Dihedral : 4.459 29.895 1632 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.90 % Allowed : 17.94 % Favored : 80.16 % 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: -2.62 (0.20), residues: 1486 helix: -1.08 (0.27), residues: 355 sheet: -1.95 (0.24), residues: 380 loop : -1.89 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 76 TYR 0.017 0.001 TYR A 746 PHE 0.022 0.001 PHE C 199 TRP 0.008 0.001 TRP C 169 HIS 0.004 0.001 HIS C 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (11939) covalent geometry : angle 0.53631 / 0.28 (16177) hydrogen bonds : bond 0.03265 / 2.20 ( 330) hydrogen bonds : angle 4.98127 / 3.45 ( 936) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.471 Fit side-chains REVERT: A 199 ARG cc_start: 0.7910 (tmm160) cc_final: 0.7557 (tpp80) REVERT: A 289 ASP cc_start: 0.7908 (m-30) cc_final: 0.6731 (p0) REVERT: A 349 MET cc_start: 0.8103 (tpp) cc_final: 0.7661 (tpp) REVERT: A 609 ARG cc_start: 0.8404 (ttp-170) cc_final: 0.8169 (ttp80) REVERT: A 750 ASP cc_start: 0.8194 (m-30) cc_final: 0.7816 (m-30) REVERT: B 32 GLN cc_start: 0.7696 (tm-30) cc_final: 0.7229 (pt0) REVERT: B 55 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7735 (tt) REVERT: B 138 GLU cc_start: 0.8461 (tp30) cc_final: 0.8206 (tp30) REVERT: B 188 MET cc_start: 0.9025 (mmt) cc_final: 0.8642 (mmt) REVERT: G 18 GLN cc_start: 0.8553 (mt0) cc_final: 0.8311 (mt0) REVERT: C 9 GLN cc_start: 0.7995 (pp30) cc_final: 0.7648 (pp30) REVERT: C 48 ARG cc_start: 0.6533 (ttp-170) cc_final: 0.4123 (ttp-170) REVERT: C 124 TYR cc_start: 0.8430 (m-10) cc_final: 0.8130 (m-10) REVERT: C 246 ASP cc_start: 0.8023 (t0) cc_final: 0.7654 (t0) outliers start: 24 outliers final: 15 residues processed: 169 average time/residue: 0.0981 time to fit residues: 24.0600 Evaluate side-chains 166 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 189 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 3 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.125931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.096594 restraints weight = 17371.809| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.74 r_work: 0.3035 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11939 Z= 0.116 Angle : 0.514 7.253 16177 Z= 0.267 Chirality : 0.042 0.169 1826 Planarity : 0.004 0.066 2097 Dihedral : 4.338 28.455 1632 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.06 % Allowed : 18.74 % Favored : 79.21 % 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: -2.40 (0.20), residues: 1486 helix: -0.84 (0.28), residues: 355 sheet: -1.83 (0.24), residues: 374 loop : -1.78 (0.21), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 76 TYR 0.014 0.001 TYR A 746 PHE 0.019 0.001 PHE C 199 TRP 0.009 0.001 TRP C 169 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (11939) covalent geometry : angle 0.51442 / 0.27 (16177) hydrogen bonds : bond 0.03052 / 2.05 ( 330) hydrogen bonds : angle 4.86077 / 3.36 ( 936) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.438 Fit side-chains REVERT: A 199 ARG cc_start: 0.7930 (tmm160) cc_final: 0.7640 (tpp80) REVERT: A 289 ASP cc_start: 0.7880 (m-30) cc_final: 0.6637 (p0) REVERT: A 349 MET cc_start: 0.8105 (tpp) cc_final: 0.7584 (tpp) REVERT: A 383 MET cc_start: 0.8374 (ppp) cc_final: 0.7707 (mmt) REVERT: A 609 ARG cc_start: 0.8389 (ttp-170) cc_final: 0.8160 (ttp80) REVERT: A 750 ASP cc_start: 0.8167 (m-30) cc_final: 0.7693 (m-30) REVERT: B 32 GLN cc_start: 0.7693 (tm-30) cc_final: 0.7235 (pt0) REVERT: B 55 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7726 (tt) REVERT: B 138 GLU cc_start: 0.8452 (tp30) cc_final: 0.8209 (tp30) REVERT: B 188 MET cc_start: 0.9012 (mmt) cc_final: 0.8646 (mmt) REVERT: G 18 GLN cc_start: 0.8574 (mt0) cc_final: 0.8350 (mt0) REVERT: C 9 GLN cc_start: 0.7986 (pp30) cc_final: 0.7665 (pp30) REVERT: C 48 ARG cc_start: 0.6522 (ttp-170) cc_final: 0.4103 (ttp-170) REVERT: C 124 TYR cc_start: 0.8462 (m-10) cc_final: 0.8115 (m-10) REVERT: C 246 ASP cc_start: 0.8024 (t0) cc_final: 0.7669 (t0) outliers start: 26 outliers final: 19 residues processed: 171 average time/residue: 0.0930 time to fit residues: 23.1496 Evaluate side-chains 172 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 65 optimal weight: 0.6980 chunk 148 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.129933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.101353 restraints weight = 17182.408| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.38 r_work: 0.3149 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11939 Z= 0.134 Angle : 0.531 7.607 16177 Z= 0.274 Chirality : 0.043 0.147 1826 Planarity : 0.004 0.069 2097 Dihedral : 4.418 28.171 1632 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.37 % Allowed : 19.21 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.34 (0.20), residues: 1486 helix: -0.77 (0.28), residues: 355 sheet: -1.83 (0.24), residues: 377 loop : -1.73 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 729 TYR 0.018 0.001 TYR B 124 PHE 0.018 0.001 PHE C 199 TRP 0.011 0.001 TRP C 169 HIS 0.005 0.001 HIS D 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (11939) covalent geometry : angle 0.53101 / 0.27 (16177) hydrogen bonds : bond 0.03136 / 2.11 ( 330) hydrogen bonds : angle 4.88267 / 3.38 ( 936) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.482 Fit side-chains REVERT: A 199 ARG cc_start: 0.8007 (tmm160) cc_final: 0.7736 (tpp80) REVERT: A 289 ASP cc_start: 0.7927 (m-30) cc_final: 0.6825 (p0) REVERT: A 349 MET cc_start: 0.8366 (tpp) cc_final: 0.7869 (tpp) REVERT: A 750 ASP cc_start: 0.8418 (m-30) cc_final: 0.8112 (m-30) REVERT: B 32 GLN cc_start: 0.7833 (tm-30) cc_final: 0.7396 (pt0) REVERT: B 55 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7750 (tt) REVERT: B 124 TYR cc_start: 0.8693 (m-80) cc_final: 0.8428 (m-10) REVERT: B 138 GLU cc_start: 0.8355 (tp30) cc_final: 0.8126 (tp30) REVERT: B 188 MET cc_start: 0.9165 (mmt) cc_final: 0.8844 (mmt) REVERT: G 18 GLN cc_start: 0.8577 (mt0) cc_final: 0.8375 (mt0) REVERT: C 9 GLN cc_start: 0.8024 (pp30) cc_final: 0.7639 (pp30) REVERT: C 48 ARG cc_start: 0.6898 (ttp-170) cc_final: 0.4401 (mmm160) REVERT: C 124 TYR cc_start: 0.8686 (m-10) cc_final: 0.8329 (m-10) REVERT: C 246 ASP cc_start: 0.8094 (t0) cc_final: 0.7753 (t0) REVERT: C 262 MET cc_start: 0.5835 (tpp) cc_final: 0.5258 (tpp) outliers start: 30 outliers final: 24 residues processed: 171 average time/residue: 0.1006 time to fit residues: 24.7874 Evaluate side-chains 176 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain D residue 37 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 124 optimal weight: 0.0050 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.129867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.103136 restraints weight = 17080.392| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.23 r_work: 0.3164 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11939 Z= 0.136 Angle : 0.535 8.302 16177 Z= 0.277 Chirality : 0.043 0.136 1826 Planarity : 0.004 0.074 2097 Dihedral : 4.427 28.136 1632 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.06 % Allowed : 19.45 % Favored : 78.50 % 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: -2.24 (0.21), residues: 1486 helix: -0.68 (0.28), residues: 355 sheet: -1.79 (0.25), residues: 377 loop : -1.66 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 729 TYR 0.016 0.001 TYR A 746 PHE 0.016 0.001 PHE C 199 TRP 0.011 0.001 TRP C 169 HIS 0.008 0.001 HIS D 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (11939) covalent geometry : angle 0.53506 / 0.28 (16177) hydrogen bonds : bond 0.03125 / 2.10 ( 330) hydrogen bonds : angle 4.85673 / 3.35 ( 936) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.493 Fit side-chains REVERT: A 199 ARG cc_start: 0.7993 (tmm160) cc_final: 0.7739 (tpp80) REVERT: A 289 ASP cc_start: 0.7918 (m-30) cc_final: 0.6826 (p0) REVERT: A 349 MET cc_start: 0.8356 (tpp) cc_final: 0.7839 (tpp) REVERT: A 383 MET cc_start: 0.8332 (ppp) cc_final: 0.7627 (mmt) REVERT: A 750 ASP cc_start: 0.8379 (m-30) cc_final: 0.8069 (m-30) REVERT: B 32 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7432 (pt0) REVERT: B 55 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7729 (tt) REVERT: B 124 TYR cc_start: 0.8699 (m-80) cc_final: 0.8435 (m-10) REVERT: B 138 GLU cc_start: 0.8324 (tp30) cc_final: 0.8091 (tp30) REVERT: B 188 MET cc_start: 0.9148 (mmt) cc_final: 0.8833 (mmt) REVERT: C 9 GLN cc_start: 0.8030 (pp30) cc_final: 0.7636 (pp30) REVERT: C 48 ARG cc_start: 0.6901 (ttp-170) cc_final: 0.4415 (mmm160) REVERT: C 124 TYR cc_start: 0.8704 (m-10) cc_final: 0.8378 (m-10) REVERT: C 246 ASP cc_start: 0.8063 (t0) cc_final: 0.7729 (t0) REVERT: C 262 MET cc_start: 0.5840 (tpp) cc_final: 0.5333 (tpp) outliers start: 26 outliers final: 24 residues processed: 168 average time/residue: 0.1086 time to fit residues: 26.1718 Evaluate side-chains 174 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain D residue 37 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 81 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 9 optimal weight: 0.0000 chunk 107 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 51 optimal weight: 0.0980 chunk 103 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.132076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.104207 restraints weight = 16905.949| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.26 r_work: 0.3193 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11939 Z= 0.096 Angle : 0.506 7.891 16177 Z= 0.262 Chirality : 0.042 0.161 1826 Planarity : 0.003 0.073 2097 Dihedral : 4.204 28.175 1632 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.82 % Allowed : 20.08 % Favored : 78.10 % 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: -2.06 (0.21), residues: 1486 helix: -0.43 (0.29), residues: 357 sheet: -1.66 (0.25), residues: 374 loop : -1.62 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 729 TYR 0.012 0.001 TYR B 124 PHE 0.016 0.001 PHE C 199 TRP 0.009 0.001 TRP C 169 HIS 0.003 0.001 HIS D 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (11939) covalent geometry : angle 0.50608 / 0.26 (16177) hydrogen bonds : bond 0.02800 / 1.89 ( 330) hydrogen bonds : angle 4.73592 / 3.24 ( 936) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.432 Fit side-chains REVERT: A 199 ARG cc_start: 0.7957 (tmm160) cc_final: 0.7703 (tpp80) REVERT: A 289 ASP cc_start: 0.7918 (m-30) cc_final: 0.6780 (p0) REVERT: A 383 MET cc_start: 0.8320 (ppp) cc_final: 0.7583 (mmt) REVERT: B 32 GLN cc_start: 0.7779 (tm-30) cc_final: 0.7371 (pt0) REVERT: B 55 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7739 (tt) REVERT: B 138 GLU cc_start: 0.8323 (tp30) cc_final: 0.8082 (tp30) REVERT: B 188 MET cc_start: 0.9132 (mmt) cc_final: 0.8855 (mmt) REVERT: C 9 GLN cc_start: 0.7997 (pp30) cc_final: 0.7595 (pp30) REVERT: C 48 ARG cc_start: 0.6818 (ttp-170) cc_final: 0.4159 (ttp-170) REVERT: C 124 TYR cc_start: 0.8590 (m-10) cc_final: 0.8265 (m-10) REVERT: C 246 ASP cc_start: 0.8052 (t0) cc_final: 0.7723 (t0) REVERT: C 262 MET cc_start: 0.5867 (tpp) cc_final: 0.5369 (tpp) outliers start: 23 outliers final: 21 residues processed: 169 average time/residue: 0.1143 time to fit residues: 27.3209 Evaluate side-chains 174 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain D residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 69 optimal weight: 0.0970 chunk 104 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 99 optimal weight: 0.0770 chunk 72 optimal weight: 6.9990 chunk 73 optimal weight: 0.4980 chunk 141 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.9338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.131105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.102569 restraints weight = 17160.270| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.39 r_work: 0.3167 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11939 Z= 0.120 Angle : 0.534 8.878 16177 Z= 0.274 Chirality : 0.043 0.173 1826 Planarity : 0.004 0.076 2097 Dihedral : 4.204 24.461 1632 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.74 % Allowed : 20.55 % Favored : 77.71 % 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: -2.04 (0.21), residues: 1486 helix: -0.42 (0.28), residues: 357 sheet: -1.66 (0.25), residues: 376 loop : -1.60 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 729 TYR 0.014 0.001 TYR A 746 PHE 0.015 0.001 PHE C 199 TRP 0.015 0.001 TRP C 169 HIS 0.005 0.001 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (11939) covalent geometry : angle 0.53371 / 0.27 (16177) hydrogen bonds : bond 0.02936 / 1.98 ( 330) hydrogen bonds : angle 4.78594 / 3.30 ( 936) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.444 Fit side-chains REVERT: A 199 ARG cc_start: 0.7982 (tmm160) cc_final: 0.7716 (tpp80) REVERT: A 289 ASP cc_start: 0.7939 (m-30) cc_final: 0.6777 (p0) REVERT: B 32 GLN cc_start: 0.7804 (tm-30) cc_final: 0.7381 (pt0) REVERT: B 55 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7749 (tt) REVERT: B 138 GLU cc_start: 0.8303 (tp30) cc_final: 0.8022 (tp30) REVERT: B 188 MET cc_start: 0.9173 (mmt) cc_final: 0.8852 (mmt) REVERT: C 9 GLN cc_start: 0.8009 (pp30) cc_final: 0.7630 (pp30) REVERT: C 48 ARG cc_start: 0.6816 (ttp-170) cc_final: 0.4204 (mmm160) REVERT: C 124 TYR cc_start: 0.8647 (m-10) cc_final: 0.8315 (m-10) REVERT: C 246 ASP cc_start: 0.7990 (t0) cc_final: 0.7682 (t0) REVERT: C 262 MET cc_start: 0.5869 (tpp) cc_final: 0.5337 (tpp) outliers start: 22 outliers final: 21 residues processed: 161 average time/residue: 0.1137 time to fit residues: 26.1805 Evaluate side-chains 170 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain D residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 chunk 104 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.127757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.099853 restraints weight = 17250.334| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.26 r_work: 0.3137 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 11939 Z= 0.200 Angle : 0.592 9.156 16177 Z= 0.305 Chirality : 0.045 0.182 1826 Planarity : 0.004 0.079 2097 Dihedral : 4.601 30.201 1632 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.13 % Allowed : 20.24 % Favored : 77.63 % 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: -2.26 (0.21), residues: 1486 helix: -0.65 (0.28), residues: 355 sheet: -1.83 (0.24), residues: 390 loop : -1.66 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 729 TYR 0.021 0.002 TYR A 746 PHE 0.018 0.002 PHE A 216 TRP 0.022 0.001 TRP C 169 HIS 0.005 0.001 HIS C 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.20 (11939) covalent geometry : angle 0.59235 / 0.31 (16177) hydrogen bonds : bond 0.03520 / 2.38 ( 330) hydrogen bonds : angle 5.04917 / 3.50 ( 936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2722.16 seconds wall clock time: 47 minutes 29.05 seconds (2849.05 seconds total)