Starting phenix.real_space_refine on Sun Aug 24 15:54:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8emx_28268/08_2025/8emx_28268.cif Found real_map, /net/cci-nas-00/data/ceres_data/8emx_28268/08_2025/8emx_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_28268/08_2025/8emx_28268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8emx_28268/08_2025/8emx_28268.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8emx_28268/08_2025/8emx_28268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8emx_28268/08_2025/8emx_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 1.94, per 1000 atoms: 0.17 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: 0.70 Conformation dependent library (CDL) restraints added in 399.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.35 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: 1.57 Time building geometry restraints manager: 0.97 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: 3.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.020 Find NCS groups from input model: 0.090 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 aren 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 covalent geometry : bond 0.00561 (11939) covalent geometry : angle 0.80867 (16177) hydrogen bonds : bond 0.22573 ( 330) hydrogen bonds : angle 8.38535 ( 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 : 0.435 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: 0.7786 (mtp85) REVERT: B 188 MET cc_start: 0.8526 (mmt) cc_final: 0.8183 (mmt) REVERT: G 14 LYS cc_start: 0.8085 (tppp) cc_final: 0.7617 (tppp) REVERT: G 27 ARG cc_start: 0.7433 (mtp85) cc_final: 0.7150 (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: 0.1072 time to fit residues: 27.4786 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 : 0.302 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3591 r_free = 0.3591 target = 0.124307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.093752 restraints weight = 17529.429| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.84 r_work: 0.3029 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1243 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 8.875 16177 Z= 0.310 Chirality : 0.044 0.152 1826 Planarity : 0.005 0.081 2097 Dihedral : 5.186 35.298 1632 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.42 % Allowed : 13.52 % Favored : 85.06 % 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 aren not related in a simple way. whole: -3.68 (0.19), residues: 1486 helix: -2.37 (0.24), residues: 352 sheet: -2.56 (0.22), residues: 380 loop : -2.35 (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 0.012 0.001 TRP C 82 HIS 0.007 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00374 (11939) covalent geometry : angle 0.58473 (16177) hydrogen bonds : bond 0.04360 ( 330) hydrogen bonds : angle 5.78388 ( 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 185 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.305 Fit side-chains REVERT: A 289 ASP cc_start: 0.7869 (m-30) cc_final: 0.6692 (p0) REVERT: A 383 MET cc_start: 0.8386 (ppp) cc_final: 0.7917 (mmt) REVERT: A 750 ASP cc_start: 0.8215 (m-30) cc_final: 0.7823 (m-30) REVERT: B 32 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7254 (pt0) REVERT: B 55 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7713 (tt) REVERT: B 163 ASP cc_start: 0.8337 (t70) cc_final: 0.8088 (t0) REVERT: B 188 MET cc_start: 0.8993 (mmt) cc_final: 0.8670 (mmt) REVERT: C 45 MET cc_start: 0.8130 (mtp) cc_final: 0.7856 (mtp) REVERT: C 48 ARG cc_start: 0.6502 (ttp-170) cc_final: 0.4117 (ttp-170) REVERT: C 246 ASP cc_start: 0.8163 (t0) cc_final: 0.7695 (t0) outliers start: 18 outliers final: 13 residues processed: 178 average time/residue: 0.0891 time to fit residues: 22.5013 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 : 0.397 ------------------------------------------------------------------------------- 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: 4.9990 chunk 14 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN C 295 ASN D 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.125185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.094593 restraints weight = 17613.558| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.86 r_work: 0.3037 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11939 Z= 0.126 Angle : 0.542 8.012 16177 Z= 0.283 Chirality : 0.043 0.140 1826 Planarity : 0.004 0.076 2097 Dihedral : 4.737 33.628 1632 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.66 % Allowed : 15.81 % Favored : 82.53 % 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 aren not related in a simple way. whole: -3.18 (0.20), residues: 1486 helix: -1.71 (0.26), residues: 354 sheet: -2.27 (0.23), residues: 386 loop : -2.15 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 8 TYR 0.016 0.001 TYR D 40 PHE 0.012 0.001 PHE B 241 TRP 0.012 0.001 TRP C 169 HIS 0.008 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00298 (11939) covalent geometry : angle 0.54230 (16177) hydrogen bonds : bond 0.03540 ( 330) hydrogen bonds : angle 5.23921 ( 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 178 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.335 Fit side-chains REVERT: A 140 MET cc_start: 0.8250 (mmt) cc_final: 0.8037 (mmt) REVERT: A 199 ARG cc_start: 0.7683 (ttm110) cc_final: 0.7376 (ttm110) REVERT: A 289 ASP cc_start: 0.7869 (m-30) cc_final: 0.6770 (p0) REVERT: A 291 MET cc_start: 0.8681 (ttm) cc_final: 0.8451 (ttt) REVERT: A 750 ASP cc_start: 0.8132 (m-30) cc_final: 0.7741 (m-30) REVERT: B 32 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7268 (pt0) REVERT: B 55 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7715 (tt) REVERT: B 138 GLU cc_start: 0.8328 (tp30) cc_final: 0.8124 (tp30) REVERT: B 163 ASP cc_start: 0.8259 (t70) cc_final: 0.8033 (t0) REVERT: B 188 MET cc_start: 0.9013 (mmt) cc_final: 0.8660 (mmt) REVERT: G 18 GLN cc_start: 0.8416 (mt0) cc_final: 0.8133 (mt0) REVERT: C 9 GLN cc_start: 0.7996 (pp30) cc_final: 0.7703 (pp30) REVERT: C 48 ARG cc_start: 0.6545 (ttp-170) cc_final: 0.4126 (ttp-170) REVERT: C 124 TYR cc_start: 0.8397 (m-10) cc_final: 0.8026 (m-10) REVERT: C 246 ASP cc_start: 0.8014 (t0) cc_final: 0.7648 (t0) outliers start: 21 outliers final: 14 residues processed: 170 average time/residue: 0.0957 time to fit residues: 22.9489 Evaluate side-chains 165 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 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 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: 0.3980 chunk 93 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 770 ASN B 17 GLN D 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.124857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.094779 restraints weight = 17519.457| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.78 r_work: 0.3030 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11939 Z= 0.142 Angle : 0.542 7.847 16177 Z= 0.281 Chirality : 0.043 0.145 1826 Planarity : 0.004 0.066 2097 Dihedral : 4.624 32.953 1632 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.74 % Allowed : 17.00 % Favored : 81.26 % 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 aren not related in a simple way. whole: -2.90 (0.20), residues: 1486 helix: -1.41 (0.27), residues: 354 sheet: -2.08 (0.23), residues: 386 loop : -2.03 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 8 TYR 0.017 0.001 TYR A 746 PHE 0.030 0.001 PHE C 199 TRP 0.008 0.001 TRP C 82 HIS 0.005 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00341 (11939) covalent geometry : angle 0.54195 (16177) hydrogen bonds : bond 0.03372 ( 330) hydrogen bonds : angle 5.09097 ( 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 180 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.417 Fit side-chains REVERT: A 289 ASP cc_start: 0.7876 (m-30) cc_final: 0.6664 (p0) REVERT: A 383 MET cc_start: 0.8396 (ppp) cc_final: 0.7795 (mmt) REVERT: A 729 ARG cc_start: 0.8575 (mtp85) cc_final: 0.8367 (mtp85) REVERT: A 750 ASP cc_start: 0.8170 (m-30) cc_final: 0.7786 (m-30) REVERT: B 32 GLN cc_start: 0.7703 (tm-30) cc_final: 0.7230 (pt0) REVERT: B 55 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7709 (tt) REVERT: B 138 GLU cc_start: 0.8381 (tp30) cc_final: 0.8155 (tp30) REVERT: B 188 MET cc_start: 0.9027 (mmt) cc_final: 0.8635 (mmt) REVERT: C 9 GLN cc_start: 0.8004 (pp30) cc_final: 0.7664 (pp30) REVERT: C 48 ARG cc_start: 0.6544 (ttp-170) cc_final: 0.4151 (ttp-170) REVERT: C 246 ASP cc_start: 0.8039 (t0) cc_final: 0.7646 (t0) outliers start: 22 outliers final: 16 residues processed: 169 average time/residue: 0.0887 time to fit residues: 21.3540 Evaluate side-chains 169 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 739 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 179 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain D residue 37 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN D 18 GLN D 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.127662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.100830 restraints weight = 17252.985| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.23 r_work: 0.3123 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 11939 Z= 0.185 Angle : 0.570 8.136 16177 Z= 0.295 Chirality : 0.044 0.141 1826 Planarity : 0.004 0.065 2097 Dihedral : 4.712 33.955 1632 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.77 % Allowed : 17.47 % Favored : 79.76 % 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 aren not related in a simple way. whole: -2.79 (0.20), residues: 1486 helix: -1.25 (0.27), residues: 354 sheet: -2.01 (0.24), residues: 384 loop : -2.00 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 76 TYR 0.026 0.002 TYR G 40 PHE 0.023 0.002 PHE C 199 TRP 0.010 0.001 TRP C 169 HIS 0.005 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00450 (11939) covalent geometry : angle 0.57030 (16177) hydrogen bonds : bond 0.03551 ( 330) hydrogen bonds : angle 5.12482 ( 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 187 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 0.323 Fit side-chains REVERT: A 289 ASP cc_start: 0.7940 (m-30) cc_final: 0.6896 (p0) REVERT: A 349 MET cc_start: 0.8396 (tpp) cc_final: 0.8039 (tpp) REVERT: A 750 ASP cc_start: 0.8471 (m-30) cc_final: 0.8169 (m-30) REVERT: B 32 GLN cc_start: 0.7817 (tm-30) cc_final: 0.7375 (pt0) REVERT: B 55 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7790 (tt) REVERT: B 188 MET cc_start: 0.9186 (mmt) cc_final: 0.8824 (mmt) REVERT: C 9 GLN cc_start: 0.8040 (pp30) cc_final: 0.7666 (pp30) REVERT: C 48 ARG cc_start: 0.6968 (ttp-170) cc_final: 0.4534 (mmm160) REVERT: C 246 ASP cc_start: 0.8129 (t0) cc_final: 0.7758 (t0) outliers start: 35 outliers final: 24 residues processed: 178 average time/residue: 0.0868 time to fit residues: 22.2501 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 : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 654 VAL 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 790 THR 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 243 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 3 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 138 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN D 18 GLN D 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.130046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.101642 restraints weight = 17141.319| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.36 r_work: 0.3153 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1974 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= 0.110 Angle : 0.520 7.239 16177 Z= 0.269 Chirality : 0.042 0.171 1826 Planarity : 0.003 0.066 2097 Dihedral : 4.436 30.547 1632 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.21 % Allowed : 18.42 % Favored : 79.37 % 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 aren not related in a simple way. whole: -2.53 (0.20), residues: 1486 helix: -0.96 (0.28), residues: 355 sheet: -1.91 (0.24), residues: 373 loop : -1.86 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 76 TYR 0.021 0.001 TYR G 40 PHE 0.020 0.001 PHE C 199 TRP 0.016 0.001 TRP C 169 HIS 0.006 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00259 (11939) covalent geometry : angle 0.52042 (16177) hydrogen bonds : bond 0.03067 ( 330) hydrogen bonds : angle 4.92351 ( 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 186 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.328 Fit side-chains REVERT: A 289 ASP cc_start: 0.7934 (m-30) cc_final: 0.6891 (p0) REVERT: A 349 MET cc_start: 0.8342 (tpp) cc_final: 0.7953 (tpp) REVERT: A 383 MET cc_start: 0.8406 (ppp) cc_final: 0.7721 (mmt) REVERT: A 750 ASP cc_start: 0.8399 (m-30) cc_final: 0.8094 (m-30) REVERT: B 32 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7357 (pt0) REVERT: B 55 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7739 (tt) REVERT: B 124 TYR cc_start: 0.8653 (m-80) cc_final: 0.8324 (m-10) REVERT: B 188 MET cc_start: 0.9171 (mmt) cc_final: 0.8851 (mmt) REVERT: C 9 GLN cc_start: 0.8040 (pp30) cc_final: 0.7706 (pp30) REVERT: C 48 ARG cc_start: 0.6902 (ttp-170) cc_final: 0.4480 (mmm160) REVERT: C 124 TYR cc_start: 0.8633 (m-10) cc_final: 0.8307 (m-10) REVERT: C 246 ASP cc_start: 0.8123 (t0) cc_final: 0.7758 (t0) outliers start: 28 outliers final: 22 residues processed: 174 average time/residue: 0.0932 time to fit residues: 22.8680 Evaluate side-chains 171 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 460 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 770 ASN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 65 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 143 optimal weight: 0.0970 chunk 137 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN D 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.098794 restraints weight = 17372.376| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.36 r_work: 0.3121 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 11939 Z= 0.208 Angle : 0.592 7.552 16177 Z= 0.306 Chirality : 0.045 0.161 1826 Planarity : 0.004 0.069 2097 Dihedral : 4.757 33.177 1632 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.77 % Allowed : 18.18 % Favored : 79.05 % 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 aren not related in a simple way. whole: -2.62 (0.20), residues: 1486 helix: -1.09 (0.27), residues: 355 sheet: -1.98 (0.24), residues: 377 loop : -1.86 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 76 TYR 0.020 0.002 TYR A 746 PHE 0.017 0.002 PHE C 199 TRP 0.019 0.001 TRP C 169 HIS 0.005 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00508 (11939) covalent geometry : angle 0.59225 (16177) hydrogen bonds : bond 0.03608 ( 330) hydrogen bonds : angle 5.10608 ( 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 183 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.343 Fit side-chains REVERT: A 289 ASP cc_start: 0.7983 (m-30) cc_final: 0.6864 (p0) REVERT: A 750 ASP cc_start: 0.8533 (m-30) cc_final: 0.8239 (m-30) REVERT: B 32 GLN cc_start: 0.7864 (tm-30) cc_final: 0.7442 (pt0) REVERT: B 55 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7779 (tt) REVERT: B 124 TYR cc_start: 0.8775 (m-80) cc_final: 0.8343 (m-10) REVERT: B 188 MET cc_start: 0.9202 (mmt) cc_final: 0.8847 (mmt) REVERT: G 17 GLU cc_start: 0.9243 (tp30) cc_final: 0.9001 (tp30) REVERT: C 9 GLN cc_start: 0.8055 (pp30) cc_final: 0.7680 (pp30) REVERT: C 48 ARG cc_start: 0.6952 (ttp-170) cc_final: 0.4464 (ttp-170) REVERT: C 246 ASP cc_start: 0.8134 (t0) cc_final: 0.7795 (t0) REVERT: C 262 MET cc_start: 0.5880 (tpp) cc_final: 0.5329 (tpp) outliers start: 35 outliers final: 31 residues processed: 170 average time/residue: 0.0880 time to fit residues: 21.5362 Evaluate side-chains 178 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 105 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 259 LEU 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 654 VAL 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 790 THR 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 B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL 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 C residue 270 ILE 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: 0.9980 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 77 optimal weight: 0.0070 chunk 53 optimal weight: 0.8980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.130752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.102378 restraints weight = 17045.295| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.36 r_work: 0.3164 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11939 Z= 0.098 Angle : 0.522 8.827 16177 Z= 0.269 Chirality : 0.042 0.153 1826 Planarity : 0.004 0.073 2097 Dihedral : 4.418 28.757 1632 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.06 % Allowed : 19.84 % 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 aren not related in a simple way. whole: -2.35 (0.21), residues: 1486 helix: -0.75 (0.28), residues: 352 sheet: -1.84 (0.25), residues: 376 loop : -1.75 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 76 TYR 0.016 0.001 TYR G 40 PHE 0.016 0.001 PHE C 199 TRP 0.013 0.001 TRP C 169 HIS 0.006 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00228 (11939) covalent geometry : angle 0.52195 (16177) hydrogen bonds : bond 0.02930 ( 330) hydrogen bonds : angle 4.85389 ( 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 188 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.424 Fit side-chains REVERT: A 199 ARG cc_start: 0.7692 (ttm110) cc_final: 0.7370 (ttm110) REVERT: A 383 MET cc_start: 0.8342 (ppp) cc_final: 0.7620 (mmt) REVERT: B 32 GLN cc_start: 0.7836 (tm-30) cc_final: 0.7436 (pt0) REVERT: B 55 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7736 (tt) REVERT: B 124 TYR cc_start: 0.8663 (m-80) cc_final: 0.8462 (m-10) REVERT: B 188 MET cc_start: 0.9166 (mmt) cc_final: 0.8853 (mmt) REVERT: G 20 LYS cc_start: 0.8171 (tmtt) cc_final: 0.7944 (tmtt) REVERT: C 9 GLN cc_start: 0.8035 (pp30) cc_final: 0.7619 (pp30) REVERT: C 48 ARG cc_start: 0.6887 (ttp-170) cc_final: 0.4459 (mmm160) REVERT: C 124 TYR cc_start: 0.8687 (m-10) cc_final: 0.8435 (m-10) REVERT: C 246 ASP cc_start: 0.8097 (t0) cc_final: 0.7779 (t0) REVERT: C 262 MET cc_start: 0.5829 (tpp) cc_final: 0.5319 (tpp) outliers start: 26 outliers final: 21 residues processed: 176 average time/residue: 0.0906 time to fit residues: 22.8460 Evaluate side-chains 173 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 105 THR 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 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 234 PHE Chi-restraints excluded: chain B residue 243 THR 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 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: 0.0770 chunk 107 optimal weight: 0.4980 chunk 120 optimal weight: 3.9990 chunk 31 optimal weight: 0.0870 chunk 66 optimal weight: 0.7980 chunk 110 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 103 optimal weight: 0.0670 chunk 25 optimal weight: 0.6980 overall best weight: 0.2854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.133015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105063 restraints weight = 16892.992| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.26 r_work: 0.3210 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11939 Z= 0.087 Angle : 0.510 8.977 16177 Z= 0.263 Chirality : 0.042 0.141 1826 Planarity : 0.003 0.073 2097 Dihedral : 4.140 29.321 1632 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.74 % Allowed : 20.79 % Favored : 77.47 % 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 aren not related in a simple way. whole: -2.08 (0.21), residues: 1486 helix: -0.56 (0.28), residues: 358 sheet: -1.65 (0.25), residues: 369 loop : -1.59 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 76 TYR 0.017 0.001 TYR D 40 PHE 0.017 0.001 PHE C 199 TRP 0.010 0.001 TRP C 169 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00195 (11939) covalent geometry : angle 0.50982 (16177) hydrogen bonds : bond 0.02724 ( 330) hydrogen bonds : angle 4.69492 ( 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 184 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.294 Fit side-chains REVERT: B 32 GLN cc_start: 0.7851 (tm-30) cc_final: 0.7440 (pt0) REVERT: B 55 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7759 (tt) REVERT: B 91 HIS cc_start: 0.8341 (m90) cc_final: 0.8135 (m90) REVERT: B 188 MET cc_start: 0.9116 (mmt) cc_final: 0.8822 (mmt) REVERT: C 9 GLN cc_start: 0.8035 (pp30) cc_final: 0.7644 (pp30) REVERT: C 48 ARG cc_start: 0.6806 (ttp-170) cc_final: 0.4333 (mmm160) REVERT: C 89 LYS cc_start: 0.8703 (mttt) cc_final: 0.8412 (mttt) REVERT: C 246 ASP cc_start: 0.7887 (t0) cc_final: 0.7569 (t0) REVERT: C 262 MET cc_start: 0.5889 (tpp) cc_final: 0.5411 (tpp) outliers start: 22 outliers final: 18 residues processed: 176 average time/residue: 0.0918 time to fit residues: 22.6282 Evaluate side-chains 171 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 214 GLU 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 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 87 THR 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 112 VAL Chi-restraints excluded: chain C residue 179 THR 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: 2.9990 chunk 104 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 73 optimal weight: 0.0020 chunk 141 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.129139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.101717 restraints weight = 17338.739| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.34 r_work: 0.3138 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11939 Z= 0.171 Angle : 0.578 8.881 16177 Z= 0.296 Chirality : 0.044 0.186 1826 Planarity : 0.004 0.076 2097 Dihedral : 4.446 29.501 1632 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.82 % Allowed : 21.19 % Favored : 77.00 % 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 aren not related in a simple way. whole: -2.18 (0.21), residues: 1486 helix: -0.69 (0.28), residues: 355 sheet: -1.72 (0.25), residues: 377 loop : -1.61 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 729 TYR 0.018 0.002 TYR B 124 PHE 0.016 0.001 PHE A 216 TRP 0.023 0.001 TRP C 169 HIS 0.004 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00418 (11939) covalent geometry : angle 0.57751 (16177) hydrogen bonds : bond 0.03297 ( 330) hydrogen bonds : angle 4.88385 ( 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 172 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.324 Fit side-chains REVERT: A 750 ASP cc_start: 0.8458 (m-30) cc_final: 0.8166 (m-30) REVERT: B 32 GLN cc_start: 0.7873 (tm-30) cc_final: 0.7453 (pt0) REVERT: B 55 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7779 (tt) REVERT: B 188 MET cc_start: 0.9192 (mmt) cc_final: 0.8826 (mmt) REVERT: B 234 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.7749 (t80) REVERT: C 9 GLN cc_start: 0.8059 (pp30) cc_final: 0.7854 (pp30) REVERT: C 48 ARG cc_start: 0.6971 (ttp-170) cc_final: 0.4409 (ttp-170) REVERT: C 246 ASP cc_start: 0.8051 (t0) cc_final: 0.7720 (t0) REVERT: C 262 MET cc_start: 0.5974 (tpp) cc_final: 0.5411 (tpp) outliers start: 23 outliers final: 21 residues processed: 163 average time/residue: 0.0872 time to fit residues: 20.0908 Evaluate side-chains 171 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 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 87 THR 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 95 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 179 THR 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: 0.7980 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 104 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.131415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.102754 restraints weight = 17135.045| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.40 r_work: 0.3170 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11939 Z= 0.108 Angle : 0.535 8.757 16177 Z= 0.274 Chirality : 0.043 0.173 1826 Planarity : 0.004 0.078 2097 Dihedral : 4.292 29.775 1632 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.74 % Allowed : 21.19 % Favored : 77.08 % 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 aren not related in a simple way. whole: -2.05 (0.21), residues: 1486 helix: -0.52 (0.28), residues: 357 sheet: -1.61 (0.25), residues: 374 loop : -1.58 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 729 TYR 0.015 0.001 TYR G 40 PHE 0.015 0.001 PHE C 199 TRP 0.016 0.001 TRP C 169 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00258 (11939) covalent geometry : angle 0.53538 (16177) hydrogen bonds : bond 0.02926 ( 330) hydrogen bonds : angle 4.78602 ( 936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2509.23 seconds wall clock time: 43 minutes 35.28 seconds (2615.28 seconds total)