Starting phenix.real_space_refine on Wed Jun 18 10:16:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8emx_28268/06_2025/8emx_28268.cif Found real_map, /net/cci-nas-00/data/ceres_data/8emx_28268/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8emx_28268/06_2025/8emx_28268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8emx_28268/06_2025/8emx_28268.map" model { file = "/net/cci-nas-00/data/ceres_data/8emx_28268/06_2025/8emx_28268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8emx_28268/06_2025/8emx_28268.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} 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: {'GLU:plan': 1, 'ARG: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: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'ARG:plan': 3} 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: 7.00, per 1000 atoms: 0.60 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: 2.44 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.38 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: 4.16 Time building geometry restraints manager: 3.01 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: 3.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 30.100 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.020 ------------------------------------------------------------------------------- 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 : 4.73 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.002 TRP A 356 HIS 0.007 0.002 HIS C 183 PHE 0.024 0.002 PHE B 241 TYR 0.024 0.002 TYR A 746 ARG 0.004 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.22573 ( 330) hydrogen bonds : angle 8.38535 ( 936) covalent geometry : bond 0.00561 (11939) covalent geometry : angle 0.80867 (16177) *********************** 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 : 1.392 Fit side-chains REVERT: A 228 LYS cc_start: 0.8261 (tmmt) cc_final: 0.8002 (tttt) REVERT: A 729 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7787 (mtp85) REVERT: B 188 MET cc_start: 0.8526 (mmt) cc_final: 0.8182 (mmt) REVERT: G 14 LYS cc_start: 0.8085 (tppp) cc_final: 0.7658 (tppp) REVERT: G 18 GLN cc_start: 0.7988 (mt0) cc_final: 0.7765 (mt0) REVERT: G 27 ARG cc_start: 0.7433 (mtp85) cc_final: 0.7151 (mtp85) REVERT: C 45 MET cc_start: 0.7567 (mtp) cc_final: 0.7181 (mtp) REVERT: C 48 ARG cc_start: 0.6597 (ttp-170) cc_final: 0.4370 (ttp-170) REVERT: C 246 ASP cc_start: 0.7772 (t0) cc_final: 0.7321 (t0) REVERT: D 17 GLU cc_start: 0.8301 (tp30) cc_final: 0.7328 (mm-30) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2878 time to fit residues: 73.9599 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 : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 0.1980 chunk 86 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.122320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.091861 restraints weight = 17550.996| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.81 r_work: 0.2993 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 11939 Z= 0.235 Angle : 0.642 9.879 16177 Z= 0.339 Chirality : 0.045 0.155 1826 Planarity : 0.005 0.083 2097 Dihedral : 5.407 37.712 1632 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.06 % Allowed : 13.83 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.18), residues: 1486 helix: -2.46 (0.23), residues: 353 sheet: -2.66 (0.21), residues: 385 loop : -2.44 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 169 HIS 0.009 0.001 HIS C 183 PHE 0.018 0.002 PHE B 241 TYR 0.022 0.002 TYR A 746 ARG 0.007 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.04704 ( 330) hydrogen bonds : angle 5.83611 ( 936) covalent geometry : bond 0.00569 (11939) covalent geometry : angle 0.64192 (16177) *********************** 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 187 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 1.246 Fit side-chains REVERT: A 289 ASP cc_start: 0.7866 (m-30) cc_final: 0.6660 (p0) REVERT: A 383 MET cc_start: 0.8403 (ppp) cc_final: 0.7962 (mmt) REVERT: A 750 ASP cc_start: 0.8365 (m-30) cc_final: 0.8004 (m-30) REVERT: B 32 GLN cc_start: 0.7811 (tm-30) cc_final: 0.7276 (pt0) REVERT: B 55 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7737 (tt) REVERT: B 163 ASP cc_start: 0.8360 (t70) cc_final: 0.8111 (t0) REVERT: G 14 LYS cc_start: 0.8029 (tppp) cc_final: 0.7825 (tppt) REVERT: G 18 GLN cc_start: 0.8656 (mt0) cc_final: 0.8358 (mt0) REVERT: G 32 LYS cc_start: 0.8826 (tptm) cc_final: 0.8619 (tppt) REVERT: C 45 MET cc_start: 0.8182 (mtp) cc_final: 0.7913 (mtp) REVERT: C 48 ARG cc_start: 0.6569 (ttp-170) cc_final: 0.4182 (ttp-170) REVERT: C 246 ASP cc_start: 0.8134 (t0) cc_final: 0.7647 (t0) outliers start: 26 outliers final: 21 residues processed: 174 average time/residue: 0.2561 time to fit residues: 62.9318 Evaluate side-chains 174 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 344 THR 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 739 SER 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 120 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 128 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 146 optimal weight: 7.9990 chunk 92 optimal weight: 0.0980 chunk 116 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 D 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.124533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.093962 restraints weight = 17697.186| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.87 r_work: 0.3036 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11939 Z= 0.122 Angle : 0.544 8.142 16177 Z= 0.284 Chirality : 0.043 0.141 1826 Planarity : 0.004 0.076 2097 Dihedral : 4.830 34.426 1632 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.90 % Allowed : 16.28 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.19), residues: 1486 helix: -1.74 (0.26), residues: 351 sheet: -2.34 (0.23), residues: 381 loop : -2.15 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.006 0.001 HIS D 44 PHE 0.012 0.001 PHE B 241 TYR 0.015 0.001 TYR A 746 ARG 0.006 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 330) hydrogen bonds : angle 5.30112 ( 936) covalent geometry : bond 0.00286 (11939) covalent geometry : angle 0.54426 (16177) *********************** 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 181 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 1.271 Fit side-chains REVERT: A 140 MET cc_start: 0.8231 (mmt) cc_final: 0.8025 (mmt) REVERT: A 199 ARG cc_start: 0.7828 (tmm160) cc_final: 0.7423 (ttm110) REVERT: A 289 ASP cc_start: 0.7888 (m-30) cc_final: 0.6690 (p0) REVERT: A 750 ASP cc_start: 0.8158 (m-30) cc_final: 0.7772 (m-30) REVERT: B 32 GLN cc_start: 0.7746 (tm-30) cc_final: 0.7248 (pt0) REVERT: B 55 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7712 (tt) REVERT: B 91 HIS cc_start: 0.8414 (m90) cc_final: 0.8083 (m-70) REVERT: B 138 GLU cc_start: 0.8300 (tp30) cc_final: 0.8071 (tp30) REVERT: B 163 ASP cc_start: 0.8248 (t70) cc_final: 0.8029 (t0) REVERT: B 188 MET cc_start: 0.9018 (mmt) cc_final: 0.8644 (mmt) REVERT: G 14 LYS cc_start: 0.8056 (tppp) cc_final: 0.7814 (tppt) REVERT: G 18 GLN cc_start: 0.8643 (mt0) cc_final: 0.8332 (mt0) REVERT: G 32 LYS cc_start: 0.8766 (tptm) cc_final: 0.8528 (tppt) REVERT: C 9 GLN cc_start: 0.7974 (pp30) cc_final: 0.7680 (pp30) REVERT: C 45 MET cc_start: 0.8142 (mtp) cc_final: 0.7847 (mtp) REVERT: C 48 ARG cc_start: 0.6529 (ttp-170) cc_final: 0.4152 (ttp-170) REVERT: C 246 ASP cc_start: 0.8064 (t0) cc_final: 0.7695 (t0) outliers start: 24 outliers final: 15 residues processed: 171 average time/residue: 0.2655 time to fit residues: 63.8628 Evaluate side-chains 164 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 344 THR 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 179 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain D residue 37 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 15 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 104 optimal weight: 0.0170 chunk 47 optimal weight: 3.9990 overall best weight: 2.3624 ------------------------------------------------------------------------------- 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 C 32 GLN C 295 ASN D 44 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.126290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.099356 restraints weight = 17293.217| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.38 r_work: 0.3095 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 11939 Z= 0.240 Angle : 0.625 8.726 16177 Z= 0.323 Chirality : 0.046 0.164 1826 Planarity : 0.004 0.068 2097 Dihedral : 5.033 36.653 1632 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.08 % Allowed : 16.76 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.20), residues: 1486 helix: -1.63 (0.26), residues: 353 sheet: -2.29 (0.23), residues: 384 loop : -2.17 (0.20), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 169 HIS 0.006 0.001 HIS C 183 PHE 0.030 0.002 PHE C 199 TYR 0.022 0.002 TYR A 746 ARG 0.003 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 330) hydrogen bonds : angle 5.36603 ( 936) covalent geometry : bond 0.00586 (11939) covalent geometry : angle 0.62461 (16177) *********************** 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 191 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 1.222 Fit side-chains REVERT: A 199 ARG cc_start: 0.8019 (tmm160) cc_final: 0.7728 (ttm110) REVERT: A 289 ASP cc_start: 0.7995 (m-30) cc_final: 0.6906 (p0) REVERT: A 383 MET cc_start: 0.8450 (ppp) cc_final: 0.7898 (mmt) REVERT: A 750 ASP cc_start: 0.8597 (m-30) cc_final: 0.8297 (m-30) REVERT: B 32 GLN cc_start: 0.7814 (tm-30) cc_final: 0.7347 (pt0) REVERT: B 55 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7823 (tt) REVERT: G 14 LYS cc_start: 0.8174 (tppp) cc_final: 0.7970 (tppt) REVERT: G 18 GLN cc_start: 0.8658 (mt0) cc_final: 0.8426 (mt0) REVERT: C 9 GLN cc_start: 0.8030 (pp30) cc_final: 0.7690 (pp30) REVERT: C 48 ARG cc_start: 0.6914 (ttp-170) cc_final: 0.4461 (ttp-170) REVERT: C 246 ASP cc_start: 0.8223 (t0) cc_final: 0.7885 (t0) outliers start: 39 outliers final: 28 residues processed: 179 average time/residue: 0.2386 time to fit residues: 60.6665 Evaluate side-chains 177 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 1.262 ------------------------------------------------------------------------------- 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 172 VAL Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 344 THR 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 771 SER Chi-restraints excluded: chain A residue 790 THR 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 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 D residue 37 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 139 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 30 optimal weight: 0.0670 chunk 141 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 overall best weight: 2.1724 ------------------------------------------------------------------------------- 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 D 18 GLN D 44 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.126190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.099129 restraints weight = 17242.950| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.33 r_work: 0.3105 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 11939 Z= 0.221 Angle : 0.608 8.726 16177 Z= 0.315 Chirality : 0.045 0.187 1826 Planarity : 0.004 0.069 2097 Dihedral : 5.007 35.780 1632 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.16 % Allowed : 17.87 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.20), residues: 1486 helix: -1.49 (0.26), residues: 353 sheet: -2.22 (0.23), residues: 381 loop : -2.14 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.004 0.001 HIS C 183 PHE 0.022 0.002 PHE C 199 TYR 0.024 0.002 TYR D 40 ARG 0.004 0.000 ARG A 729 Details of bonding type rmsd hydrogen bonds : bond 0.03811 ( 330) hydrogen bonds : angle 5.29782 ( 936) covalent geometry : bond 0.00541 (11939) covalent geometry : angle 0.60844 (16177) *********************** 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 189 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 1.214 Fit side-chains REVERT: A 199 ARG cc_start: 0.8025 (tmm160) cc_final: 0.7761 (ttm110) REVERT: A 289 ASP cc_start: 0.8004 (m-30) cc_final: 0.6956 (p0) REVERT: A 750 ASP cc_start: 0.8543 (m-30) cc_final: 0.8250 (m-30) REVERT: B 32 GLN cc_start: 0.7840 (tm-30) cc_final: 0.7391 (pt0) REVERT: B 55 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7794 (tt) REVERT: B 124 TYR cc_start: 0.8820 (m-80) cc_final: 0.8156 (m-10) REVERT: G 14 LYS cc_start: 0.8189 (tppp) cc_final: 0.7984 (tppt) REVERT: G 18 GLN cc_start: 0.8659 (mt0) cc_final: 0.8448 (mt0) REVERT: C 9 GLN cc_start: 0.8040 (pp30) cc_final: 0.7673 (pp30) REVERT: C 48 ARG cc_start: 0.6956 (ttp-170) cc_final: 0.4520 (ttp-170) REVERT: C 246 ASP cc_start: 0.8197 (t0) cc_final: 0.7833 (t0) REVERT: C 262 MET cc_start: 0.5829 (tpp) cc_final: 0.5218 (tpp) outliers start: 40 outliers final: 32 residues processed: 178 average time/residue: 0.2397 time to fit residues: 61.2533 Evaluate side-chains 178 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL 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 73 ARG Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 344 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 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 B residue 243 THR Chi-restraints excluded: chain B residue 321 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 137 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 D 18 GLN D 44 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.128001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.100777 restraints weight = 17254.732| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.42 r_work: 0.3117 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11939 Z= 0.146 Angle : 0.554 7.840 16177 Z= 0.287 Chirality : 0.043 0.172 1826 Planarity : 0.004 0.070 2097 Dihedral : 4.742 32.874 1632 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.16 % Allowed : 18.42 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.20), residues: 1486 helix: -1.27 (0.27), residues: 354 sheet: -2.11 (0.24), residues: 374 loop : -1.98 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.007 0.001 HIS D 44 PHE 0.019 0.001 PHE C 199 TYR 0.016 0.001 TYR A 746 ARG 0.003 0.000 ARG A 729 Details of bonding type rmsd hydrogen bonds : bond 0.03366 ( 330) hydrogen bonds : angle 5.08793 ( 936) covalent geometry : bond 0.00354 (11939) covalent geometry : angle 0.55411 (16177) *********************** 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 195 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 1.282 Fit side-chains REVERT: A 199 ARG cc_start: 0.8071 (tmm160) cc_final: 0.7572 (ttm110) REVERT: A 289 ASP cc_start: 0.7975 (m-30) cc_final: 0.6837 (p0) REVERT: A 383 MET cc_start: 0.8430 (ppp) cc_final: 0.7804 (mmt) REVERT: A 750 ASP cc_start: 0.8489 (m-30) cc_final: 0.8185 (m-30) REVERT: B 32 GLN cc_start: 0.7837 (tm-30) cc_final: 0.7419 (pt0) REVERT: B 55 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7752 (tt) REVERT: B 124 TYR cc_start: 0.8795 (m-80) cc_final: 0.8206 (m-10) REVERT: B 188 MET cc_start: 0.9189 (mmt) cc_final: 0.8847 (mmt) REVERT: G 14 LYS cc_start: 0.8142 (tppp) cc_final: 0.7888 (tppp) REVERT: G 18 GLN cc_start: 0.8643 (mt0) cc_final: 0.8438 (mt0) REVERT: C 9 GLN cc_start: 0.8037 (pp30) cc_final: 0.7677 (pp30) REVERT: C 48 ARG cc_start: 0.6903 (ttp-170) cc_final: 0.4462 (ttp-170) REVERT: C 246 ASP cc_start: 0.8162 (t0) cc_final: 0.7837 (t0) REVERT: D 32 LYS cc_start: 0.8981 (ttpt) cc_final: 0.8762 (ttpt) outliers start: 40 outliers final: 34 residues processed: 182 average time/residue: 0.2440 time to fit residues: 63.3551 Evaluate side-chains 181 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 21 THR 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 330 SER Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 764 THR 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 47 THR 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 321 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 95 LEU 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 48 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** 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 = 0.3616 r_free = 0.3616 target = 0.126539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.099793 restraints weight = 17468.009| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.34 r_work: 0.3118 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 11939 Z= 0.203 Angle : 0.598 8.208 16177 Z= 0.309 Chirality : 0.045 0.156 1826 Planarity : 0.004 0.072 2097 Dihedral : 4.896 33.976 1632 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.48 % Allowed : 18.97 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.20), residues: 1486 helix: -1.31 (0.27), residues: 358 sheet: -2.06 (0.24), residues: 375 loop : -2.01 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 169 HIS 0.007 0.001 HIS D 44 PHE 0.018 0.002 PHE C 199 TYR 0.028 0.002 TYR G 40 ARG 0.006 0.000 ARG A 729 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 330) hydrogen bonds : angle 5.17637 ( 936) covalent geometry : bond 0.00497 (11939) covalent geometry : angle 0.59817 (16177) *********************** 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 194 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 1.330 Fit side-chains REVERT: A 199 ARG cc_start: 0.8061 (tmm160) cc_final: 0.7587 (ttm110) REVERT: A 289 ASP cc_start: 0.7984 (m-30) cc_final: 0.6867 (p0) REVERT: A 729 ARG cc_start: 0.8725 (mtp85) cc_final: 0.8491 (mtp85) REVERT: A 750 ASP cc_start: 0.8499 (m-30) cc_final: 0.8209 (m-30) REVERT: B 32 GLN cc_start: 0.7856 (tm-30) cc_final: 0.7446 (pt0) REVERT: B 55 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7779 (tt) REVERT: G 14 LYS cc_start: 0.8181 (tppp) cc_final: 0.7919 (tppp) REVERT: G 48 ASP cc_start: 0.7553 (t0) cc_final: 0.7312 (m-30) REVERT: C 48 ARG cc_start: 0.6929 (ttp-170) cc_final: 0.4544 (ttp-170) REVERT: C 246 ASP cc_start: 0.8100 (t0) cc_final: 0.7793 (t0) REVERT: C 262 MET cc_start: 0.5934 (tpp) cc_final: 0.5427 (tpp) REVERT: D 32 LYS cc_start: 0.8979 (ttpt) cc_final: 0.8742 (ttpt) outliers start: 44 outliers final: 39 residues processed: 179 average time/residue: 0.2385 time to fit residues: 61.1588 Evaluate side-chains 187 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL 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 73 ARG Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 764 THR 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 47 THR 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 B residue 243 THR Chi-restraints excluded: chain B residue 321 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 243 THR 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 6 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 25 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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** D 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.130249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.101872 restraints weight = 17193.703| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.36 r_work: 0.3157 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11939 Z= 0.102 Angle : 0.535 9.350 16177 Z= 0.276 Chirality : 0.043 0.142 1826 Planarity : 0.004 0.072 2097 Dihedral : 4.537 29.627 1632 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.53 % Allowed : 19.68 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.20), residues: 1486 helix: -0.89 (0.28), residues: 353 sheet: -1.93 (0.24), residues: 374 loop : -1.81 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.003 0.001 HIS C 311 PHE 0.017 0.001 PHE C 199 TYR 0.023 0.001 TYR G 40 ARG 0.009 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.03010 ( 330) hydrogen bonds : angle 4.91837 ( 936) covalent geometry : bond 0.00238 (11939) covalent geometry : angle 0.53510 (16177) *********************** 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 189 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 1.287 Fit side-chains REVERT: A 199 ARG cc_start: 0.8050 (tmm160) cc_final: 0.7681 (tpp80) REVERT: A 289 ASP cc_start: 0.7914 (m-30) cc_final: 0.6832 (p0) REVERT: A 383 MET cc_start: 0.8340 (ppp) cc_final: 0.7617 (mmt) REVERT: A 750 ASP cc_start: 0.8375 (m-30) cc_final: 0.8081 (m-30) REVERT: B 32 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7465 (pt0) REVERT: B 55 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7744 (tt) REVERT: B 124 TYR cc_start: 0.8833 (m-10) cc_final: 0.8518 (m-10) REVERT: B 188 MET cc_start: 0.9181 (mmt) cc_final: 0.8875 (mmt) REVERT: G 14 LYS cc_start: 0.8085 (tppp) cc_final: 0.7739 (tppp) REVERT: C 9 GLN cc_start: 0.7942 (pp30) cc_final: 0.7718 (pp30) REVERT: C 48 ARG cc_start: 0.6890 (ttp-170) cc_final: 0.4458 (ttp-170) REVERT: C 246 ASP cc_start: 0.8075 (t0) cc_final: 0.7771 (t0) REVERT: C 262 MET cc_start: 0.5927 (tpp) cc_final: 0.5413 (tpp) outliers start: 32 outliers final: 28 residues processed: 176 average time/residue: 0.2567 time to fit residues: 63.5737 Evaluate side-chains 175 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 47 THR 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 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 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 92 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 chunk 142 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 128 optimal weight: 0.2980 chunk 72 optimal weight: 6.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.126458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.099882 restraints weight = 17350.982| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.20 r_work: 0.3121 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 11939 Z= 0.229 Angle : 0.617 10.027 16177 Z= 0.317 Chirality : 0.046 0.200 1826 Planarity : 0.004 0.074 2097 Dihedral : 4.858 32.954 1632 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.00 % Allowed : 20.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.20), residues: 1486 helix: -1.14 (0.27), residues: 358 sheet: -1.95 (0.24), residues: 379 loop : -1.91 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 169 HIS 0.005 0.001 HIS D 44 PHE 0.018 0.002 PHE A 216 TYR 0.022 0.002 TYR G 40 ARG 0.006 0.000 ARG A 729 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 330) hydrogen bonds : angle 5.13521 ( 936) covalent geometry : bond 0.00560 (11939) covalent geometry : angle 0.61671 (16177) *********************** 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 186 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 1.330 Fit side-chains REVERT: A 199 ARG cc_start: 0.8055 (tmm160) cc_final: 0.7701 (tpp80) REVERT: A 289 ASP cc_start: 0.7950 (m-30) cc_final: 0.6837 (p0) REVERT: A 750 ASP cc_start: 0.8476 (m-30) cc_final: 0.8186 (m-30) REVERT: B 32 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7495 (pt0) REVERT: B 55 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7795 (tt) REVERT: G 14 LYS cc_start: 0.8106 (tppp) cc_final: 0.7829 (tppp) REVERT: C 9 GLN cc_start: 0.7979 (pp30) cc_final: 0.7750 (pp30) REVERT: C 48 ARG cc_start: 0.6943 (ttp-170) cc_final: 0.3793 (mmm160) REVERT: C 246 ASP cc_start: 0.8058 (t0) cc_final: 0.7753 (t0) REVERT: C 262 MET cc_start: 0.5946 (tpp) cc_final: 0.5413 (tpp) outliers start: 38 outliers final: 37 residues processed: 175 average time/residue: 0.2529 time to fit residues: 62.5121 Evaluate side-chains 185 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 47 THR 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 B residue 243 THR Chi-restraints excluded: chain B residue 321 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 95 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 152 LEU 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 243 THR 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 118 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 48 optimal weight: 0.0670 chunk 123 optimal weight: 0.8980 chunk 115 optimal weight: 0.0770 chunk 60 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 137 optimal weight: 0.0170 chunk 44 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 overall best weight: 0.2914 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.132314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.105195 restraints weight = 16983.613| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.31 r_work: 0.3178 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11939 Z= 0.091 Angle : 0.528 8.933 16177 Z= 0.272 Chirality : 0.042 0.146 1826 Planarity : 0.004 0.073 2097 Dihedral : 4.380 30.440 1632 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.98 % Allowed : 21.11 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.21), residues: 1486 helix: -0.68 (0.28), residues: 351 sheet: -1.83 (0.25), residues: 372 loop : -1.73 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS C 225 PHE 0.015 0.001 PHE C 199 TYR 0.020 0.001 TYR G 40 ARG 0.004 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.02794 ( 330) hydrogen bonds : angle 4.81933 ( 936) covalent geometry : bond 0.00205 (11939) covalent geometry : angle 0.52807 (16177) ********************** 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 186 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 1.362 Fit side-chains REVERT: A 199 ARG cc_start: 0.8031 (tmm160) cc_final: 0.7725 (tpp80) REVERT: A 289 ASP cc_start: 0.7897 (m-30) cc_final: 0.6824 (p0) REVERT: A 383 MET cc_start: 0.8296 (ppp) cc_final: 0.7460 (mmt) REVERT: A 750 ASP cc_start: 0.8295 (m-30) cc_final: 0.8024 (m-30) REVERT: B 32 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7529 (pt0) REVERT: B 55 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7728 (tt) REVERT: B 188 MET cc_start: 0.9184 (mmt) cc_final: 0.8888 (mmt) REVERT: C 9 GLN cc_start: 0.7958 (pp30) cc_final: 0.7682 (pp30) REVERT: C 48 ARG cc_start: 0.6867 (ttp-170) cc_final: 0.4283 (ttp-170) REVERT: C 246 ASP cc_start: 0.7942 (t0) cc_final: 0.7623 (t0) REVERT: C 262 MET cc_start: 0.5975 (tpp) cc_final: 0.5503 (tpp) outliers start: 25 outliers final: 20 residues processed: 177 average time/residue: 0.2677 time to fit residues: 66.4360 Evaluate side-chains 169 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 344 THR 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 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 C residue 243 THR 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 13 optimal weight: 0.0980 chunk 19 optimal weight: 2.9990 chunk 42 optimal weight: 0.1980 chunk 67 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.134487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.110040 restraints weight = 17273.582| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.12 r_work: 0.3248 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11939 Z= 0.102 Angle : 0.531 8.448 16177 Z= 0.273 Chirality : 0.043 0.149 1826 Planarity : 0.004 0.076 2097 Dihedral : 4.248 23.282 1632 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.66 % Allowed : 21.82 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.21), residues: 1486 helix: -0.56 (0.28), residues: 355 sheet: -1.70 (0.25), residues: 373 loop : -1.62 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.004 0.001 HIS C 225 PHE 0.016 0.001 PHE C 199 TYR 0.020 0.001 TYR G 40 ARG 0.008 0.000 ARG A 729 Details of bonding type rmsd hydrogen bonds : bond 0.02853 ( 330) hydrogen bonds : angle 4.77722 ( 936) covalent geometry : bond 0.00238 (11939) covalent geometry : angle 0.53148 (16177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6797.20 seconds wall clock time: 116 minutes 52.58 seconds (7012.58 seconds total)