Starting phenix.real_space_refine on Mon Jun 9 03:04:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wk1_32555/06_2025/7wk1_32555.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wk1_32555/06_2025/7wk1_32555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wk1_32555/06_2025/7wk1_32555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wk1_32555/06_2025/7wk1_32555.map" model { file = "/net/cci-nas-00/data/ceres_data/7wk1_32555/06_2025/7wk1_32555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wk1_32555/06_2025/7wk1_32555.cif" } resolution = 3.25 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 42 5.16 5 Cl 2 4.86 5 C 6656 2.51 5 N 1684 2.21 5 O 1816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 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: 10200 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.74, per 1000 atoms: 0.66 Number of scatterers: 10200 At special positions: 0 Unit cell: (86.818, 126.566, 117.152, 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) Cl 2 17.00 S 42 16.00 O 1816 8.00 N 1684 7.00 C 6656 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: 2.68 Conformation dependent library (CDL) restraints added in 1.2 seconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 7 sheets defined 66.8% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.602A pdb=" N CYS A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.882A pdb=" N ALA A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 removed outlier: 4.054A pdb=" N TRP A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 75' Processing helix chain 'A' and resid 79 through 106 removed outlier: 4.909A pdb=" N LEU A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 120 removed outlier: 3.851A pdb=" N GLY A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 141 through 156 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.804A pdb=" N HIS A 160 " --> pdb=" O PRO A 157 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 161 " --> pdb=" O ASP A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 161' Processing helix chain 'A' and resid 179 through 206 removed outlier: 3.883A pdb=" N ALA A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.563A pdb=" N VAL A 212 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR A 214 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 241 Processing helix chain 'A' and resid 251 through 263 Processing helix chain 'A' and resid 268 through 292 Processing helix chain 'A' and resid 301 through 317 removed outlier: 3.621A pdb=" N ALA A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 374 Processing helix chain 'A' and resid 380 through 397 removed outlier: 3.758A pdb=" N GLU A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 417 removed outlier: 3.716A pdb=" N VAL A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 437 removed outlier: 3.662A pdb=" N VAL A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 458 removed outlier: 3.784A pdb=" N LEU A 450 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 475 through 492 removed outlier: 3.515A pdb=" N ALA A 479 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 490 " --> pdb=" O CYS A 486 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 515 removed outlier: 3.569A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 573 through 595 removed outlier: 3.782A pdb=" N TYR A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 591 " --> pdb=" O ARG A 587 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 686 removed outlier: 3.754A pdb=" N SER A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 706 removed outlier: 3.562A pdb=" N GLN A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 718 removed outlier: 3.529A pdb=" N ARG A 717 " --> pdb=" O ARG A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 removed outlier: 3.857A pdb=" N ALA A 725 " --> pdb=" O THR A 721 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 726 " --> pdb=" O VAL A 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.552A pdb=" N LEU B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 removed outlier: 3.752A pdb=" N ALA B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 4.080A pdb=" N TRP B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 105 removed outlier: 3.729A pdb=" N SER B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 110 Processing helix chain 'B' and resid 113 through 119 removed outlier: 3.978A pdb=" N LEU B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 119 " --> pdb=" O PHE B 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 113 through 119' Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 141 through 156 removed outlier: 3.659A pdb=" N VAL B 151 " --> pdb=" O MET B 147 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.571A pdb=" N HIS B 160 " --> pdb=" O PRO B 157 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 161' Processing helix chain 'B' and resid 180 through 206 removed outlier: 3.981A pdb=" N ALA B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.590A pdb=" N VAL B 212 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR B 214 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 241 removed outlier: 3.569A pdb=" N PHE B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 268 through 292 removed outlier: 3.641A pdb=" N THR B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 317 removed outlier: 3.514A pdb=" N ALA B 317 " --> pdb=" O ILE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 376 removed outlier: 3.795A pdb=" N SER B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS B 375 " --> pdb=" O TYR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 397 removed outlier: 3.963A pdb=" N GLU B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 416 removed outlier: 3.740A pdb=" N VAL B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 437 removed outlier: 3.611A pdb=" N VAL B 436 " --> pdb=" O MET B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 458 removed outlier: 3.779A pdb=" N LEU B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 475 through 492 removed outlier: 3.550A pdb=" N ALA B 479 " --> pdb=" O ASN B 475 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE B 490 " --> pdb=" O CYS B 486 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 515 removed outlier: 3.544A pdb=" N LEU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 571 Processing helix chain 'B' and resid 573 through 595 removed outlier: 3.845A pdb=" N TYR B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG B 587 " --> pdb=" O LYS B 583 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS B 593 " --> pdb=" O GLN B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 685 removed outlier: 4.733A pdb=" N SER B 675 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 676 " --> pdb=" O GLY B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 706 removed outlier: 3.828A pdb=" N LYS B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 718 removed outlier: 3.551A pdb=" N ARG B 717 " --> pdb=" O ARG B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 736 removed outlier: 3.803A pdb=" N ALA B 725 " --> pdb=" O THR B 721 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 726 " --> pdb=" O VAL B 722 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 25 removed outlier: 3.607A pdb=" N VAL A 22 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 22 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA3, first strand: chain 'A' and resid 522 through 523 Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 549 removed outlier: 6.670A pdb=" N LYS A 546 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASP A 661 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU A 548 " --> pdb=" O ASP A 661 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AA6, first strand: chain 'B' and resid 522 through 523 Processing sheet with id=AA7, first strand: chain 'B' and resid 545 through 549 removed outlier: 6.675A pdb=" N LYS B 546 " --> pdb=" O VAL B 659 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASP B 661 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU B 548 " --> pdb=" O ASP B 661 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1674 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.04 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3212 1.34 - 1.46: 2260 1.46 - 1.58: 4864 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 10400 Sorted by residual: bond pdb=" CA VAL A 163 " pdb=" CB VAL A 163 " ideal model delta sigma weight residual 1.540 1.527 0.014 1.23e-02 6.61e+03 1.21e+00 bond pdb=" C VAL B 653 " pdb=" N PRO B 654 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.04e-01 bond pdb=" C VAL A 653 " pdb=" N PRO A 654 " ideal model delta sigma weight residual 1.334 1.353 -0.020 2.34e-02 1.83e+03 6.95e-01 bond pdb=" CA ASP A 669 " pdb=" C ASP A 669 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.34e-02 5.57e+03 5.79e-01 bond pdb=" C GLY B 166 " pdb=" N ASN B 167 " ideal model delta sigma weight residual 1.328 1.338 -0.010 1.30e-02 5.92e+03 5.79e-01 ... (remaining 10395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 13817 1.22 - 2.43: 242 2.43 - 3.65: 55 3.65 - 4.87: 14 4.87 - 6.08: 8 Bond angle restraints: 14136 Sorted by residual: angle pdb=" C ASP B 467 " pdb=" N VAL B 468 " pdb=" CA VAL B 468 " ideal model delta sigma weight residual 120.33 122.69 -2.36 8.00e-01 1.56e+00 8.69e+00 angle pdb=" C ASP A 669 " pdb=" N VAL A 670 " pdb=" CA VAL A 670 " ideal model delta sigma weight residual 121.97 126.24 -4.27 1.80e+00 3.09e-01 5.62e+00 angle pdb=" N VAL A 80 " pdb=" CA VAL A 80 " pdb=" C VAL A 80 " ideal model delta sigma weight residual 109.34 113.75 -4.41 2.08e+00 2.31e-01 4.49e+00 angle pdb=" C ARG A 79 " pdb=" N VAL A 80 " pdb=" CA VAL A 80 " ideal model delta sigma weight residual 121.97 125.66 -3.69 1.80e+00 3.09e-01 4.20e+00 angle pdb=" C ASP B 669 " pdb=" N VAL B 670 " pdb=" CA VAL B 670 " ideal model delta sigma weight residual 121.97 125.56 -3.59 1.80e+00 3.09e-01 3.99e+00 ... (remaining 14131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 5999 17.18 - 34.36: 150 34.36 - 51.53: 22 51.53 - 68.71: 6 68.71 - 85.89: 5 Dihedral angle restraints: 6182 sinusoidal: 2346 harmonic: 3836 Sorted by residual: dihedral pdb=" CA ASP A 669 " pdb=" C ASP A 669 " pdb=" N VAL A 670 " pdb=" CA VAL A 670 " ideal model delta harmonic sigma weight residual -180.00 -164.27 -15.73 0 5.00e+00 4.00e-02 9.90e+00 dihedral pdb=" N LYS A 681 " pdb=" CA LYS A 681 " pdb=" CB LYS A 681 " pdb=" CG LYS A 681 " ideal model delta sinusoidal sigma weight residual -180.00 -121.99 -58.01 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N LEU A 496 " pdb=" CA LEU A 496 " pdb=" CB LEU A 496 " pdb=" CG LEU A 496 " ideal model delta sinusoidal sigma weight residual -60.00 -113.85 53.85 3 1.50e+01 4.44e-03 9.24e+00 ... (remaining 6179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 985 0.026 - 0.053: 479 0.053 - 0.079: 171 0.079 - 0.105: 65 0.105 - 0.131: 18 Chirality restraints: 1718 Sorted by residual: chirality pdb=" CA PRO A 553 " pdb=" N PRO A 553 " pdb=" C PRO A 553 " pdb=" CB PRO A 553 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA PRO B 553 " pdb=" N PRO B 553 " pdb=" C PRO B 553 " pdb=" CB PRO B 553 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE A 331 " pdb=" N ILE A 331 " pdb=" C ILE A 331 " pdb=" CB ILE A 331 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 1715 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 552 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO B 553 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 553 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 553 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 552 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO A 553 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 553 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 553 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 111 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO A 112 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " 0.018 5.00e-02 4.00e+02 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1226 2.75 - 3.29: 10788 3.29 - 3.82: 16684 3.82 - 4.36: 19765 4.36 - 4.90: 33560 Nonbonded interactions: 82023 Sorted by model distance: nonbonded pdb=" OH TYR A 78 " pdb=" OD2 ASP A 87 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR A 118 " pdb=" O GLY A 334 " model vdw 2.225 3.040 nonbonded pdb=" O ASP A 669 " pdb=" N GLY A 672 " model vdw 2.238 3.120 nonbonded pdb=" OD1 ASN A 475 " pdb=" OG1 THR A 477 " model vdw 2.244 3.040 nonbonded pdb=" OD1 ASN B 475 " pdb=" OG1 THR B 477 " model vdw 2.248 3.040 ... (remaining 82018 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.460 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10400 Z= 0.091 Angle : 0.443 6.082 14136 Z= 0.251 Chirality : 0.037 0.131 1718 Planarity : 0.003 0.035 1758 Dihedral : 8.422 85.889 3710 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 2.94 % Allowed : 4.72 % Favored : 92.34 % 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: -4.01 (0.19), residues: 1322 helix: -2.20 (0.14), residues: 860 sheet: -3.22 (0.77), residues: 36 loop : -3.28 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 83 HIS 0.002 0.000 HIS A 656 PHE 0.009 0.001 PHE B 555 TYR 0.008 0.001 TYR A 127 ARG 0.001 0.000 ARG B 512 Details of bonding type rmsd hydrogen bonds : bond 0.23680 ( 570) hydrogen bonds : angle 7.26712 ( 1674) covalent geometry : bond 0.00169 (10400) covalent geometry : angle 0.44270 (14136) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 314 time to evaluate : 1.035 Fit side-chains REVERT: A 73 ASP cc_start: 0.7646 (t0) cc_final: 0.7313 (m-30) REVERT: A 119 SER cc_start: 0.8633 (t) cc_final: 0.8415 (p) REVERT: A 269 ILE cc_start: 0.8302 (pt) cc_final: 0.7931 (pt) REVERT: A 273 ILE cc_start: 0.8837 (mt) cc_final: 0.8585 (mt) REVERT: A 345 LEU cc_start: 0.6245 (mt) cc_final: 0.5738 (mt) REVERT: A 350 LEU cc_start: 0.5830 (OUTLIER) cc_final: 0.5410 (pt) REVERT: A 369 LYS cc_start: 0.8083 (mmtt) cc_final: 0.7580 (mttm) REVERT: A 385 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.7073 (t80) REVERT: A 560 ASP cc_start: 0.7912 (m-30) cc_final: 0.7648 (m-30) REVERT: A 580 LYS cc_start: 0.8180 (mmtt) cc_final: 0.7786 (mtpt) REVERT: B 66 LYS cc_start: 0.8607 (tppt) cc_final: 0.8018 (mttm) REVERT: B 73 ASP cc_start: 0.7799 (t0) cc_final: 0.7562 (t0) REVERT: B 77 LYS cc_start: 0.7489 (pttm) cc_final: 0.7013 (tptt) REVERT: B 134 ARG cc_start: 0.7776 (mtt90) cc_final: 0.7362 (mtp180) REVERT: B 350 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.5900 (tm) REVERT: B 355 SER cc_start: 0.8950 (m) cc_final: 0.8617 (t) REVERT: B 366 SER cc_start: 0.8939 (t) cc_final: 0.8231 (m) REVERT: B 560 ASP cc_start: 0.7781 (m-30) cc_final: 0.7536 (m-30) REVERT: B 580 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7937 (mtpt) outliers start: 33 outliers final: 6 residues processed: 336 average time/residue: 0.2247 time to fit residues: 103.9823 Evaluate side-chains 184 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 175 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 496 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.0970 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 119 optimal weight: 0.4980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 230 GLN A 421 GLN A 656 HIS A 728 HIS A 730 GLN B 135 HIS B 160 HIS B 421 GLN B 656 HIS B 728 HIS B 730 GLN B 731 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.154433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.120937 restraints weight = 14119.119| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.07 r_work: 0.3327 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10400 Z= 0.151 Angle : 0.575 5.844 14136 Z= 0.302 Chirality : 0.043 0.212 1718 Planarity : 0.005 0.047 1758 Dihedral : 4.675 54.131 1431 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.92 % Allowed : 11.94 % Favored : 84.14 % 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: -1.90 (0.22), residues: 1322 helix: -0.32 (0.17), residues: 856 sheet: -3.61 (0.63), residues: 50 loop : -2.84 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 518 HIS 0.009 0.001 HIS A 656 PHE 0.024 0.002 PHE A 130 TYR 0.026 0.001 TYR A 371 ARG 0.006 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.04886 ( 570) hydrogen bonds : angle 4.39582 ( 1674) covalent geometry : bond 0.00340 (10400) covalent geometry : angle 0.57521 (14136) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 1.124 Fit side-chains REVERT: A 73 ASP cc_start: 0.7816 (t0) cc_final: 0.7364 (t0) REVERT: A 78 TYR cc_start: 0.6282 (t80) cc_final: 0.6076 (t80) REVERT: A 119 SER cc_start: 0.9002 (t) cc_final: 0.8698 (p) REVERT: A 269 ILE cc_start: 0.8409 (pt) cc_final: 0.8012 (pt) REVERT: A 273 ILE cc_start: 0.8995 (mt) cc_final: 0.8754 (mt) REVERT: A 309 ILE cc_start: 0.9512 (OUTLIER) cc_final: 0.9308 (mp) REVERT: A 345 LEU cc_start: 0.6649 (mt) cc_final: 0.6246 (mt) REVERT: A 350 LEU cc_start: 0.5860 (OUTLIER) cc_final: 0.5396 (pt) REVERT: A 369 LYS cc_start: 0.7961 (mmtt) cc_final: 0.7517 (mttm) REVERT: A 385 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7344 (t80) REVERT: A 386 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8676 (pt) REVERT: A 580 LYS cc_start: 0.8390 (mmtt) cc_final: 0.7928 (mtpt) REVERT: B 66 LYS cc_start: 0.8725 (tppt) cc_final: 0.8065 (mttm) REVERT: B 73 ASP cc_start: 0.8112 (t0) cc_final: 0.7763 (t0) REVERT: B 134 ARG cc_start: 0.8291 (mtt90) cc_final: 0.7610 (mtm-85) REVERT: B 194 LEU cc_start: 0.8093 (tp) cc_final: 0.7881 (mp) REVERT: B 247 TYR cc_start: 0.8281 (m-10) cc_final: 0.8065 (m-10) REVERT: B 303 GLU cc_start: 0.8196 (mp0) cc_final: 0.7959 (mp0) REVERT: B 350 LEU cc_start: 0.6143 (OUTLIER) cc_final: 0.5811 (tp) REVERT: B 366 SER cc_start: 0.8777 (t) cc_final: 0.8093 (m) REVERT: B 580 LYS cc_start: 0.8502 (mmtt) cc_final: 0.8187 (mtpt) REVERT: B 590 LYS cc_start: 0.5736 (OUTLIER) cc_final: 0.5479 (pttp) REVERT: B 714 ARG cc_start: 0.8324 (mtm-85) cc_final: 0.7892 (mtp-110) outliers start: 44 outliers final: 21 residues processed: 212 average time/residue: 0.2104 time to fit residues: 63.8203 Evaluate side-chains 183 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 695 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 130 optimal weight: 0.4980 chunk 107 optimal weight: 0.5980 chunk 43 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 160 HIS A 656 HIS A 731 ASN B 160 HIS B 656 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.150684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.118144 restraints weight = 14375.649| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.99 r_work: 0.3295 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10400 Z= 0.144 Angle : 0.556 10.163 14136 Z= 0.290 Chirality : 0.043 0.199 1718 Planarity : 0.004 0.050 1758 Dihedral : 4.465 55.965 1426 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.30 % Favored : 94.63 % Rotamer: Outliers : 3.65 % Allowed : 12.30 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.10 (0.23), residues: 1322 helix: 0.34 (0.18), residues: 866 sheet: -3.34 (0.67), residues: 50 loop : -2.69 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 482 HIS 0.011 0.001 HIS A 656 PHE 0.021 0.002 PHE A 122 TYR 0.015 0.001 TYR A 247 ARG 0.006 0.000 ARG B 677 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 570) hydrogen bonds : angle 4.06284 ( 1674) covalent geometry : bond 0.00331 (10400) covalent geometry : angle 0.55584 (14136) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 73 ASP cc_start: 0.7794 (t0) cc_final: 0.7320 (t0) REVERT: A 78 TYR cc_start: 0.6344 (t80) cc_final: 0.5884 (t80) REVERT: A 119 SER cc_start: 0.9116 (t) cc_final: 0.8770 (p) REVERT: A 269 ILE cc_start: 0.8356 (pt) cc_final: 0.7962 (pt) REVERT: A 273 ILE cc_start: 0.8964 (mt) cc_final: 0.8720 (mt) REVERT: A 303 GLU cc_start: 0.8276 (mp0) cc_final: 0.7944 (mp0) REVERT: A 345 LEU cc_start: 0.6572 (mt) cc_final: 0.6301 (mt) REVERT: A 350 LEU cc_start: 0.5845 (OUTLIER) cc_final: 0.5303 (pt) REVERT: A 369 LYS cc_start: 0.7913 (mmtt) cc_final: 0.7463 (mttm) REVERT: A 385 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7397 (t80) REVERT: A 398 PHE cc_start: 0.7567 (m-80) cc_final: 0.7285 (m-80) REVERT: A 432 MET cc_start: 0.8007 (tpp) cc_final: 0.7783 (tpp) REVERT: A 580 LYS cc_start: 0.8343 (mmtt) cc_final: 0.7869 (mtpt) REVERT: B 50 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6703 (tt) REVERT: B 66 LYS cc_start: 0.8657 (tppt) cc_final: 0.8017 (mttm) REVERT: B 73 ASP cc_start: 0.8275 (t0) cc_final: 0.7973 (t0) REVERT: B 77 LYS cc_start: 0.7958 (mptt) cc_final: 0.7480 (mttt) REVERT: B 134 ARG cc_start: 0.8281 (mtt90) cc_final: 0.7497 (mtp180) REVERT: B 194 LEU cc_start: 0.7986 (tp) cc_final: 0.7775 (mp) REVERT: B 247 TYR cc_start: 0.8239 (m-10) cc_final: 0.8001 (m-10) REVERT: B 350 LEU cc_start: 0.6535 (OUTLIER) cc_final: 0.6168 (tp) REVERT: B 369 LYS cc_start: 0.8188 (mmtt) cc_final: 0.7686 (mttm) REVERT: B 398 PHE cc_start: 0.7476 (m-80) cc_final: 0.7081 (m-80) REVERT: B 580 LYS cc_start: 0.8423 (mmtt) cc_final: 0.8100 (mtpt) REVERT: B 681 LYS cc_start: 0.8312 (mptt) cc_final: 0.8091 (mttp) REVERT: B 714 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.7868 (mtp-110) outliers start: 41 outliers final: 21 residues processed: 186 average time/residue: 0.2235 time to fit residues: 58.7863 Evaluate side-chains 170 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 590 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 110 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 23 optimal weight: 0.0980 chunk 85 optimal weight: 0.0770 chunk 130 optimal weight: 0.8980 chunk 51 optimal weight: 0.0060 chunk 24 optimal weight: 0.9980 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 656 HIS B 160 HIS B 464 GLN B 656 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.152956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.119180 restraints weight = 14169.040| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.09 r_work: 0.3295 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10400 Z= 0.111 Angle : 0.518 8.150 14136 Z= 0.268 Chirality : 0.041 0.174 1718 Planarity : 0.004 0.045 1758 Dihedral : 4.406 54.449 1426 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.50 % Allowed : 14.35 % Favored : 83.16 % 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: -0.65 (0.24), residues: 1322 helix: 0.70 (0.18), residues: 866 sheet: -3.24 (0.70), residues: 50 loop : -2.53 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 482 HIS 0.010 0.001 HIS B 656 PHE 0.010 0.001 PHE A 115 TYR 0.011 0.001 TYR A 247 ARG 0.005 0.000 ARG B 576 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 570) hydrogen bonds : angle 3.91116 ( 1674) covalent geometry : bond 0.00239 (10400) covalent geometry : angle 0.51786 (14136) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 1.032 Fit side-chains REVERT: A 73 ASP cc_start: 0.7793 (t0) cc_final: 0.7343 (t0) REVERT: A 119 SER cc_start: 0.9077 (t) cc_final: 0.8699 (p) REVERT: A 269 ILE cc_start: 0.8242 (pt) cc_final: 0.7828 (pt) REVERT: A 273 ILE cc_start: 0.8977 (mt) cc_final: 0.8727 (mt) REVERT: A 350 LEU cc_start: 0.5898 (OUTLIER) cc_final: 0.5356 (pt) REVERT: A 369 LYS cc_start: 0.7883 (mmtt) cc_final: 0.7408 (mttm) REVERT: A 385 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7499 (t80) REVERT: A 580 LYS cc_start: 0.8441 (mmtt) cc_final: 0.7991 (mtpt) REVERT: B 66 LYS cc_start: 0.8605 (tppt) cc_final: 0.7996 (mttm) REVERT: B 73 ASP cc_start: 0.8282 (t0) cc_final: 0.7904 (t0) REVERT: B 134 ARG cc_start: 0.8295 (mtt90) cc_final: 0.7564 (mtp180) REVERT: B 247 TYR cc_start: 0.8203 (m-10) cc_final: 0.7971 (m-10) REVERT: B 303 GLU cc_start: 0.8195 (mp0) cc_final: 0.7966 (mp0) REVERT: B 350 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.6186 (tp) REVERT: B 369 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7738 (mttm) REVERT: B 398 PHE cc_start: 0.7499 (m-80) cc_final: 0.7225 (m-80) REVERT: B 580 LYS cc_start: 0.8503 (mmtt) cc_final: 0.8158 (mtpt) REVERT: B 590 LYS cc_start: 0.5460 (OUTLIER) cc_final: 0.5237 (pttp) REVERT: B 714 ARG cc_start: 0.8333 (mtm-85) cc_final: 0.7916 (mtp-110) outliers start: 28 outliers final: 18 residues processed: 175 average time/residue: 0.2210 time to fit residues: 54.4937 Evaluate side-chains 163 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 590 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 10 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 chunk 72 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 656 HIS B 160 HIS B 656 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.148602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.115643 restraints weight = 14202.611| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.04 r_work: 0.3229 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10400 Z= 0.144 Angle : 0.538 7.109 14136 Z= 0.282 Chirality : 0.042 0.180 1718 Planarity : 0.004 0.054 1758 Dihedral : 4.534 55.567 1426 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.14 % Favored : 94.78 % Rotamer: Outliers : 3.39 % Allowed : 14.80 % 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: -0.40 (0.24), residues: 1322 helix: 0.90 (0.18), residues: 864 sheet: -3.02 (0.73), residues: 50 loop : -2.46 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 518 HIS 0.010 0.002 HIS B 656 PHE 0.014 0.001 PHE A 115 TYR 0.016 0.001 TYR A 247 ARG 0.005 0.000 ARG B 576 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 570) hydrogen bonds : angle 3.86888 ( 1674) covalent geometry : bond 0.00335 (10400) covalent geometry : angle 0.53790 (14136) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 1.052 Fit side-chains REVERT: A 73 ASP cc_start: 0.7782 (t0) cc_final: 0.7259 (t0) REVERT: A 119 SER cc_start: 0.9120 (t) cc_final: 0.8716 (p) REVERT: A 269 ILE cc_start: 0.8295 (pt) cc_final: 0.7925 (pt) REVERT: A 273 ILE cc_start: 0.8984 (mt) cc_final: 0.8731 (mt) REVERT: A 350 LEU cc_start: 0.5902 (OUTLIER) cc_final: 0.5407 (tp) REVERT: A 369 LYS cc_start: 0.7975 (mmtt) cc_final: 0.7559 (mttm) REVERT: A 385 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7554 (t80) REVERT: A 580 LYS cc_start: 0.8486 (mmtt) cc_final: 0.8056 (mtpt) REVERT: B 66 LYS cc_start: 0.8609 (tppt) cc_final: 0.8384 (mttm) REVERT: B 73 ASP cc_start: 0.8355 (t0) cc_final: 0.7523 (m-30) REVERT: B 134 ARG cc_start: 0.8177 (mtt90) cc_final: 0.7451 (mtp180) REVERT: B 247 TYR cc_start: 0.8260 (m-10) cc_final: 0.8013 (m-10) REVERT: B 273 ILE cc_start: 0.9081 (mm) cc_final: 0.8860 (mp) REVERT: B 350 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6312 (tp) REVERT: B 369 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7646 (mttm) REVERT: B 398 PHE cc_start: 0.7538 (m-80) cc_final: 0.7267 (m-80) REVERT: B 405 THR cc_start: 0.9181 (m) cc_final: 0.8807 (t) REVERT: B 580 LYS cc_start: 0.8562 (mmtt) cc_final: 0.8188 (mtpt) REVERT: B 590 LYS cc_start: 0.5404 (OUTLIER) cc_final: 0.5174 (pttp) REVERT: B 714 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.7931 (mtp-110) outliers start: 38 outliers final: 24 residues processed: 173 average time/residue: 0.2115 time to fit residues: 52.1317 Evaluate side-chains 165 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.0070 chunk 37 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 656 HIS B 160 HIS B 656 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.147484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114707 restraints weight = 14367.361| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.08 r_work: 0.3212 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10400 Z= 0.147 Angle : 0.534 6.497 14136 Z= 0.281 Chirality : 0.041 0.162 1718 Planarity : 0.004 0.054 1758 Dihedral : 4.649 55.259 1426 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.65 % Allowed : 15.60 % Favored : 80.75 % 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: -0.23 (0.24), residues: 1322 helix: 1.01 (0.18), residues: 864 sheet: -2.85 (0.75), residues: 50 loop : -2.37 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 518 HIS 0.011 0.002 HIS B 656 PHE 0.013 0.001 PHE B 667 TYR 0.012 0.001 TYR A 247 ARG 0.006 0.000 ARG B 576 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 570) hydrogen bonds : angle 3.84021 ( 1674) covalent geometry : bond 0.00342 (10400) covalent geometry : angle 0.53413 (14136) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 1.443 Fit side-chains REVERT: A 73 ASP cc_start: 0.7738 (t0) cc_final: 0.7492 (t0) REVERT: A 77 LYS cc_start: 0.7995 (pttm) cc_final: 0.6949 (tptt) REVERT: A 119 SER cc_start: 0.9119 (t) cc_final: 0.8747 (p) REVERT: A 247 TYR cc_start: 0.8237 (m-10) cc_final: 0.8004 (m-10) REVERT: A 269 ILE cc_start: 0.8280 (pt) cc_final: 0.7900 (pt) REVERT: A 273 ILE cc_start: 0.8997 (mt) cc_final: 0.8736 (mt) REVERT: A 350 LEU cc_start: 0.5593 (OUTLIER) cc_final: 0.5359 (tp) REVERT: A 369 LYS cc_start: 0.7972 (mmtt) cc_final: 0.7559 (mttm) REVERT: A 385 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7639 (t80) REVERT: A 580 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8066 (mtpt) REVERT: B 66 LYS cc_start: 0.8579 (tppt) cc_final: 0.7899 (mttm) REVERT: B 73 ASP cc_start: 0.8338 (t0) cc_final: 0.7881 (t0) REVERT: B 100 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8328 (mm) REVERT: B 134 ARG cc_start: 0.8337 (mtt90) cc_final: 0.7624 (mtp180) REVERT: B 247 TYR cc_start: 0.8214 (m-10) cc_final: 0.7962 (m-10) REVERT: B 273 ILE cc_start: 0.9104 (mm) cc_final: 0.8856 (mp) REVERT: B 350 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6161 (tp) REVERT: B 369 LYS cc_start: 0.8151 (mmtt) cc_final: 0.7610 (mttm) REVERT: B 405 THR cc_start: 0.9212 (m) cc_final: 0.8924 (t) REVERT: B 580 LYS cc_start: 0.8575 (mmtt) cc_final: 0.8196 (mtpt) REVERT: B 590 LYS cc_start: 0.5501 (OUTLIER) cc_final: 0.5289 (pttp) REVERT: B 714 ARG cc_start: 0.8428 (mtm-85) cc_final: 0.7945 (mtp180) outliers start: 41 outliers final: 27 residues processed: 171 average time/residue: 0.2271 time to fit residues: 55.5061 Evaluate side-chains 166 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 87 optimal weight: 0.1980 chunk 130 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 22 optimal weight: 0.4980 chunk 60 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 61 optimal weight: 0.2980 chunk 7 optimal weight: 2.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 656 HIS B 289 ASN B 656 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.149966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.117270 restraints weight = 14460.072| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.07 r_work: 0.3252 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10400 Z= 0.119 Angle : 0.525 9.424 14136 Z= 0.274 Chirality : 0.041 0.160 1718 Planarity : 0.004 0.052 1758 Dihedral : 4.578 54.501 1426 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 3.03 % Allowed : 16.22 % Favored : 80.75 % 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: -0.09 (0.24), residues: 1322 helix: 1.12 (0.18), residues: 864 sheet: -2.83 (0.74), residues: 50 loop : -2.28 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 482 HIS 0.011 0.001 HIS B 656 PHE 0.014 0.001 PHE B 398 TYR 0.009 0.001 TYR A 20 ARG 0.007 0.000 ARG B 576 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 570) hydrogen bonds : angle 3.78304 ( 1674) covalent geometry : bond 0.00267 (10400) covalent geometry : angle 0.52517 (14136) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 1.121 Fit side-chains REVERT: A 73 ASP cc_start: 0.7644 (t0) cc_final: 0.7400 (t0) REVERT: A 77 LYS cc_start: 0.7977 (pttm) cc_final: 0.6946 (tptt) REVERT: A 119 SER cc_start: 0.9175 (t) cc_final: 0.8749 (p) REVERT: A 247 TYR cc_start: 0.8245 (m-10) cc_final: 0.8006 (m-10) REVERT: A 269 ILE cc_start: 0.8150 (pt) cc_final: 0.7771 (pt) REVERT: A 273 ILE cc_start: 0.8930 (mt) cc_final: 0.8665 (mt) REVERT: A 292 PHE cc_start: 0.7605 (m-80) cc_final: 0.7402 (m-80) REVERT: A 313 ILE cc_start: 0.9159 (mm) cc_final: 0.8943 (mm) REVERT: A 369 LYS cc_start: 0.7921 (mmtt) cc_final: 0.7495 (mttm) REVERT: A 385 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7601 (t80) REVERT: A 580 LYS cc_start: 0.8444 (mmtt) cc_final: 0.7998 (mtpt) REVERT: B 66 LYS cc_start: 0.8513 (tppt) cc_final: 0.8253 (mttm) REVERT: B 73 ASP cc_start: 0.8377 (t0) cc_final: 0.7498 (m-30) REVERT: B 134 ARG cc_start: 0.8312 (mtt90) cc_final: 0.7530 (mtp180) REVERT: B 247 TYR cc_start: 0.8182 (m-10) cc_final: 0.7906 (m-10) REVERT: B 273 ILE cc_start: 0.9004 (mm) cc_final: 0.8732 (mp) REVERT: B 303 GLU cc_start: 0.8164 (mp0) cc_final: 0.7891 (mp0) REVERT: B 350 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.6046 (tp) REVERT: B 369 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7499 (mttm) REVERT: B 405 THR cc_start: 0.9187 (m) cc_final: 0.8892 (t) REVERT: B 580 LYS cc_start: 0.8521 (mmtt) cc_final: 0.8122 (mtpt) REVERT: B 714 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.7871 (mtp180) outliers start: 34 outliers final: 25 residues processed: 166 average time/residue: 0.2234 time to fit residues: 52.5496 Evaluate side-chains 164 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 42 optimal weight: 0.8980 chunk 43 optimal weight: 0.0980 chunk 71 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 126 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 656 HIS B 656 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.148142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.116163 restraints weight = 14409.565| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.14 r_work: 0.3221 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10400 Z= 0.132 Angle : 0.538 10.417 14136 Z= 0.279 Chirality : 0.041 0.149 1718 Planarity : 0.004 0.055 1758 Dihedral : 4.520 54.625 1424 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.90 % Favored : 94.02 % Rotamer: Outliers : 2.85 % Allowed : 16.67 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.01 (0.25), residues: 1322 helix: 1.17 (0.18), residues: 864 sheet: -2.77 (0.75), residues: 50 loop : -2.25 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 482 HIS 0.011 0.002 HIS B 656 PHE 0.013 0.001 PHE B 667 TYR 0.018 0.001 TYR A 371 ARG 0.008 0.000 ARG B 576 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 570) hydrogen bonds : angle 3.77904 ( 1674) covalent geometry : bond 0.00304 (10400) covalent geometry : angle 0.53836 (14136) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 1.131 Fit side-chains REVERT: A 73 ASP cc_start: 0.7697 (t0) cc_final: 0.7345 (m-30) REVERT: A 77 LYS cc_start: 0.8009 (pttm) cc_final: 0.7152 (tptt) REVERT: A 119 SER cc_start: 0.9182 (t) cc_final: 0.8753 (p) REVERT: A 247 TYR cc_start: 0.8108 (m-10) cc_final: 0.7880 (m-10) REVERT: A 269 ILE cc_start: 0.8136 (pt) cc_final: 0.7769 (pt) REVERT: A 273 ILE cc_start: 0.8931 (mt) cc_final: 0.8660 (mt) REVERT: A 313 ILE cc_start: 0.9175 (mm) cc_final: 0.8940 (mm) REVERT: A 369 LYS cc_start: 0.7838 (mmtt) cc_final: 0.7371 (mttm) REVERT: A 385 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7575 (t80) REVERT: A 580 LYS cc_start: 0.8481 (mmtt) cc_final: 0.8037 (mtpt) REVERT: B 66 LYS cc_start: 0.8579 (tppt) cc_final: 0.8294 (mttm) REVERT: B 73 ASP cc_start: 0.8336 (t0) cc_final: 0.7493 (m-30) REVERT: B 134 ARG cc_start: 0.8324 (mtt90) cc_final: 0.7608 (mtp180) REVERT: B 247 TYR cc_start: 0.8170 (m-10) cc_final: 0.7887 (m-10) REVERT: B 273 ILE cc_start: 0.9002 (mm) cc_final: 0.8732 (mp) REVERT: B 303 GLU cc_start: 0.8220 (mp0) cc_final: 0.7964 (mp0) REVERT: B 350 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6125 (tp) REVERT: B 369 LYS cc_start: 0.8094 (mmtt) cc_final: 0.7570 (mttm) REVERT: B 398 PHE cc_start: 0.7499 (m-80) cc_final: 0.7104 (m-80) REVERT: B 405 THR cc_start: 0.9125 (m) cc_final: 0.8843 (t) REVERT: B 580 LYS cc_start: 0.8555 (mmtt) cc_final: 0.8138 (mtpt) REVERT: B 714 ARG cc_start: 0.8419 (mtm-85) cc_final: 0.7883 (mtp-110) outliers start: 32 outliers final: 25 residues processed: 163 average time/residue: 0.2370 time to fit residues: 54.1909 Evaluate side-chains 165 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 119 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 656 HIS B 656 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.145590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113804 restraints weight = 14497.153| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.13 r_work: 0.3183 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10400 Z= 0.168 Angle : 0.580 10.231 14136 Z= 0.301 Chirality : 0.042 0.150 1718 Planarity : 0.004 0.061 1758 Dihedral : 4.689 55.849 1424 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.05 % Favored : 93.87 % Rotamer: Outliers : 2.85 % Allowed : 17.11 % Favored : 80.04 % 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: -0.04 (0.25), residues: 1322 helix: 1.14 (0.18), residues: 864 sheet: -2.69 (0.75), residues: 50 loop : -2.23 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 518 HIS 0.011 0.002 HIS B 656 PHE 0.018 0.001 PHE A 130 TYR 0.023 0.001 TYR A 371 ARG 0.007 0.000 ARG B 576 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 570) hydrogen bonds : angle 3.81504 ( 1674) covalent geometry : bond 0.00400 (10400) covalent geometry : angle 0.58010 (14136) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 1.090 Fit side-chains REVERT: A 73 ASP cc_start: 0.7754 (t0) cc_final: 0.7431 (m-30) REVERT: A 77 LYS cc_start: 0.8061 (pttm) cc_final: 0.7414 (tptt) REVERT: A 119 SER cc_start: 0.9113 (t) cc_final: 0.8654 (p) REVERT: A 269 ILE cc_start: 0.8221 (pt) cc_final: 0.7717 (pt) REVERT: A 273 ILE cc_start: 0.8982 (mt) cc_final: 0.8683 (mp) REVERT: A 313 ILE cc_start: 0.9210 (mm) cc_final: 0.9005 (mm) REVERT: A 369 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7427 (mttm) REVERT: A 385 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7656 (t80) REVERT: A 580 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8071 (mtpt) REVERT: B 66 LYS cc_start: 0.8640 (tppt) cc_final: 0.8348 (mttm) REVERT: B 73 ASP cc_start: 0.8334 (t0) cc_final: 0.7508 (m-30) REVERT: B 134 ARG cc_start: 0.8313 (mtt90) cc_final: 0.7649 (mtm-85) REVERT: B 247 TYR cc_start: 0.8164 (m-10) cc_final: 0.7884 (m-10) REVERT: B 273 ILE cc_start: 0.9022 (mm) cc_final: 0.8751 (mp) REVERT: B 303 GLU cc_start: 0.8222 (mp0) cc_final: 0.7950 (mp0) REVERT: B 350 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.6090 (tp) REVERT: B 369 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7655 (mttm) REVERT: B 398 PHE cc_start: 0.7510 (m-80) cc_final: 0.7142 (m-80) REVERT: B 405 THR cc_start: 0.9142 (m) cc_final: 0.8904 (t) REVERT: B 580 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8161 (mtpt) REVERT: B 714 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.7894 (mtp-110) outliers start: 32 outliers final: 27 residues processed: 165 average time/residue: 0.2593 time to fit residues: 61.4428 Evaluate side-chains 169 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 724 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 105 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 0.0020 chunk 63 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 656 HIS B 656 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.147636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.115735 restraints weight = 14503.788| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.16 r_work: 0.3223 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10400 Z= 0.126 Angle : 0.552 10.013 14136 Z= 0.286 Chirality : 0.041 0.153 1718 Planarity : 0.004 0.055 1758 Dihedral : 4.619 55.382 1424 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.76 % Allowed : 17.47 % Favored : 79.77 % 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: 0.07 (0.25), residues: 1322 helix: 1.23 (0.18), residues: 862 sheet: -2.67 (0.75), residues: 50 loop : -2.20 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 482 HIS 0.011 0.002 HIS B 656 PHE 0.020 0.001 PHE A 130 TYR 0.024 0.001 TYR A 247 ARG 0.008 0.000 ARG B 576 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 570) hydrogen bonds : angle 3.77532 ( 1674) covalent geometry : bond 0.00287 (10400) covalent geometry : angle 0.55176 (14136) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 1.549 Fit side-chains REVERT: A 73 ASP cc_start: 0.7738 (t0) cc_final: 0.7424 (m-30) REVERT: A 77 LYS cc_start: 0.8028 (pttm) cc_final: 0.7251 (tppt) REVERT: A 269 ILE cc_start: 0.8203 (pt) cc_final: 0.7777 (pt) REVERT: A 273 ILE cc_start: 0.8930 (mt) cc_final: 0.8634 (mt) REVERT: A 313 ILE cc_start: 0.9185 (mm) cc_final: 0.8975 (mm) REVERT: A 369 LYS cc_start: 0.7761 (mmtt) cc_final: 0.7326 (mttm) REVERT: A 385 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7692 (t80) REVERT: A 580 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8056 (mtpt) REVERT: B 66 LYS cc_start: 0.8581 (tppt) cc_final: 0.8317 (mttm) REVERT: B 73 ASP cc_start: 0.8296 (t0) cc_final: 0.7463 (m-30) REVERT: B 134 ARG cc_start: 0.8287 (mtt90) cc_final: 0.7598 (mtm-85) REVERT: B 247 TYR cc_start: 0.8174 (m-10) cc_final: 0.7847 (m-10) REVERT: B 273 ILE cc_start: 0.8984 (mm) cc_final: 0.8712 (mp) REVERT: B 303 GLU cc_start: 0.8163 (mp0) cc_final: 0.7883 (mp0) REVERT: B 350 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.6075 (tp) REVERT: B 369 LYS cc_start: 0.8143 (mmtt) cc_final: 0.7629 (mttm) REVERT: B 398 PHE cc_start: 0.7485 (m-80) cc_final: 0.7113 (m-80) REVERT: B 405 THR cc_start: 0.9116 (m) cc_final: 0.8855 (t) REVERT: B 580 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8146 (mtpt) REVERT: B 714 ARG cc_start: 0.8418 (mtm-85) cc_final: 0.7880 (mtp180) outliers start: 31 outliers final: 25 residues processed: 162 average time/residue: 0.2659 time to fit residues: 61.7698 Evaluate side-chains 166 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 24 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 0.0570 chunk 93 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 97 optimal weight: 0.0020 overall best weight: 0.5106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 656 HIS B 656 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.147297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.114834 restraints weight = 14402.443| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.11 r_work: 0.3205 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10400 Z= 0.131 Angle : 0.556 9.881 14136 Z= 0.289 Chirality : 0.041 0.152 1718 Planarity : 0.004 0.057 1758 Dihedral : 4.615 55.779 1424 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.60 % Favored : 94.33 % Rotamer: Outliers : 2.76 % Allowed : 17.65 % Favored : 79.59 % 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: 0.13 (0.25), residues: 1322 helix: 1.25 (0.18), residues: 864 sheet: -2.66 (0.75), residues: 50 loop : -2.11 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 482 HIS 0.011 0.002 HIS A 656 PHE 0.021 0.001 PHE A 130 TYR 0.022 0.001 TYR A 247 ARG 0.008 0.000 ARG B 576 Details of bonding type rmsd hydrogen bonds : bond 0.03501 ( 570) hydrogen bonds : angle 3.76704 ( 1674) covalent geometry : bond 0.00300 (10400) covalent geometry : angle 0.55552 (14136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6331.10 seconds wall clock time: 111 minutes 15.63 seconds (6675.63 seconds total)