Starting phenix.real_space_refine on Fri Feb 14 12:41:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wk1_32555/02_2025/7wk1_32555.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wk1_32555/02_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_32555/02_2025/7wk1_32555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wk1_32555/02_2025/7wk1_32555.map" model { file = "/net/cci-nas-00/data/ceres_data/7wk1_32555/02_2025/7wk1_32555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wk1_32555/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.79, per 1000 atoms: 0.67 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: 2.48 Conformation dependent library (CDL) restraints added in 989.6 milliseconds 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: 1.04 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: 3.11 Time building geometry restraints manager: 2.81 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: 2.910 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: 0.100 Process input model: 24.800 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.460 ------------------------------------------------------------------------------- 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= 0.111 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 *********************** 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 : 1.348 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: 0.2530 time to fit residues: 116.6173 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 : 1.327 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.153507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.120433 restraints weight = 14083.527| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.16 r_work: 0.3320 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 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= 0.220 Angle : 0.575 5.842 14136 Z= 0.302 Chirality : 0.043 0.213 1718 Planarity : 0.005 0.047 1758 Dihedral : 4.675 54.125 1431 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.95 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 *********************** 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 : 1.236 Fit side-chains REVERT: A 73 ASP cc_start: 0.7818 (t0) cc_final: 0.7365 (t0) REVERT: A 78 TYR cc_start: 0.6288 (t80) cc_final: 0.6070 (t80) REVERT: A 119 SER cc_start: 0.8973 (t) cc_final: 0.8704 (p) REVERT: A 269 ILE cc_start: 0.8419 (pt) cc_final: 0.8023 (pt) REVERT: A 273 ILE cc_start: 0.9016 (mt) cc_final: 0.8780 (mt) REVERT: A 309 ILE cc_start: 0.9521 (OUTLIER) cc_final: 0.9320 (mp) REVERT: A 345 LEU cc_start: 0.6644 (mt) cc_final: 0.6254 (mt) REVERT: A 350 LEU cc_start: 0.5892 (OUTLIER) cc_final: 0.5425 (pt) REVERT: A 369 LYS cc_start: 0.7990 (mmtt) cc_final: 0.7555 (mttm) REVERT: A 385 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7372 (t80) REVERT: A 580 LYS cc_start: 0.8410 (mmtt) cc_final: 0.7961 (mtpt) REVERT: B 66 LYS cc_start: 0.8737 (tppt) cc_final: 0.8078 (mttm) REVERT: B 73 ASP cc_start: 0.8108 (t0) cc_final: 0.7768 (t0) REVERT: B 134 ARG cc_start: 0.8299 (mtt90) cc_final: 0.7638 (mtm-85) REVERT: B 194 LEU cc_start: 0.8140 (tp) cc_final: 0.7933 (mp) REVERT: B 247 TYR cc_start: 0.8276 (m-10) cc_final: 0.8067 (m-10) REVERT: B 303 GLU cc_start: 0.8175 (mp0) cc_final: 0.7941 (mp0) REVERT: B 350 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5838 (tp) REVERT: B 366 SER cc_start: 0.8827 (t) cc_final: 0.8149 (m) REVERT: B 580 LYS cc_start: 0.8521 (mmtt) cc_final: 0.8218 (mtpt) REVERT: B 590 LYS cc_start: 0.5758 (OUTLIER) cc_final: 0.5501 (pttp) REVERT: B 714 ARG cc_start: 0.8326 (mtm-85) cc_final: 0.7926 (mtp-110) outliers start: 44 outliers final: 21 residues processed: 212 average time/residue: 0.2119 time to fit residues: 63.9313 Evaluate side-chains 182 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 107 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.150132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.116180 restraints weight = 14440.213| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.24 r_work: 0.3267 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10400 Z= 0.246 Angle : 0.569 10.075 14136 Z= 0.298 Chirality : 0.043 0.217 1718 Planarity : 0.004 0.054 1758 Dihedral : 4.510 56.451 1426 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 3.65 % Allowed : 12.39 % Favored : 83.96 % 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: -1.14 (0.23), residues: 1322 helix: 0.28 (0.18), residues: 870 sheet: -3.31 (0.68), residues: 50 loop : -2.67 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 482 HIS 0.010 0.002 HIS A 656 PHE 0.020 0.002 PHE A 122 TYR 0.013 0.001 TYR A 27 ARG 0.005 0.000 ARG B 677 *********************** 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 200 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 159 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: A 73 ASP cc_start: 0.7828 (t0) cc_final: 0.7353 (t0) REVERT: A 78 TYR cc_start: 0.6374 (t80) cc_final: 0.5905 (t80) REVERT: A 119 SER cc_start: 0.9121 (t) cc_final: 0.8805 (p) REVERT: A 269 ILE cc_start: 0.8342 (pt) cc_final: 0.7952 (pt) REVERT: A 273 ILE cc_start: 0.8990 (mt) cc_final: 0.8750 (mt) REVERT: A 303 GLU cc_start: 0.8259 (mp0) cc_final: 0.7924 (mp0) REVERT: A 345 LEU cc_start: 0.6620 (mt) cc_final: 0.6358 (mt) REVERT: A 350 LEU cc_start: 0.5907 (OUTLIER) cc_final: 0.5339 (pt) REVERT: A 369 LYS cc_start: 0.8001 (mmtt) cc_final: 0.7555 (mttm) REVERT: A 385 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7617 (t80) REVERT: A 432 MET cc_start: 0.8003 (tpp) cc_final: 0.7713 (tpp) REVERT: A 580 LYS cc_start: 0.8381 (mmtt) cc_final: 0.7918 (mtpt) REVERT: B 50 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6704 (tt) REVERT: B 66 LYS cc_start: 0.8674 (tppt) cc_final: 0.8023 (mttm) REVERT: B 73 ASP cc_start: 0.8318 (t0) cc_final: 0.7934 (t0) REVERT: B 134 ARG cc_start: 0.8319 (mtt90) cc_final: 0.7619 (mtm-85) REVERT: B 194 LEU cc_start: 0.8051 (tp) cc_final: 0.7835 (mp) REVERT: B 247 TYR cc_start: 0.8268 (m-10) cc_final: 0.8054 (m-10) REVERT: B 350 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.6173 (tp) REVERT: B 369 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7699 (mttm) REVERT: B 398 PHE cc_start: 0.7493 (m-80) cc_final: 0.7093 (m-80) REVERT: B 580 LYS cc_start: 0.8458 (mmtt) cc_final: 0.8131 (mtpt) REVERT: B 714 ARG cc_start: 0.8379 (mtm-85) cc_final: 0.7909 (mtp-110) outliers start: 41 outliers final: 23 residues processed: 187 average time/residue: 0.2264 time to fit residues: 59.4368 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 : 1.111 ------------------------------------------------------------------------------- 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 199 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 253 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 331 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 110 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 130 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.147311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114280 restraints weight = 14269.697| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.05 r_work: 0.3211 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10400 Z= 0.239 Angle : 0.554 7.980 14136 Z= 0.289 Chirality : 0.042 0.171 1718 Planarity : 0.004 0.058 1758 Dihedral : 4.636 55.837 1426 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.98 % Favored : 93.95 % Rotamer: Outliers : 3.57 % Allowed : 13.99 % Favored : 82.44 % 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: -0.74 (0.24), residues: 1322 helix: 0.61 (0.18), residues: 870 sheet: -3.20 (0.70), residues: 50 loop : -2.56 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 518 HIS 0.010 0.002 HIS A 656 PHE 0.014 0.001 PHE B 667 TYR 0.014 0.001 TYR A 247 ARG 0.006 0.000 ARG B 576 *********************** 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: 40 poor density : 144 time to evaluate : 1.061 Fit side-chains REVERT: A 73 ASP cc_start: 0.7849 (t0) cc_final: 0.7644 (t0) REVERT: A 77 LYS cc_start: 0.8082 (pttm) cc_final: 0.6962 (tptt) REVERT: A 78 TYR cc_start: 0.6657 (t80) cc_final: 0.6059 (t80) REVERT: A 119 SER cc_start: 0.9129 (t) cc_final: 0.8834 (p) REVERT: A 269 ILE cc_start: 0.8254 (pt) cc_final: 0.7718 (pt) REVERT: A 273 ILE cc_start: 0.8970 (mt) cc_final: 0.8681 (mp) REVERT: A 350 LEU cc_start: 0.6065 (OUTLIER) cc_final: 0.5552 (tp) REVERT: A 369 LYS cc_start: 0.7972 (mmtt) cc_final: 0.7548 (mttm) REVERT: A 385 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7724 (t80) REVERT: A 432 MET cc_start: 0.8233 (tpp) cc_final: 0.8003 (tpp) REVERT: A 580 LYS cc_start: 0.8503 (mmtt) cc_final: 0.8081 (mtpt) REVERT: B 66 LYS cc_start: 0.8674 (tppt) cc_final: 0.8041 (mttm) REVERT: B 73 ASP cc_start: 0.8354 (t0) cc_final: 0.7925 (t0) REVERT: B 134 ARG cc_start: 0.8354 (mtt90) cc_final: 0.7601 (mtp180) REVERT: B 247 TYR cc_start: 0.8215 (m-10) cc_final: 0.7944 (m-10) REVERT: B 273 ILE cc_start: 0.9132 (mm) cc_final: 0.8927 (mp) REVERT: B 303 GLU cc_start: 0.8267 (mp0) cc_final: 0.8057 (mp0) REVERT: B 350 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6270 (tp) REVERT: B 369 LYS cc_start: 0.8282 (mmtt) cc_final: 0.7761 (mttm) REVERT: B 398 PHE cc_start: 0.7584 (m-80) cc_final: 0.7291 (m-80) REVERT: B 580 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8215 (mtpt) REVERT: B 590 LYS cc_start: 0.5561 (OUTLIER) cc_final: 0.5333 (pttp) REVERT: B 714 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.7932 (mtp-110) outliers start: 40 outliers final: 24 residues processed: 175 average time/residue: 0.2241 time to fit residues: 55.2030 Evaluate side-chains 162 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 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 348 ASP Chi-restraints excluded: chain A residue 350 LEU 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 565 CYS 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 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 331 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.145708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.113339 restraints weight = 14284.043| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.03 r_work: 0.3204 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10400 Z= 0.258 Angle : 0.563 7.982 14136 Z= 0.296 Chirality : 0.042 0.178 1718 Planarity : 0.004 0.065 1758 Dihedral : 4.736 55.918 1426 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.90 % Favored : 94.02 % Rotamer: Outliers : 3.65 % Allowed : 14.80 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.24), residues: 1322 helix: 0.74 (0.18), residues: 870 sheet: -3.03 (0.72), residues: 50 loop : -2.48 (0.31), residues: 402 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 0.018 0.001 PHE B 667 TYR 0.017 0.001 TYR A 247 ARG 0.006 0.000 ARG B 576 *********************** 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 186 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 1.146 Fit side-chains REVERT: A 73 ASP cc_start: 0.7791 (t0) cc_final: 0.7562 (t0) REVERT: A 77 LYS cc_start: 0.7998 (pttm) cc_final: 0.7012 (tppt) REVERT: A 78 TYR cc_start: 0.6749 (t80) cc_final: 0.6100 (t80) REVERT: A 119 SER cc_start: 0.9178 (t) cc_final: 0.8715 (p) REVERT: A 269 ILE cc_start: 0.8263 (pt) cc_final: 0.7755 (pt) REVERT: A 273 ILE cc_start: 0.8953 (mt) cc_final: 0.8669 (mp) REVERT: A 303 GLU cc_start: 0.8371 (mp0) cc_final: 0.8140 (mp0) REVERT: A 350 LEU cc_start: 0.5719 (OUTLIER) cc_final: 0.5399 (tp) REVERT: A 369 LYS cc_start: 0.7936 (mmtt) cc_final: 0.7520 (mttm) REVERT: A 385 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7736 (t80) REVERT: A 580 LYS cc_start: 0.8447 (mmtt) cc_final: 0.8006 (mtpt) REVERT: B 66 LYS cc_start: 0.8641 (tppt) cc_final: 0.8008 (mttm) REVERT: B 73 ASP cc_start: 0.8376 (t0) cc_final: 0.7908 (t0) REVERT: B 134 ARG cc_start: 0.8278 (mtt90) cc_final: 0.7435 (mtp180) REVERT: B 247 TYR cc_start: 0.8244 (m-10) cc_final: 0.7931 (m-10) REVERT: B 273 ILE cc_start: 0.9077 (mm) cc_final: 0.8833 (mp) REVERT: B 303 GLU cc_start: 0.8232 (mp0) cc_final: 0.8026 (mp0) REVERT: B 350 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.6179 (tp) REVERT: B 369 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7633 (mttm) REVERT: B 398 PHE cc_start: 0.7603 (m-80) cc_final: 0.7341 (m-80) REVERT: B 580 LYS cc_start: 0.8542 (mmtt) cc_final: 0.8129 (mtpt) REVERT: B 590 LYS cc_start: 0.5416 (OUTLIER) cc_final: 0.5198 (pttp) REVERT: B 714 ARG cc_start: 0.8402 (mtm-85) cc_final: 0.7882 (mtp180) outliers start: 41 outliers final: 30 residues processed: 177 average time/residue: 0.2266 time to fit residues: 56.6128 Evaluate side-chains 170 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 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 89 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 331 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 575 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 666 SER 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: 1.9990 chunk 37 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 65 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 656 HIS B 656 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.145580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.112925 restraints weight = 14434.462| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.09 r_work: 0.3177 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10400 Z= 0.248 Angle : 0.557 7.463 14136 Z= 0.292 Chirality : 0.042 0.163 1718 Planarity : 0.004 0.066 1758 Dihedral : 4.782 55.760 1426 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.75 % Favored : 94.18 % Rotamer: Outliers : 4.01 % Allowed : 15.69 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.38 (0.24), residues: 1322 helix: 0.86 (0.18), residues: 870 sheet: -2.91 (0.73), residues: 50 loop : -2.36 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 482 HIS 0.011 0.002 HIS B 656 PHE 0.016 0.001 PHE B 667 TYR 0.017 0.001 TYR A 247 ARG 0.006 0.000 ARG B 576 *********************** 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 190 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 1.071 Fit side-chains REVERT: A 77 LYS cc_start: 0.8037 (pttm) cc_final: 0.7121 (tppt) REVERT: A 78 TYR cc_start: 0.6868 (t80) cc_final: 0.6196 (t80) REVERT: A 119 SER cc_start: 0.9161 (t) cc_final: 0.8750 (p) REVERT: A 269 ILE cc_start: 0.8239 (pt) cc_final: 0.7721 (pt) REVERT: A 273 ILE cc_start: 0.8984 (mt) cc_final: 0.8694 (mp) REVERT: A 369 LYS cc_start: 0.7957 (mmtt) cc_final: 0.7549 (mttm) REVERT: A 414 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7329 (tm-30) REVERT: A 432 MET cc_start: 0.8287 (tpp) cc_final: 0.8002 (tpp) REVERT: A 580 LYS cc_start: 0.8546 (mmtt) cc_final: 0.8106 (mtpt) REVERT: B 66 LYS cc_start: 0.8712 (tppt) cc_final: 0.8041 (mttm) REVERT: B 73 ASP cc_start: 0.8465 (t0) cc_final: 0.8057 (t0) REVERT: B 100 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8368 (mm) REVERT: B 134 ARG cc_start: 0.8418 (mtt90) cc_final: 0.7666 (mtp180) REVERT: B 247 TYR cc_start: 0.8264 (m-10) cc_final: 0.7985 (m-10) REVERT: B 273 ILE cc_start: 0.9064 (mm) cc_final: 0.8783 (mp) REVERT: B 303 GLU cc_start: 0.8238 (mp0) cc_final: 0.8028 (mp0) REVERT: B 350 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.6122 (tp) REVERT: B 369 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7693 (mttm) REVERT: B 580 LYS cc_start: 0.8606 (mmtt) cc_final: 0.8193 (mtpt) REVERT: B 590 LYS cc_start: 0.5548 (OUTLIER) cc_final: 0.5333 (pttp) REVERT: B 714 ARG cc_start: 0.8478 (mtm-85) cc_final: 0.7969 (mtp180) outliers start: 45 outliers final: 34 residues processed: 180 average time/residue: 0.2281 time to fit residues: 57.5352 Evaluate side-chains 173 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 1.234 ------------------------------------------------------------------------------- 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 365 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 458 LEU 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 A residue 703 MET Chi-restraints excluded: chain A residue 724 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 ILE 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 331 ILE Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 463 MET 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 575 ILE Chi-restraints excluded: chain B residue 590 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 87 optimal weight: 0.3980 chunk 130 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 110 optimal weight: 0.2980 chunk 72 optimal weight: 3.9990 chunk 22 optimal weight: 0.0170 chunk 60 optimal weight: 0.0970 chunk 52 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3805 r_free = 0.3805 target = 0.148498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.116556 restraints weight = 14359.828| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.08 r_work: 0.3235 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4163 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= 0.154 Angle : 0.526 6.993 14136 Z= 0.275 Chirality : 0.040 0.162 1718 Planarity : 0.004 0.056 1758 Dihedral : 4.541 54.928 1424 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.85 % Allowed : 17.02 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.15 (0.24), residues: 1322 helix: 1.03 (0.18), residues: 870 sheet: -2.85 (0.75), residues: 50 loop : -2.26 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 482 HIS 0.011 0.001 HIS B 656 PHE 0.018 0.001 PHE A 130 TYR 0.020 0.001 TYR A 247 ARG 0.007 0.000 ARG B 576 *********************** 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 175 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 1.180 Fit side-chains REVERT: A 77 LYS cc_start: 0.8124 (pttm) cc_final: 0.7048 (tptt) REVERT: A 119 SER cc_start: 0.9120 (t) cc_final: 0.8702 (p) REVERT: A 269 ILE cc_start: 0.8238 (pt) cc_final: 0.7681 (pt) REVERT: A 273 ILE cc_start: 0.8952 (mt) cc_final: 0.8639 (mp) REVERT: A 313 ILE cc_start: 0.9176 (mm) cc_final: 0.8962 (mm) REVERT: A 369 LYS cc_start: 0.7956 (mmtt) cc_final: 0.7490 (mttm) REVERT: A 385 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7958 (t80) REVERT: A 580 LYS cc_start: 0.8533 (mmtt) cc_final: 0.8106 (mtpt) REVERT: B 66 LYS cc_start: 0.8618 (tppt) cc_final: 0.8299 (mttm) REVERT: B 73 ASP cc_start: 0.8317 (t0) cc_final: 0.7396 (m-30) REVERT: B 100 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8327 (mm) REVERT: B 134 ARG cc_start: 0.8356 (mtt90) cc_final: 0.7610 (mtp180) REVERT: B 247 TYR cc_start: 0.8215 (m-10) cc_final: 0.7919 (m-10) REVERT: B 273 ILE cc_start: 0.9063 (mm) cc_final: 0.8800 (mp) REVERT: B 303 GLU cc_start: 0.8171 (mp0) cc_final: 0.7844 (mp0) REVERT: B 350 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.6119 (tp) REVERT: B 369 LYS cc_start: 0.8186 (mmtt) cc_final: 0.7654 (mttm) REVERT: B 580 LYS cc_start: 0.8614 (mmtt) cc_final: 0.8182 (mtpt) REVERT: B 590 LYS cc_start: 0.5460 (OUTLIER) cc_final: 0.5253 (pttp) REVERT: B 714 ARG cc_start: 0.8432 (mtm-85) cc_final: 0.7943 (mtp180) outliers start: 32 outliers final: 22 residues processed: 168 average time/residue: 0.2309 time to fit residues: 55.0485 Evaluate side-chains 166 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 138 VAL 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 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 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 590 LYS 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: 0.8980 chunk 71 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 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 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.145154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113149 restraints weight = 14548.010| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.06 r_work: 0.3179 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4299 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= 0.255 Angle : 0.564 8.865 14136 Z= 0.294 Chirality : 0.042 0.163 1718 Planarity : 0.004 0.068 1758 Dihedral : 4.689 57.604 1424 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.82 % Favored : 94.10 % Rotamer: Outliers : 3.21 % Allowed : 16.84 % Favored : 79.95 % 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: -0.11 (0.25), residues: 1322 helix: 1.06 (0.18), residues: 864 sheet: -2.75 (0.74), residues: 50 loop : -2.20 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 518 HIS 0.011 0.002 HIS B 656 PHE 0.017 0.001 PHE B 667 TYR 0.012 0.001 TYR A 20 ARG 0.008 0.000 ARG B 576 *********************** 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 178 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 1.391 Fit side-chains REVERT: A 77 LYS cc_start: 0.8031 (pttm) cc_final: 0.7266 (tptt) REVERT: A 119 SER cc_start: 0.9170 (t) cc_final: 0.8687 (p) REVERT: A 269 ILE cc_start: 0.8210 (pt) cc_final: 0.7693 (pt) REVERT: A 273 ILE cc_start: 0.8967 (mt) cc_final: 0.8662 (mp) REVERT: A 303 GLU cc_start: 0.8252 (mp0) cc_final: 0.7955 (mp0) REVERT: A 313 ILE cc_start: 0.9193 (mm) cc_final: 0.8974 (mm) REVERT: A 369 LYS cc_start: 0.8002 (mmtt) cc_final: 0.7551 (mttm) REVERT: A 414 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7321 (tm-30) REVERT: A 580 LYS cc_start: 0.8512 (mmtt) cc_final: 0.8084 (mtpt) REVERT: B 66 LYS cc_start: 0.8679 (tppt) cc_final: 0.8339 (mttm) REVERT: B 73 ASP cc_start: 0.8294 (t0) cc_final: 0.7358 (m-30) REVERT: B 100 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8329 (mm) REVERT: B 134 ARG cc_start: 0.8362 (mtt90) cc_final: 0.7651 (mtp180) REVERT: B 247 TYR cc_start: 0.8214 (m-10) cc_final: 0.7915 (m-10) REVERT: B 273 ILE cc_start: 0.9057 (mm) cc_final: 0.8791 (mp) REVERT: B 303 GLU cc_start: 0.8220 (mp0) cc_final: 0.7877 (mp0) REVERT: B 350 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6146 (tp) REVERT: B 369 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7677 (mttm) REVERT: B 580 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8161 (mtpt) REVERT: B 590 LYS cc_start: 0.5551 (OUTLIER) cc_final: 0.5344 (pttp) REVERT: B 714 ARG cc_start: 0.8411 (mtm-85) cc_final: 0.7890 (mtp-110) outliers start: 36 outliers final: 30 residues processed: 169 average time/residue: 0.2848 time to fit residues: 67.7829 Evaluate side-chains 171 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 1.405 ------------------------------------------------------------------------------- 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 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 100 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 590 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 119 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.145937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.113766 restraints weight = 14508.443| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.02 r_work: 0.3192 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4369 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= 0.216 Angle : 0.552 8.890 14136 Z= 0.289 Chirality : 0.041 0.163 1718 Planarity : 0.004 0.064 1758 Dihedral : 4.696 57.496 1424 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.67 % Favored : 94.25 % Rotamer: Outliers : 3.39 % Allowed : 17.02 % 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: -0.08 (0.25), residues: 1322 helix: 1.03 (0.18), residues: 870 sheet: -2.69 (0.75), residues: 50 loop : -2.11 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 482 HIS 0.012 0.002 HIS B 656 PHE 0.014 0.001 PHE B 667 TYR 0.013 0.001 TYR A 247 ARG 0.009 0.000 ARG B 576 *********************** 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 177 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 1.147 Fit side-chains REVERT: A 77 LYS cc_start: 0.8212 (pttm) cc_final: 0.7088 (tptt) REVERT: A 78 TYR cc_start: 0.6870 (t80) cc_final: 0.6207 (t80) REVERT: A 119 SER cc_start: 0.9062 (t) cc_final: 0.8625 (p) REVERT: A 269 ILE cc_start: 0.8141 (pt) cc_final: 0.7610 (pt) REVERT: A 273 ILE cc_start: 0.8966 (mt) cc_final: 0.8659 (mp) REVERT: A 303 GLU cc_start: 0.8224 (mp0) cc_final: 0.7945 (mp0) REVERT: A 313 ILE cc_start: 0.9187 (mm) cc_final: 0.8964 (mm) REVERT: A 369 LYS cc_start: 0.7958 (mmtt) cc_final: 0.7529 (mttm) REVERT: A 414 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7301 (tm-30) REVERT: A 580 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8082 (mtpt) REVERT: B 66 LYS cc_start: 0.8679 (tppt) cc_final: 0.8340 (mttm) REVERT: B 73 ASP cc_start: 0.8249 (t0) cc_final: 0.7351 (m-30) REVERT: B 100 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8273 (mm) REVERT: B 134 ARG cc_start: 0.8366 (mtt90) cc_final: 0.7651 (mtp180) REVERT: B 247 TYR cc_start: 0.8208 (m-10) cc_final: 0.7920 (m-10) REVERT: B 273 ILE cc_start: 0.9051 (mm) cc_final: 0.8783 (mp) REVERT: B 303 GLU cc_start: 0.8224 (mp0) cc_final: 0.7868 (mp0) REVERT: B 350 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6109 (tp) REVERT: B 369 LYS cc_start: 0.8216 (mmtt) cc_final: 0.7669 (mttm) REVERT: B 580 LYS cc_start: 0.8582 (mmtt) cc_final: 0.8141 (mtpt) REVERT: B 714 ARG cc_start: 0.8432 (mtm-85) cc_final: 0.7926 (mtp-110) outliers start: 38 outliers final: 29 residues processed: 168 average time/residue: 0.2334 time to fit residues: 55.6816 Evaluate side-chains 169 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 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 A residue 724 ASP 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 103 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 350 LEU 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: 4.9990 chunk 107 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 0.0570 chunk 63 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.145912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114225 restraints weight = 14511.287| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.14 r_work: 0.3189 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4396 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= 0.209 Angle : 0.552 9.698 14136 Z= 0.288 Chirality : 0.041 0.169 1718 Planarity : 0.004 0.065 1758 Dihedral : 4.698 58.010 1424 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.20 % Favored : 93.72 % Rotamer: Outliers : 3.12 % Allowed : 17.56 % Favored : 79.32 % 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: -0.02 (0.25), residues: 1322 helix: 1.10 (0.18), residues: 864 sheet: -2.67 (0.75), residues: 50 loop : -2.10 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 482 HIS 0.012 0.002 HIS B 656 PHE 0.014 0.001 PHE A 130 TYR 0.023 0.001 TYR A 247 ARG 0.008 0.000 ARG B 576 ********************** 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 174 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 1.140 Fit side-chains REVERT: A 77 LYS cc_start: 0.8107 (pttm) cc_final: 0.7228 (tptt) REVERT: A 78 TYR cc_start: 0.6822 (t80) cc_final: 0.6146 (t80) REVERT: A 119 SER cc_start: 0.9089 (t) cc_final: 0.8615 (p) REVERT: A 269 ILE cc_start: 0.8149 (pt) cc_final: 0.7621 (pt) REVERT: A 273 ILE cc_start: 0.8937 (mt) cc_final: 0.8616 (mp) REVERT: A 303 GLU cc_start: 0.8235 (mp0) cc_final: 0.7939 (mp0) REVERT: A 313 ILE cc_start: 0.9194 (mm) cc_final: 0.8978 (mm) REVERT: A 369 LYS cc_start: 0.7882 (mmtt) cc_final: 0.7448 (mttm) REVERT: A 414 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7296 (tm-30) REVERT: A 580 LYS cc_start: 0.8481 (mmtt) cc_final: 0.8043 (mtpt) REVERT: B 66 LYS cc_start: 0.8676 (tppt) cc_final: 0.8341 (mttm) REVERT: B 73 ASP cc_start: 0.8229 (t0) cc_final: 0.7310 (m-30) REVERT: B 100 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8243 (mm) REVERT: B 134 ARG cc_start: 0.8331 (mtt90) cc_final: 0.7591 (mtp180) REVERT: B 247 TYR cc_start: 0.8197 (m-10) cc_final: 0.7882 (m-10) REVERT: B 273 ILE cc_start: 0.8988 (mm) cc_final: 0.8713 (mp) REVERT: B 350 LEU cc_start: 0.6501 (OUTLIER) cc_final: 0.6071 (tp) REVERT: B 369 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7634 (mttm) REVERT: B 414 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7815 (tm-30) REVERT: B 580 LYS cc_start: 0.8556 (mmtt) cc_final: 0.8099 (mtpt) REVERT: B 714 ARG cc_start: 0.8438 (mtm-85) cc_final: 0.7882 (mtp-110) outliers start: 35 outliers final: 28 residues processed: 165 average time/residue: 0.2308 time to fit residues: 53.4534 Evaluate side-chains 167 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 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 A residue 724 ASP 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 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 350 LEU 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 24 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 93 optimal weight: 0.0030 chunk 57 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 97 optimal weight: 0.0010 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.145850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.114122 restraints weight = 14407.207| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.08 r_work: 0.3189 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10400 Z= 0.211 Angle : 0.557 9.460 14136 Z= 0.292 Chirality : 0.041 0.165 1718 Planarity : 0.004 0.064 1758 Dihedral : 4.715 58.283 1424 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.75 % Favored : 94.18 % Rotamer: Outliers : 3.39 % Allowed : 17.29 % Favored : 79.32 % 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: 1.12 (0.18), residues: 864 sheet: -2.66 (0.75), residues: 50 loop : -2.08 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 482 HIS 0.012 0.002 HIS B 656 PHE 0.014 0.001 PHE A 130 TYR 0.022 0.001 TYR A 247 ARG 0.009 0.000 ARG B 576 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5911.38 seconds wall clock time: 105 minutes 27.32 seconds (6327.32 seconds total)