Starting phenix.real_space_refine on Wed Mar 4 02:29:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wl8_32577/03_2026/7wl8_32577.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wl8_32577/03_2026/7wl8_32577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wl8_32577/03_2026/7wl8_32577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wl8_32577/03_2026/7wl8_32577.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wl8_32577/03_2026/7wl8_32577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wl8_32577/03_2026/7wl8_32577.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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: 4 Type Number sf(0) Gaussians S 42 5.16 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 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10198 Number of models: 1 Model: "" Number of chains: 2 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 Time building chain proxies: 2.62, per 1000 atoms: 0.26 Number of scatterers: 10198 At special positions: 0 Unit cell: (85.12, 127.68, 115.976, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) 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: 0.95 Conformation dependent library (CDL) restraints added in 587.6 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: 66 helices and 7 sheets defined 67.7% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.613A pdb=" N CYS A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.869A pdb=" N ALA A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.890A pdb=" N TRP A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 106 removed outlier: 5.132A pdb=" N LEU A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 120 removed outlier: 4.018A pdb=" N GLY A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 117 " --> pdb=" O VAL A 113 " (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: 3.598A pdb=" N HIS A 160 " --> pdb=" O PRO A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 206 Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.592A pdb=" N VAL A 212 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.897A 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 262 Processing helix chain 'A' and resid 268 through 292 Processing helix chain 'A' and resid 301 through 317 removed outlier: 3.752A pdb=" N ALA A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 348 Processing helix chain 'A' and resid 349 through 375 Processing helix chain 'A' and resid 380 through 397 removed outlier: 3.539A pdb=" N PHE A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 416 removed outlier: 3.660A pdb=" N VAL A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 437 removed outlier: 3.513A pdb=" N VAL A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 430 " --> pdb=" O ILE A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 446 through 458 removed outlier: 3.708A pdb=" N LEU A 450 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 4.352A 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: 3.561A pdb=" N ALA A 479 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 490 " --> pdb=" O CYS A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 515 removed outlier: 3.702A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 573 through 595 removed outlier: 3.814A pdb=" N TYR A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ARG A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 591 " --> pdb=" O ARG A 587 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LYS A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 686 removed outlier: 3.716A pdb=" N SER A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 706 removed outlier: 3.615A pdb=" N LYS A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 718 removed outlier: 3.567A pdb=" N ARG A 717 " --> pdb=" O ARG A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 removed outlier: 3.718A pdb=" N ALA A 725 " --> pdb=" O THR A 721 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 726 " --> pdb=" O VAL A 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.512A pdb=" N LEU B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 removed outlier: 3.843A pdb=" N ALA B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.918A pdb=" N TRP B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 105 removed outlier: 3.688A pdb=" N SER B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 110 Processing helix chain 'B' and resid 113 through 119 removed outlier: 3.864A pdb=" N LEU B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 141 through 156 removed outlier: 3.613A pdb=" N VAL B 151 " --> pdb=" O MET B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.507A pdb=" N HIS B 160 " --> pdb=" O PRO B 157 " (cutoff:3.500A) removed outlier: 3.529A 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 179 through 206 removed outlier: 3.628A pdb=" N LEU B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.597A pdb=" N VAL B 212 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR B 214 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 241 removed outlier: 3.793A 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 Processing helix chain 'B' and resid 301 through 317 removed outlier: 3.742A pdb=" N THR B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 309 " --> pdb=" O ILE B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 348 No H-bonds generated for 'chain 'B' and resid 346 through 348' Processing helix chain 'B' and resid 349 through 375 removed outlier: 3.513A pdb=" N TYR B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 397 removed outlier: 3.771A pdb=" N GLU B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 416 removed outlier: 3.662A pdb=" N VAL B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 437 Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 446 through 458 removed outlier: 3.692A pdb=" N LEU B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN B 457 " --> pdb=" O VAL B 453 " (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: 3.578A pdb=" N ALA B 479 " --> pdb=" O ASN B 475 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 490 " --> pdb=" O CYS B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 515 removed outlier: 3.680A pdb=" N LEU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 504 " --> pdb=" O ALA B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 571 Processing helix chain 'B' and resid 573 through 595 removed outlier: 3.832A pdb=" N TYR B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 586 " --> pdb=" O LEU B 582 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG B 587 " --> pdb=" O LYS B 583 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 591 " --> pdb=" O ARG B 587 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LYS B 593 " --> pdb=" O GLN B 589 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 595 " --> pdb=" O LEU B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 686 removed outlier: 3.597A pdb=" N VAL B 673 " --> pdb=" O ASP B 669 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N SER B 675 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 676 " --> pdb=" O GLY B 672 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 685 " --> pdb=" O LYS B 681 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 706 removed outlier: 3.951A pdb=" N LYS B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 718 removed outlier: 3.607A pdb=" N ARG B 717 " --> pdb=" O ARG B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 736 removed outlier: 3.577A pdb=" N ALA B 725 " --> pdb=" O THR B 721 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 25 removed outlier: 3.592A pdb=" N VAL A 22 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 3.608A 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: 6.472A pdb=" N LYS A 546 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ASP A 661 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 548 " --> pdb=" O ASP A 661 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU A 658 " --> pdb=" O TYR A 691 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 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: 6.494A pdb=" N LYS B 546 " --> pdb=" O VAL B 659 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASP B 661 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU B 548 " --> pdb=" O ASP B 661 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU B 658 " --> pdb=" O TYR B 691 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 569 hydrogen bonds defined for protein. 1653 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.56 Time building geometry restraints manager: 1.26 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: 3214 1.34 - 1.46: 2147 1.46 - 1.58: 4975 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 10400 Sorted by residual: bond pdb=" N LYS B 329 " pdb=" CA LYS B 329 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.89e-01 bond pdb=" CA ASP B 669 " pdb=" C ASP B 669 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 9.03e-01 bond pdb=" C TYR A 127 " pdb=" N PHE A 128 " ideal model delta sigma weight residual 1.332 1.320 0.013 1.40e-02 5.10e+03 7.99e-01 bond pdb=" CA ASP A 669 " pdb=" C ASP A 669 " ideal model delta sigma weight residual 1.532 1.524 0.008 9.60e-03 1.09e+04 7.21e-01 bond pdb=" C VAL B 653 " pdb=" N PRO B 654 " ideal model delta sigma weight residual 1.334 1.353 -0.019 2.34e-02 1.83e+03 6.52e-01 ... (remaining 10395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 13606 1.08 - 2.15: 417 2.15 - 3.23: 81 3.23 - 4.30: 19 4.30 - 5.38: 13 Bond angle restraints: 14136 Sorted by residual: angle pdb=" C ARG A 79 " pdb=" N VAL A 80 " pdb=" CA VAL A 80 " ideal model delta sigma weight residual 120.62 125.21 -4.59 1.64e+00 3.72e-01 7.83e+00 angle pdb=" C ASP A 669 " pdb=" N VAL A 670 " pdb=" CA VAL A 670 " ideal model delta sigma weight residual 121.97 126.47 -4.50 1.80e+00 3.09e-01 6.24e+00 angle pdb=" C VAL A 97 " pdb=" N GLY A 98 " pdb=" CA GLY A 98 " ideal model delta sigma weight residual 120.00 122.58 -2.58 1.10e+00 8.26e-01 5.50e+00 angle pdb=" C VAL A 328 " pdb=" N LYS A 329 " pdb=" CA LYS A 329 " ideal model delta sigma weight residual 122.08 125.34 -3.26 1.47e+00 4.63e-01 4.93e+00 angle pdb=" C ASP B 669 " pdb=" N VAL B 670 " pdb=" CA VAL B 670 " ideal model delta sigma weight residual 121.97 125.93 -3.96 1.80e+00 3.09e-01 4.85e+00 ... (remaining 14131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 5955 17.10 - 34.20: 183 34.20 - 51.29: 34 51.29 - 68.39: 6 68.39 - 85.49: 4 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 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" N LEU A 727 " pdb=" CA LEU A 727 " pdb=" CB LEU A 727 " pdb=" CG LEU A 727 " ideal model delta sinusoidal sigma weight residual -60.00 -119.14 59.14 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N PHE A 385 " pdb=" CA PHE A 385 " pdb=" CB PHE A 385 " pdb=" CG PHE A 385 " ideal model delta sinusoidal sigma weight residual -60.00 -116.37 56.37 3 1.50e+01 4.44e-03 9.40e+00 ... (remaining 6179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 952 0.024 - 0.049: 440 0.049 - 0.073: 221 0.073 - 0.097: 78 0.097 - 0.122: 27 Chirality restraints: 1718 Sorted by residual: chirality pdb=" CA ILE B 331 " pdb=" N ILE B 331 " pdb=" C ILE B 331 " pdb=" CB ILE B 331 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CA VAL A 524 " pdb=" N VAL A 524 " pdb=" C VAL A 524 " pdb=" CB VAL A 524 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.64e-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 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 1715 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 111 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.75e+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 delta sigma weight rms_deltas residual plane pdb=" C SER A 552 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO A 553 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 553 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 553 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 552 " 0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO B 553 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 553 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 553 " 0.017 5.00e-02 4.00e+02 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2418 2.78 - 3.31: 10339 3.31 - 3.84: 16528 3.84 - 4.37: 19575 4.37 - 4.90: 33014 Nonbonded interactions: 81874 Sorted by model distance: nonbonded pdb=" OH TYR B 118 " pdb=" O GLY B 334 " model vdw 2.251 3.040 nonbonded pdb=" OH TYR A 118 " pdb=" O GLY A 334 " model vdw 2.252 3.040 nonbonded pdb=" O THR A 485 " pdb=" OG SER A 489 " model vdw 2.253 3.040 nonbonded pdb=" OG SER A 90 " pdb=" O GLY A 417 " model vdw 2.265 3.040 nonbonded pdb=" O ASP A 669 " pdb=" N GLY A 672 " model vdw 2.279 3.120 ... (remaining 81869 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: 0.01 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: 2.890 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.230 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 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 0.024 10400 Z= 0.105 Angle : 0.489 5.381 14136 Z= 0.299 Chirality : 0.037 0.122 1718 Planarity : 0.003 0.033 1758 Dihedral : 9.001 85.490 3710 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 1.87 % Allowed : 6.51 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.89 (0.19), residues: 1322 helix: -2.31 (0.14), residues: 850 sheet: -2.48 (0.84), residues: 34 loop : -2.82 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 512 TYR 0.008 0.001 TYR A 377 PHE 0.007 0.001 PHE A 555 TRP 0.003 0.000 TRP B 83 HIS 0.001 0.000 HIS B 656 Details of bonding type rmsd covalent geometry : bond 0.00179 (10400) covalent geometry : angle 0.48939 (14136) hydrogen bonds : bond 0.23343 ( 569) hydrogen bonds : angle 6.98647 ( 1653) *********************** 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 356 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 335 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.8676 (tt) cc_final: 0.8458 (tp) REVERT: A 145 SER cc_start: 0.8133 (m) cc_final: 0.7892 (p) REVERT: A 155 MET cc_start: 0.6791 (mpp) cc_final: 0.6328 (mpp) REVERT: A 237 LYS cc_start: 0.8816 (ttpp) cc_final: 0.8549 (ttpp) REVERT: A 272 PHE cc_start: 0.8190 (t80) cc_final: 0.7901 (t80) REVERT: A 276 LEU cc_start: 0.8917 (mm) cc_final: 0.8417 (mm) REVERT: A 277 LEU cc_start: 0.8861 (mm) cc_final: 0.8438 (mt) REVERT: A 288 LEU cc_start: 0.8462 (tp) cc_final: 0.8250 (tp) REVERT: A 318 ASN cc_start: 0.7476 (t0) cc_final: 0.7242 (t0) REVERT: A 394 PHE cc_start: 0.8609 (t80) cc_final: 0.8393 (t80) REVERT: A 473 LYS cc_start: 0.8346 (mmmm) cc_final: 0.8125 (mmmm) REVERT: A 477 THR cc_start: 0.8346 (p) cc_final: 0.7977 (t) REVERT: A 499 LEU cc_start: 0.8817 (tp) cc_final: 0.8525 (tt) REVERT: A 575 ILE cc_start: 0.8309 (mm) cc_final: 0.7098 (mm) REVERT: A 580 LYS cc_start: 0.7500 (tttt) cc_final: 0.6732 (tttp) REVERT: A 582 LEU cc_start: 0.8749 (mt) cc_final: 0.8234 (mp) REVERT: A 652 LYS cc_start: 0.6318 (pttt) cc_final: 0.6118 (pttm) REVERT: A 681 LYS cc_start: 0.8718 (tppt) cc_final: 0.8479 (tppp) REVERT: A 687 ASP cc_start: 0.8089 (t70) cc_final: 0.7721 (t0) REVERT: A 698 ASP cc_start: 0.7693 (t70) cc_final: 0.7351 (t0) REVERT: A 704 GLU cc_start: 0.7515 (tm-30) cc_final: 0.6382 (tm-30) REVERT: A 706 CYS cc_start: 0.7633 (m) cc_final: 0.6372 (m) REVERT: B 66 LYS cc_start: 0.8414 (tptt) cc_final: 0.7971 (tppt) REVERT: B 157 PRO cc_start: 0.9182 (Cg_endo) cc_final: 0.8664 (Cg_exo) REVERT: B 161 PHE cc_start: 0.7927 (m-80) cc_final: 0.7621 (m-80) REVERT: B 210 PHE cc_start: 0.7891 (p90) cc_final: 0.7635 (p90) REVERT: B 276 LEU cc_start: 0.8957 (mm) cc_final: 0.8756 (tp) REVERT: B 277 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8618 (mm) REVERT: B 286 LYS cc_start: 0.8950 (tppt) cc_final: 0.8498 (tppt) REVERT: B 293 LYS cc_start: 0.8587 (tppt) cc_final: 0.8244 (tppt) REVERT: B 477 THR cc_start: 0.8501 (p) cc_final: 0.7894 (p) REVERT: B 486 CYS cc_start: 0.8379 (t) cc_final: 0.8159 (t) REVERT: B 496 LEU cc_start: 0.9104 (mm) cc_final: 0.8870 (mt) REVERT: B 580 LYS cc_start: 0.7844 (tttt) cc_final: 0.7305 (tttm) REVERT: B 583 LYS cc_start: 0.8405 (tmtt) cc_final: 0.8097 (tmtt) REVERT: B 668 LEU cc_start: 0.6839 (mt) cc_final: 0.6195 (mt) REVERT: B 670 VAL cc_start: 0.7689 (p) cc_final: 0.6898 (p) REVERT: B 698 ASP cc_start: 0.7684 (t70) cc_final: 0.7359 (t0) REVERT: B 701 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7355 (mm-30) REVERT: B 704 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6377 (tm-30) REVERT: B 706 CYS cc_start: 0.7405 (m) cc_final: 0.6302 (m) REVERT: B 728 HIS cc_start: 0.8536 (t70) cc_final: 0.8328 (t-90) REVERT: B 731 ASN cc_start: 0.7033 (m-40) cc_final: 0.6826 (m-40) outliers start: 21 outliers final: 8 residues processed: 352 average time/residue: 0.1382 time to fit residues: 62.3862 Evaluate side-chains 277 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 268 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 543 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 289 ASN A 421 GLN A 589 GLN A 656 HIS A 696 GLN A 712 ASN A 730 GLN A 731 ASN B 375 HIS B 421 GLN B 589 GLN B 656 HIS B 696 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.114865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.098037 restraints weight = 21109.131| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.97 r_work: 0.3167 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10400 Z= 0.159 Angle : 0.635 9.220 14136 Z= 0.325 Chirality : 0.043 0.169 1718 Planarity : 0.005 0.053 1758 Dihedral : 5.423 79.875 1433 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.41 % Allowed : 15.86 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.22), residues: 1322 helix: -0.40 (0.17), residues: 848 sheet: -2.30 (0.84), residues: 36 loop : -2.59 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 576 TYR 0.021 0.001 TYR A 377 PHE 0.019 0.001 PHE A 210 TRP 0.011 0.001 TRP B 518 HIS 0.011 0.001 HIS B 656 Details of bonding type rmsd covalent geometry : bond 0.00348 (10400) covalent geometry : angle 0.63515 (14136) hydrogen bonds : bond 0.04263 ( 569) hydrogen bonds : angle 4.36473 ( 1653) *********************** 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 298 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 271 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7789 (mpp) cc_final: 0.7223 (mpp) REVERT: A 213 ARG cc_start: 0.8399 (mtt180) cc_final: 0.8122 (mtt180) REVERT: A 237 LYS cc_start: 0.9063 (ttpp) cc_final: 0.8787 (ttpp) REVERT: A 272 PHE cc_start: 0.8781 (t80) cc_final: 0.8340 (t80) REVERT: A 276 LEU cc_start: 0.9103 (mm) cc_final: 0.8529 (mm) REVERT: A 283 MET cc_start: 0.8692 (mmm) cc_final: 0.8432 (mmm) REVERT: A 293 LYS cc_start: 0.8643 (tppt) cc_final: 0.8180 (tppt) REVERT: A 318 ASN cc_start: 0.8288 (t0) cc_final: 0.7567 (t0) REVERT: A 463 MET cc_start: 0.8693 (mmm) cc_final: 0.8356 (mmm) REVERT: A 472 TRP cc_start: 0.9171 (t-100) cc_final: 0.8759 (t-100) REVERT: A 488 MET cc_start: 0.8477 (mmm) cc_final: 0.8153 (mmm) REVERT: A 496 LEU cc_start: 0.9264 (mm) cc_final: 0.9030 (mt) REVERT: A 518 TRP cc_start: 0.8839 (p-90) cc_final: 0.8367 (p-90) REVERT: A 541 GLU cc_start: 0.8158 (mp0) cc_final: 0.7941 (mp0) REVERT: A 580 LYS cc_start: 0.7384 (tttt) cc_final: 0.6632 (tttm) REVERT: A 582 LEU cc_start: 0.8904 (mt) cc_final: 0.8652 (mp) REVERT: A 681 LYS cc_start: 0.8995 (tppt) cc_final: 0.8728 (tppp) REVERT: A 682 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8278 (mt-10) REVERT: A 685 ARG cc_start: 0.8528 (mtm180) cc_final: 0.7947 (mtm110) REVERT: A 687 ASP cc_start: 0.8830 (t70) cc_final: 0.8446 (t0) REVERT: A 696 GLN cc_start: 0.7439 (mt0) cc_final: 0.7221 (mt0) REVERT: A 698 ASP cc_start: 0.8401 (t70) cc_final: 0.8001 (t0) REVERT: A 701 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8296 (mm-30) REVERT: B 66 LYS cc_start: 0.8827 (tptt) cc_final: 0.8363 (tppt) REVERT: B 77 LYS cc_start: 0.8785 (ttpp) cc_final: 0.8503 (ttpp) REVERT: B 195 LEU cc_start: 0.8526 (tp) cc_final: 0.8222 (tt) REVERT: B 213 ARG cc_start: 0.8390 (mtt180) cc_final: 0.8047 (mtm180) REVERT: B 277 LEU cc_start: 0.9215 (mm) cc_final: 0.8889 (mm) REVERT: B 287 GLU cc_start: 0.8241 (pp20) cc_final: 0.7918 (pp20) REVERT: B 293 LYS cc_start: 0.8805 (tppt) cc_final: 0.8257 (tppt) REVERT: B 318 ASN cc_start: 0.8367 (t0) cc_final: 0.8118 (t0) REVERT: B 376 ASP cc_start: 0.8085 (t0) cc_final: 0.7498 (t0) REVERT: B 486 CYS cc_start: 0.9179 (t) cc_final: 0.8906 (t) REVERT: B 517 SER cc_start: 0.8431 (p) cc_final: 0.8215 (p) REVERT: B 537 LYS cc_start: 0.8916 (tptt) cc_final: 0.8564 (tptt) REVERT: B 549 ARG cc_start: 0.8589 (ttt180) cc_final: 0.8304 (ttt180) REVERT: B 573 ASP cc_start: 0.7795 (t0) cc_final: 0.7347 (t0) REVERT: B 576 ARG cc_start: 0.8035 (mmm160) cc_final: 0.7434 (mmm160) REVERT: B 583 LYS cc_start: 0.8889 (tmtt) cc_final: 0.8548 (tmtt) REVERT: B 698 ASP cc_start: 0.8434 (t70) cc_final: 0.7994 (t0) REVERT: B 704 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7412 (tm-30) REVERT: B 705 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7453 (mm-40) REVERT: B 728 HIS cc_start: 0.8779 (t70) cc_final: 0.8342 (t70) outliers start: 27 outliers final: 14 residues processed: 289 average time/residue: 0.1220 time to fit residues: 46.6952 Evaluate side-chains 268 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 254 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 585 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 69 optimal weight: 30.0000 chunk 81 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 128 optimal weight: 0.4980 chunk 96 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 119 optimal weight: 0.0000 chunk 94 optimal weight: 2.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 731 ASN ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 HIS B 728 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.110769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.093637 restraints weight = 21150.463| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.96 r_work: 0.3088 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10400 Z= 0.204 Angle : 0.631 7.715 14136 Z= 0.329 Chirality : 0.044 0.198 1718 Planarity : 0.005 0.046 1758 Dihedral : 5.441 80.286 1430 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.90 % Favored : 94.02 % Rotamer: Outliers : 3.12 % Allowed : 18.81 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.23), residues: 1322 helix: 0.20 (0.17), residues: 854 sheet: -1.59 (0.91), residues: 36 loop : -2.33 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 38 TYR 0.022 0.001 TYR B 377 PHE 0.025 0.002 PHE A 210 TRP 0.014 0.002 TRP A 83 HIS 0.011 0.001 HIS B 656 Details of bonding type rmsd covalent geometry : bond 0.00448 (10400) covalent geometry : angle 0.63140 (14136) hydrogen bonds : bond 0.04230 ( 569) hydrogen bonds : angle 4.16400 ( 1653) *********************** 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 293 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 258 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8714 (mm) REVERT: A 237 LYS cc_start: 0.9036 (ttpp) cc_final: 0.8771 (ttpp) REVERT: A 245 LYS cc_start: 0.8459 (mtmm) cc_final: 0.8225 (mtmm) REVERT: A 264 ILE cc_start: 0.9034 (mm) cc_final: 0.8809 (mm) REVERT: A 272 PHE cc_start: 0.8903 (t80) cc_final: 0.8427 (t80) REVERT: A 276 LEU cc_start: 0.9171 (mm) cc_final: 0.8555 (mm) REVERT: A 283 MET cc_start: 0.8817 (mmm) cc_final: 0.8525 (mmm) REVERT: A 293 LYS cc_start: 0.8634 (tppt) cc_final: 0.8118 (tppt) REVERT: A 303 GLU cc_start: 0.8552 (mp0) cc_final: 0.8325 (mp0) REVERT: A 318 ASN cc_start: 0.8516 (t0) cc_final: 0.8091 (t0) REVERT: A 374 LYS cc_start: 0.8593 (tmmt) cc_final: 0.8087 (ttpp) REVERT: A 376 ASP cc_start: 0.8194 (t70) cc_final: 0.7986 (t0) REVERT: A 463 MET cc_start: 0.8775 (mmm) cc_final: 0.8524 (mmm) REVERT: A 472 TRP cc_start: 0.9249 (t-100) cc_final: 0.8934 (t-100) REVERT: A 473 LYS cc_start: 0.9113 (mmmm) cc_final: 0.8751 (mmmm) REVERT: A 499 LEU cc_start: 0.8780 (mm) cc_final: 0.8457 (tt) REVERT: A 537 LYS cc_start: 0.8977 (tppt) cc_final: 0.8386 (mmtt) REVERT: A 541 GLU cc_start: 0.8357 (mp0) cc_final: 0.8066 (mp0) REVERT: A 580 LYS cc_start: 0.7467 (tttt) cc_final: 0.6582 (tttm) REVERT: A 681 LYS cc_start: 0.9056 (tppt) cc_final: 0.8747 (tppp) REVERT: A 687 ASP cc_start: 0.8827 (t70) cc_final: 0.8480 (t0) REVERT: A 696 GLN cc_start: 0.7654 (mt0) cc_final: 0.7384 (mt0) REVERT: A 698 ASP cc_start: 0.8470 (t70) cc_final: 0.8099 (t0) REVERT: B 66 LYS cc_start: 0.8818 (tptt) cc_final: 0.8344 (tppt) REVERT: B 77 LYS cc_start: 0.8839 (ttpp) cc_final: 0.8537 (ttpp) REVERT: B 155 MET cc_start: 0.8129 (mpp) cc_final: 0.7714 (mpp) REVERT: B 195 LEU cc_start: 0.8513 (tp) cc_final: 0.8282 (tt) REVERT: B 213 ARG cc_start: 0.8426 (mtt180) cc_final: 0.8106 (mtm180) REVERT: B 259 GLU cc_start: 0.8852 (tt0) cc_final: 0.8454 (tm-30) REVERT: B 277 LEU cc_start: 0.9242 (mm) cc_final: 0.9016 (mm) REVERT: B 293 LYS cc_start: 0.8816 (tppt) cc_final: 0.8247 (tppt) REVERT: B 318 ASN cc_start: 0.8487 (t0) cc_final: 0.7972 (t0) REVERT: B 320 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7312 (tm-30) REVERT: B 322 ASN cc_start: 0.8385 (m-40) cc_final: 0.8147 (m-40) REVERT: B 376 ASP cc_start: 0.7899 (t0) cc_final: 0.7619 (t0) REVERT: B 384 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8192 (mm-30) REVERT: B 466 CYS cc_start: 0.8752 (m) cc_final: 0.8482 (p) REVERT: B 486 CYS cc_start: 0.9154 (t) cc_final: 0.8911 (t) REVERT: B 537 LYS cc_start: 0.8982 (tptt) cc_final: 0.8632 (tptt) REVERT: B 549 ARG cc_start: 0.8756 (ttt180) cc_final: 0.8400 (ttt180) REVERT: B 583 LYS cc_start: 0.8953 (tmtt) cc_final: 0.8608 (tmtt) REVERT: B 587 ARG cc_start: 0.7439 (mmm-85) cc_final: 0.7195 (mmm-85) REVERT: B 669 ASP cc_start: 0.7434 (t0) cc_final: 0.7186 (t70) REVERT: B 698 ASP cc_start: 0.8492 (t70) cc_final: 0.7982 (t0) REVERT: B 704 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8060 (tm-30) outliers start: 35 outliers final: 22 residues processed: 277 average time/residue: 0.1252 time to fit residues: 45.6401 Evaluate side-chains 268 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 245 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 585 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 77 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 79 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.110620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.093388 restraints weight = 21098.829| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.99 r_work: 0.3098 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10400 Z= 0.163 Angle : 0.623 12.677 14136 Z= 0.318 Chirality : 0.043 0.183 1718 Planarity : 0.004 0.045 1758 Dihedral : 5.443 81.424 1430 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.82 % Favored : 94.10 % Rotamer: Outliers : 3.39 % Allowed : 20.23 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.24), residues: 1322 helix: 0.49 (0.18), residues: 854 sheet: -0.92 (0.98), residues: 34 loop : -2.16 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 38 TYR 0.027 0.001 TYR B 377 PHE 0.026 0.001 PHE B 210 TRP 0.016 0.001 TRP A 83 HIS 0.007 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00361 (10400) covalent geometry : angle 0.62256 (14136) hydrogen bonds : bond 0.03867 ( 569) hydrogen bonds : angle 4.02866 ( 1653) *********************** 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 295 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 257 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LEU cc_start: 0.9029 (tp) cc_final: 0.8744 (tt) REVERT: A 237 LYS cc_start: 0.9049 (ttpp) cc_final: 0.8773 (ttpp) REVERT: A 245 LYS cc_start: 0.8438 (mtmm) cc_final: 0.8220 (mtmm) REVERT: A 272 PHE cc_start: 0.8890 (t80) cc_final: 0.8400 (t80) REVERT: A 276 LEU cc_start: 0.9182 (mm) cc_final: 0.8535 (mm) REVERT: A 283 MET cc_start: 0.8801 (mmm) cc_final: 0.8466 (mmm) REVERT: A 293 LYS cc_start: 0.8599 (tppt) cc_final: 0.8104 (tppt) REVERT: A 318 ASN cc_start: 0.8442 (t0) cc_final: 0.8117 (t0) REVERT: A 443 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8172 (pp20) REVERT: A 463 MET cc_start: 0.8773 (mmm) cc_final: 0.8476 (mmm) REVERT: A 537 LYS cc_start: 0.8960 (tppt) cc_final: 0.8444 (mmtm) REVERT: A 541 GLU cc_start: 0.8393 (mp0) cc_final: 0.8120 (mp0) REVERT: A 580 LYS cc_start: 0.7326 (tttt) cc_final: 0.6594 (tttp) REVERT: A 677 ARG cc_start: 0.8343 (ttp80) cc_final: 0.8073 (ttp-110) REVERT: A 687 ASP cc_start: 0.8843 (t70) cc_final: 0.8482 (t0) REVERT: A 696 GLN cc_start: 0.7666 (mt0) cc_final: 0.7364 (mt0) REVERT: A 698 ASP cc_start: 0.8475 (t70) cc_final: 0.8090 (t0) REVERT: A 704 GLU cc_start: 0.8628 (tm-30) cc_final: 0.7963 (tm-30) REVERT: A 712 ASN cc_start: 0.8550 (t0) cc_final: 0.8175 (t0) REVERT: B 66 LYS cc_start: 0.8795 (tptt) cc_final: 0.8276 (tppt) REVERT: B 77 LYS cc_start: 0.8793 (ttpp) cc_final: 0.8253 (ttpp) REVERT: B 195 LEU cc_start: 0.8516 (tp) cc_final: 0.8262 (tt) REVERT: B 213 ARG cc_start: 0.8390 (mtt180) cc_final: 0.8131 (mtm-85) REVERT: B 259 GLU cc_start: 0.8811 (tt0) cc_final: 0.8370 (tm-30) REVERT: B 293 LYS cc_start: 0.8813 (tppt) cc_final: 0.8229 (tppt) REVERT: B 318 ASN cc_start: 0.8491 (t0) cc_final: 0.7961 (t0) REVERT: B 320 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7288 (tm-30) REVERT: B 322 ASN cc_start: 0.8364 (m-40) cc_final: 0.8161 (m-40) REVERT: B 324 ASN cc_start: 0.9049 (t0) cc_final: 0.8595 (t0) REVERT: B 376 ASP cc_start: 0.7949 (t0) cc_final: 0.7637 (t0) REVERT: B 384 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8177 (mm-30) REVERT: B 466 CYS cc_start: 0.8766 (m) cc_final: 0.8479 (p) REVERT: B 486 CYS cc_start: 0.9137 (t) cc_final: 0.8871 (t) REVERT: B 517 SER cc_start: 0.8479 (p) cc_final: 0.8216 (p) REVERT: B 537 LYS cc_start: 0.8961 (tptt) cc_final: 0.8589 (tptt) REVERT: B 549 ARG cc_start: 0.8721 (ttt180) cc_final: 0.8356 (ttt180) REVERT: B 583 LYS cc_start: 0.8951 (tmtt) cc_final: 0.8519 (tmtt) REVERT: B 669 ASP cc_start: 0.7329 (t0) cc_final: 0.7039 (t0) REVERT: B 698 ASP cc_start: 0.8433 (t70) cc_final: 0.7951 (t0) REVERT: B 704 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8333 (tm-30) outliers start: 38 outliers final: 30 residues processed: 278 average time/residue: 0.1218 time to fit residues: 45.0004 Evaluate side-chains 273 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 243 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 277 LEU 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 385 PHE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 706 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 76 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 68 optimal weight: 0.0570 chunk 78 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 712 ASN A 730 GLN ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.110603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.093418 restraints weight = 21110.994| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.97 r_work: 0.3081 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10400 Z= 0.173 Angle : 0.629 13.158 14136 Z= 0.323 Chirality : 0.043 0.185 1718 Planarity : 0.004 0.050 1758 Dihedral : 5.476 81.145 1428 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.90 % Favored : 93.95 % Rotamer: Outliers : 3.39 % Allowed : 21.93 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.24), residues: 1322 helix: 0.60 (0.18), residues: 860 sheet: -0.68 (0.99), residues: 34 loop : -1.93 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 38 TYR 0.028 0.001 TYR B 377 PHE 0.026 0.001 PHE B 210 TRP 0.018 0.001 TRP A 83 HIS 0.009 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00384 (10400) covalent geometry : angle 0.62858 (14136) hydrogen bonds : bond 0.03936 ( 569) hydrogen bonds : angle 4.01267 ( 1653) *********************** 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 293 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 255 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 SER cc_start: 0.8904 (m) cc_final: 0.8525 (p) REVERT: A 236 LEU cc_start: 0.9031 (tp) cc_final: 0.8722 (tt) REVERT: A 237 LYS cc_start: 0.9052 (ttpp) cc_final: 0.8774 (ttpp) REVERT: A 262 GLN cc_start: 0.8706 (pt0) cc_final: 0.8420 (pp30) REVERT: A 272 PHE cc_start: 0.8942 (t80) cc_final: 0.8427 (t80) REVERT: A 276 LEU cc_start: 0.9169 (mm) cc_final: 0.8534 (mm) REVERT: A 283 MET cc_start: 0.8825 (mmm) cc_final: 0.8448 (mmm) REVERT: A 293 LYS cc_start: 0.8576 (tppt) cc_final: 0.8069 (tppt) REVERT: A 303 GLU cc_start: 0.8502 (mp0) cc_final: 0.8260 (mp0) REVERT: A 318 ASN cc_start: 0.8454 (t0) cc_final: 0.8111 (t0) REVERT: A 463 MET cc_start: 0.8776 (mmm) cc_final: 0.8440 (mmm) REVERT: A 473 LYS cc_start: 0.9053 (mmmm) cc_final: 0.8650 (tppp) REVERT: A 537 LYS cc_start: 0.8977 (tppt) cc_final: 0.8532 (mmtm) REVERT: A 541 GLU cc_start: 0.8432 (mp0) cc_final: 0.8160 (mp0) REVERT: A 580 LYS cc_start: 0.7346 (tttt) cc_final: 0.6634 (tttm) REVERT: A 582 LEU cc_start: 0.8932 (mp) cc_final: 0.8680 (mp) REVERT: A 687 ASP cc_start: 0.8829 (t70) cc_final: 0.8488 (t0) REVERT: A 696 GLN cc_start: 0.7711 (mt0) cc_final: 0.7424 (mt0) REVERT: A 698 ASP cc_start: 0.8471 (t70) cc_final: 0.8109 (t0) REVERT: A 704 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8086 (tm-30) REVERT: A 712 ASN cc_start: 0.8614 (t0) cc_final: 0.8232 (t0) REVERT: B 66 LYS cc_start: 0.8795 (tptt) cc_final: 0.8438 (tptp) REVERT: B 195 LEU cc_start: 0.8522 (tp) cc_final: 0.8273 (tt) REVERT: B 213 ARG cc_start: 0.8413 (mtt180) cc_final: 0.8087 (mtp85) REVERT: B 259 GLU cc_start: 0.8699 (tt0) cc_final: 0.8216 (tm-30) REVERT: B 293 LYS cc_start: 0.8804 (tppt) cc_final: 0.8234 (tppt) REVERT: B 318 ASN cc_start: 0.8511 (t0) cc_final: 0.7942 (t0) REVERT: B 320 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7351 (tm-30) REVERT: B 322 ASN cc_start: 0.8408 (m-40) cc_final: 0.8198 (m-40) REVERT: B 324 ASN cc_start: 0.9048 (t0) cc_final: 0.8565 (t0) REVERT: B 374 LYS cc_start: 0.8741 (tmtt) cc_final: 0.8471 (ttpp) REVERT: B 376 ASP cc_start: 0.7975 (t0) cc_final: 0.7568 (t0) REVERT: B 384 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8128 (mm-30) REVERT: B 400 CYS cc_start: 0.8552 (m) cc_final: 0.8317 (m) REVERT: B 466 CYS cc_start: 0.8801 (m) cc_final: 0.8507 (p) REVERT: B 486 CYS cc_start: 0.9132 (t) cc_final: 0.8876 (t) REVERT: B 517 SER cc_start: 0.8522 (p) cc_final: 0.8275 (p) REVERT: B 537 LYS cc_start: 0.8980 (tptt) cc_final: 0.8606 (tptt) REVERT: B 549 ARG cc_start: 0.8714 (ttt180) cc_final: 0.8350 (ttt180) REVERT: B 580 LYS cc_start: 0.7742 (tttt) cc_final: 0.7529 (tttt) REVERT: B 583 LYS cc_start: 0.8938 (tmtt) cc_final: 0.8482 (tmtt) REVERT: B 698 ASP cc_start: 0.8364 (t70) cc_final: 0.7891 (t0) REVERT: B 704 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8356 (tm-30) outliers start: 38 outliers final: 28 residues processed: 279 average time/residue: 0.1188 time to fit residues: 43.9231 Evaluate side-chains 277 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 249 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 706 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 49 optimal weight: 0.8980 chunk 120 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 14 optimal weight: 0.0670 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 69 optimal weight: 40.0000 chunk 44 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.111026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.093924 restraints weight = 21251.318| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.99 r_work: 0.3095 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10400 Z= 0.146 Angle : 0.631 12.893 14136 Z= 0.322 Chirality : 0.043 0.185 1718 Planarity : 0.004 0.042 1758 Dihedral : 5.511 81.865 1428 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.82 % Favored : 94.02 % Rotamer: Outliers : 3.83 % Allowed : 21.57 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.24), residues: 1322 helix: 0.70 (0.18), residues: 860 sheet: -0.44 (1.01), residues: 34 loop : -1.86 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 38 TYR 0.030 0.001 TYR B 377 PHE 0.025 0.001 PHE B 210 TRP 0.012 0.001 TRP A 83 HIS 0.006 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00326 (10400) covalent geometry : angle 0.63093 (14136) hydrogen bonds : bond 0.03733 ( 569) hydrogen bonds : angle 3.98601 ( 1653) *********************** 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 299 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 256 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 SER cc_start: 0.8894 (m) cc_final: 0.8501 (p) REVERT: A 236 LEU cc_start: 0.9011 (tp) cc_final: 0.8695 (tt) REVERT: A 259 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8365 (tm-30) REVERT: A 262 GLN cc_start: 0.8734 (pt0) cc_final: 0.8436 (pp30) REVERT: A 272 PHE cc_start: 0.8935 (t80) cc_final: 0.8421 (t80) REVERT: A 276 LEU cc_start: 0.9169 (mm) cc_final: 0.8531 (mm) REVERT: A 283 MET cc_start: 0.8854 (mmm) cc_final: 0.8460 (mmm) REVERT: A 293 LYS cc_start: 0.8555 (tppt) cc_final: 0.8049 (tppt) REVERT: A 318 ASN cc_start: 0.8453 (t0) cc_final: 0.8099 (t0) REVERT: A 374 LYS cc_start: 0.8783 (tmtt) cc_final: 0.8415 (ttpp) REVERT: A 463 MET cc_start: 0.8795 (mmm) cc_final: 0.8462 (mmm) REVERT: A 473 LYS cc_start: 0.9018 (mmmm) cc_final: 0.8716 (tppp) REVERT: A 496 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9024 (mt) REVERT: A 537 LYS cc_start: 0.8959 (tppt) cc_final: 0.8512 (mmtm) REVERT: A 541 GLU cc_start: 0.8506 (mp0) cc_final: 0.8232 (mp0) REVERT: A 575 ILE cc_start: 0.8693 (mm) cc_final: 0.7448 (mm) REVERT: A 576 ARG cc_start: 0.8133 (mmm160) cc_final: 0.7576 (mmm160) REVERT: A 580 LYS cc_start: 0.7366 (tttt) cc_final: 0.6580 (tttm) REVERT: A 687 ASP cc_start: 0.8777 (t70) cc_final: 0.8457 (t0) REVERT: A 696 GLN cc_start: 0.7727 (mt0) cc_final: 0.7442 (mt0) REVERT: A 698 ASP cc_start: 0.8487 (t70) cc_final: 0.8147 (t0) REVERT: A 704 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8165 (tm-30) REVERT: A 705 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8308 (mm-40) REVERT: A 712 ASN cc_start: 0.8633 (t0) cc_final: 0.8265 (t0) REVERT: B 66 LYS cc_start: 0.8766 (tptt) cc_final: 0.8372 (tptp) REVERT: B 195 LEU cc_start: 0.8520 (tp) cc_final: 0.8284 (tt) REVERT: B 213 ARG cc_start: 0.8386 (mtt180) cc_final: 0.7725 (mtp85) REVERT: B 259 GLU cc_start: 0.8506 (tt0) cc_final: 0.8301 (tm-30) REVERT: B 288 LEU cc_start: 0.8679 (tt) cc_final: 0.8253 (mm) REVERT: B 293 LYS cc_start: 0.8794 (tppt) cc_final: 0.8221 (tppt) REVERT: B 318 ASN cc_start: 0.8524 (t0) cc_final: 0.7956 (t0) REVERT: B 320 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7320 (tm-30) REVERT: B 322 ASN cc_start: 0.8403 (m-40) cc_final: 0.8200 (m-40) REVERT: B 324 ASN cc_start: 0.9042 (t0) cc_final: 0.8552 (t0) REVERT: B 369 LYS cc_start: 0.8840 (mttp) cc_final: 0.8639 (ttmm) REVERT: B 384 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8069 (mm-30) REVERT: B 400 CYS cc_start: 0.8535 (m) cc_final: 0.8300 (m) REVERT: B 466 CYS cc_start: 0.8745 (m) cc_final: 0.8461 (p) REVERT: B 486 CYS cc_start: 0.9127 (t) cc_final: 0.8872 (t) REVERT: B 517 SER cc_start: 0.8391 (p) cc_final: 0.8123 (p) REVERT: B 537 LYS cc_start: 0.8973 (tptt) cc_final: 0.8573 (tptt) REVERT: B 549 ARG cc_start: 0.8684 (ttt180) cc_final: 0.8336 (ttt180) REVERT: B 583 LYS cc_start: 0.8949 (tmtt) cc_final: 0.8536 (tmtt) REVERT: B 652 LYS cc_start: 0.7504 (pttt) cc_final: 0.7259 (pttt) REVERT: B 698 ASP cc_start: 0.8382 (t70) cc_final: 0.7898 (t0) REVERT: B 704 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8409 (tm-30) outliers start: 43 outliers final: 31 residues processed: 280 average time/residue: 0.1211 time to fit residues: 44.3679 Evaluate side-chains 278 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 246 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 706 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 85 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 90 optimal weight: 0.3980 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 0.0470 chunk 53 optimal weight: 0.0470 chunk 92 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.111919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.095027 restraints weight = 20991.900| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.98 r_work: 0.3113 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10400 Z= 0.133 Angle : 0.637 11.835 14136 Z= 0.323 Chirality : 0.042 0.179 1718 Planarity : 0.004 0.040 1758 Dihedral : 5.481 81.748 1428 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.98 % Favored : 93.87 % Rotamer: Outliers : 3.57 % Allowed : 22.01 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.24), residues: 1322 helix: 0.77 (0.18), residues: 862 sheet: -0.37 (1.00), residues: 34 loop : -1.83 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 587 TYR 0.032 0.001 TYR B 377 PHE 0.022 0.001 PHE A 210 TRP 0.010 0.001 TRP A 83 HIS 0.007 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00299 (10400) covalent geometry : angle 0.63750 (14136) hydrogen bonds : bond 0.03633 ( 569) hydrogen bonds : angle 3.95345 ( 1653) *********************** 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 292 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 252 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LEU cc_start: 0.8981 (tp) cc_final: 0.8677 (tt) REVERT: A 259 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8107 (tm-30) REVERT: A 262 GLN cc_start: 0.8734 (pt0) cc_final: 0.8488 (pp30) REVERT: A 272 PHE cc_start: 0.8950 (t80) cc_final: 0.8438 (t80) REVERT: A 276 LEU cc_start: 0.9165 (mm) cc_final: 0.8532 (mm) REVERT: A 283 MET cc_start: 0.8812 (mmm) cc_final: 0.8478 (mmm) REVERT: A 293 LYS cc_start: 0.8522 (tppt) cc_final: 0.7998 (tppt) REVERT: A 318 ASN cc_start: 0.8428 (t0) cc_final: 0.8069 (t0) REVERT: A 374 LYS cc_start: 0.8860 (tmtt) cc_final: 0.8459 (ttpp) REVERT: A 463 MET cc_start: 0.8783 (mmm) cc_final: 0.8439 (mmm) REVERT: A 472 TRP cc_start: 0.9216 (t-100) cc_final: 0.8813 (t-100) REVERT: A 473 LYS cc_start: 0.9050 (mmmm) cc_final: 0.8752 (tppp) REVERT: A 496 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9037 (mt) REVERT: A 537 LYS cc_start: 0.8918 (tppt) cc_final: 0.8543 (mmtt) REVERT: A 541 GLU cc_start: 0.8519 (mp0) cc_final: 0.8263 (mp0) REVERT: A 575 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.7368 (mm) REVERT: A 576 ARG cc_start: 0.8188 (mmm160) cc_final: 0.7628 (mmm160) REVERT: A 580 LYS cc_start: 0.7373 (tttt) cc_final: 0.6618 (tttm) REVERT: A 687 ASP cc_start: 0.8777 (t70) cc_final: 0.8446 (t0) REVERT: A 698 ASP cc_start: 0.8510 (t70) cc_final: 0.8164 (t0) REVERT: A 704 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8219 (tm-30) REVERT: A 705 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8412 (mm-40) REVERT: A 712 ASN cc_start: 0.8612 (t0) cc_final: 0.8241 (t0) REVERT: B 66 LYS cc_start: 0.8765 (tptt) cc_final: 0.8361 (tptp) REVERT: B 195 LEU cc_start: 0.8517 (tp) cc_final: 0.8296 (tt) REVERT: B 203 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8498 (m-80) REVERT: B 213 ARG cc_start: 0.8351 (mtt180) cc_final: 0.7827 (mtp85) REVERT: B 255 TYR cc_start: 0.8996 (m-10) cc_final: 0.8234 (m-10) REVERT: B 259 GLU cc_start: 0.8683 (tt0) cc_final: 0.8370 (tm-30) REVERT: B 288 LEU cc_start: 0.8661 (tt) cc_final: 0.8238 (mm) REVERT: B 293 LYS cc_start: 0.8774 (tppt) cc_final: 0.8186 (tppt) REVERT: B 318 ASN cc_start: 0.8491 (t0) cc_final: 0.8180 (t0) REVERT: B 320 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7285 (tm-30) REVERT: B 324 ASN cc_start: 0.9016 (t0) cc_final: 0.8551 (t0) REVERT: B 384 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8230 (mm-30) REVERT: B 400 CYS cc_start: 0.8435 (m) cc_final: 0.8199 (m) REVERT: B 466 CYS cc_start: 0.8693 (m) cc_final: 0.8439 (p) REVERT: B 486 CYS cc_start: 0.9142 (t) cc_final: 0.8880 (t) REVERT: B 517 SER cc_start: 0.8401 (p) cc_final: 0.8155 (p) REVERT: B 537 LYS cc_start: 0.8919 (tptt) cc_final: 0.8541 (tptt) REVERT: B 580 LYS cc_start: 0.7857 (tttt) cc_final: 0.7515 (tttp) REVERT: B 583 LYS cc_start: 0.8966 (tmtt) cc_final: 0.8563 (tmtt) REVERT: B 587 ARG cc_start: 0.7713 (mmm-85) cc_final: 0.7232 (mmm-85) REVERT: B 652 LYS cc_start: 0.7560 (pttt) cc_final: 0.7283 (pttt) REVERT: B 687 ASP cc_start: 0.8755 (t0) cc_final: 0.8517 (t0) REVERT: B 698 ASP cc_start: 0.8394 (t70) cc_final: 0.7926 (t0) REVERT: B 704 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8372 (tm-30) outliers start: 40 outliers final: 32 residues processed: 275 average time/residue: 0.1261 time to fit residues: 45.8035 Evaluate side-chains 281 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 246 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 706 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 85 optimal weight: 0.4980 chunk 106 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 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 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.110554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.093931 restraints weight = 21301.167| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.97 r_work: 0.3063 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4215 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= 0.196 Angle : 0.675 14.659 14136 Z= 0.344 Chirality : 0.044 0.177 1718 Planarity : 0.004 0.046 1758 Dihedral : 5.561 80.770 1428 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.58 % Favored : 93.27 % Rotamer: Outliers : 3.92 % Allowed : 22.46 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.24), residues: 1322 helix: 0.76 (0.18), residues: 862 sheet: -0.26 (1.00), residues: 34 loop : -1.77 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 38 TYR 0.028 0.001 TYR B 377 PHE 0.022 0.001 PHE A 210 TRP 0.010 0.002 TRP A 472 HIS 0.007 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00433 (10400) covalent geometry : angle 0.67543 (14136) hydrogen bonds : bond 0.03998 ( 569) hydrogen bonds : angle 3.98514 ( 1653) *********************** 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 298 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 254 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8126 (t80) cc_final: 0.7821 (t80) REVERT: A 145 SER cc_start: 0.8956 (m) cc_final: 0.8599 (p) REVERT: A 262 GLN cc_start: 0.8800 (pt0) cc_final: 0.8555 (pp30) REVERT: A 272 PHE cc_start: 0.8964 (t80) cc_final: 0.8393 (t80) REVERT: A 276 LEU cc_start: 0.9179 (mm) cc_final: 0.8539 (mm) REVERT: A 283 MET cc_start: 0.8845 (mmm) cc_final: 0.8508 (mmm) REVERT: A 293 LYS cc_start: 0.8505 (tppt) cc_final: 0.7961 (tppt) REVERT: A 318 ASN cc_start: 0.8455 (t0) cc_final: 0.8072 (t0) REVERT: A 374 LYS cc_start: 0.8872 (tmtt) cc_final: 0.8452 (ttpp) REVERT: A 440 ARG cc_start: 0.8280 (mmm160) cc_final: 0.7957 (tmm-80) REVERT: A 443 GLU cc_start: 0.8683 (pp20) cc_final: 0.8237 (mm-30) REVERT: A 463 MET cc_start: 0.8816 (mmm) cc_final: 0.8478 (mmm) REVERT: A 473 LYS cc_start: 0.9053 (mmmm) cc_final: 0.8710 (tppp) REVERT: A 496 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9051 (mt) REVERT: A 537 LYS cc_start: 0.8937 (tppt) cc_final: 0.8556 (mmtt) REVERT: A 541 GLU cc_start: 0.8575 (mp0) cc_final: 0.8314 (mp0) REVERT: A 576 ARG cc_start: 0.8248 (mmm160) cc_final: 0.7541 (mmm160) REVERT: A 580 LYS cc_start: 0.7342 (tttt) cc_final: 0.6404 (tttp) REVERT: A 681 LYS cc_start: 0.9135 (tppp) cc_final: 0.8776 (tppp) REVERT: A 687 ASP cc_start: 0.8809 (t70) cc_final: 0.8482 (t0) REVERT: A 698 ASP cc_start: 0.8526 (t70) cc_final: 0.8187 (t0) REVERT: A 704 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8179 (tm-30) REVERT: A 705 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8283 (mm-40) REVERT: A 712 ASN cc_start: 0.8629 (t0) cc_final: 0.8202 (t0) REVERT: A 732 GLN cc_start: 0.7236 (tm-30) cc_final: 0.6769 (tm-30) REVERT: B 66 LYS cc_start: 0.8814 (tptt) cc_final: 0.8188 (tppt) REVERT: B 195 LEU cc_start: 0.8548 (tp) cc_final: 0.8293 (tt) REVERT: B 203 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8453 (m-80) REVERT: B 213 ARG cc_start: 0.8384 (mtt180) cc_final: 0.7730 (mtp85) REVERT: B 245 LYS cc_start: 0.7909 (ptpp) cc_final: 0.7578 (ptpp) REVERT: B 255 TYR cc_start: 0.9042 (m-10) cc_final: 0.8414 (m-10) REVERT: B 259 GLU cc_start: 0.8705 (tt0) cc_final: 0.8354 (tm-30) REVERT: B 288 LEU cc_start: 0.8673 (tt) cc_final: 0.8232 (mm) REVERT: B 293 LYS cc_start: 0.8740 (tppt) cc_final: 0.8171 (tppt) REVERT: B 318 ASN cc_start: 0.8544 (t0) cc_final: 0.8324 (t0) REVERT: B 320 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7386 (tm-30) REVERT: B 324 ASN cc_start: 0.9027 (t0) cc_final: 0.8543 (t0) REVERT: B 374 LYS cc_start: 0.8784 (tmtt) cc_final: 0.8503 (ttpp) REVERT: B 384 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8021 (tp30) REVERT: B 400 CYS cc_start: 0.8484 (m) cc_final: 0.8259 (m) REVERT: B 466 CYS cc_start: 0.8798 (m) cc_final: 0.8482 (p) REVERT: B 472 TRP cc_start: 0.9178 (t-100) cc_final: 0.8784 (t-100) REVERT: B 486 CYS cc_start: 0.9155 (t) cc_final: 0.8907 (t) REVERT: B 517 SER cc_start: 0.8580 (p) cc_final: 0.8351 (p) REVERT: B 537 LYS cc_start: 0.8943 (tptt) cc_final: 0.8544 (tptt) REVERT: B 549 ARG cc_start: 0.8739 (ttt180) cc_final: 0.7878 (ttt180) REVERT: B 583 LYS cc_start: 0.8966 (tmtt) cc_final: 0.8604 (tmtt) REVERT: B 687 ASP cc_start: 0.8803 (t0) cc_final: 0.8470 (t0) REVERT: B 698 ASP cc_start: 0.8439 (t70) cc_final: 0.8038 (t0) REVERT: B 704 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8455 (tm-30) outliers start: 44 outliers final: 34 residues processed: 281 average time/residue: 0.1310 time to fit residues: 48.4680 Evaluate side-chains 283 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 247 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 208 ILE 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 385 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 705 GLN Chi-restraints excluded: chain B residue 706 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 31 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 66 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 HIS ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.111072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.094410 restraints weight = 21241.798| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.98 r_work: 0.3076 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10400 Z= 0.174 Angle : 0.674 15.442 14136 Z= 0.342 Chirality : 0.044 0.183 1718 Planarity : 0.004 0.043 1758 Dihedral : 5.593 81.721 1428 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.35 % Favored : 93.49 % Rotamer: Outliers : 3.57 % Allowed : 22.28 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.24), residues: 1322 helix: 0.79 (0.18), residues: 862 sheet: -0.13 (1.01), residues: 34 loop : -1.75 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 38 TYR 0.032 0.002 TYR A 361 PHE 0.026 0.001 PHE A 130 TRP 0.009 0.001 TRP B 518 HIS 0.015 0.001 HIS B 656 Details of bonding type rmsd covalent geometry : bond 0.00389 (10400) covalent geometry : angle 0.67376 (14136) hydrogen bonds : bond 0.03908 ( 569) hydrogen bonds : angle 3.98460 ( 1653) *********************** 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 289 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 249 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8076 (t80) cc_final: 0.7780 (t80) REVERT: A 145 SER cc_start: 0.8940 (m) cc_final: 0.8593 (p) REVERT: A 272 PHE cc_start: 0.8975 (t80) cc_final: 0.8406 (t80) REVERT: A 276 LEU cc_start: 0.9174 (mm) cc_final: 0.8535 (mm) REVERT: A 283 MET cc_start: 0.8866 (mmm) cc_final: 0.8524 (mmm) REVERT: A 293 LYS cc_start: 0.8472 (tppt) cc_final: 0.7947 (tppt) REVERT: A 318 ASN cc_start: 0.8419 (t0) cc_final: 0.8017 (t0) REVERT: A 374 LYS cc_start: 0.8857 (tmtt) cc_final: 0.8406 (ttpp) REVERT: A 463 MET cc_start: 0.8831 (mmm) cc_final: 0.8503 (mmm) REVERT: A 473 LYS cc_start: 0.9055 (mmmm) cc_final: 0.8706 (tppp) REVERT: A 496 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9054 (mt) REVERT: A 537 LYS cc_start: 0.8893 (tppt) cc_final: 0.8509 (mmtm) REVERT: A 541 GLU cc_start: 0.8573 (mp0) cc_final: 0.8319 (mp0) REVERT: A 580 LYS cc_start: 0.7245 (tttt) cc_final: 0.6483 (tttm) REVERT: A 681 LYS cc_start: 0.9116 (tppp) cc_final: 0.8721 (tppp) REVERT: A 687 ASP cc_start: 0.8771 (t70) cc_final: 0.8453 (t0) REVERT: A 698 ASP cc_start: 0.8485 (t70) cc_final: 0.8158 (t0) REVERT: A 704 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8142 (tm-30) REVERT: A 705 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8287 (mm-40) REVERT: A 712 ASN cc_start: 0.8613 (t0) cc_final: 0.8191 (t0) REVERT: A 714 ARG cc_start: 0.8453 (mtm180) cc_final: 0.8148 (mtm110) REVERT: A 732 GLN cc_start: 0.7244 (tm-30) cc_final: 0.6773 (tm-30) REVERT: B 66 LYS cc_start: 0.8787 (tptt) cc_final: 0.8169 (tppt) REVERT: B 195 LEU cc_start: 0.8535 (tp) cc_final: 0.8287 (tt) REVERT: B 203 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8483 (m-80) REVERT: B 245 LYS cc_start: 0.7937 (ptpp) cc_final: 0.7592 (ptpp) REVERT: B 255 TYR cc_start: 0.9054 (m-10) cc_final: 0.8322 (m-10) REVERT: B 288 LEU cc_start: 0.8644 (tt) cc_final: 0.8220 (mm) REVERT: B 293 LYS cc_start: 0.8707 (tppt) cc_final: 0.8130 (tppt) REVERT: B 318 ASN cc_start: 0.8542 (t0) cc_final: 0.8324 (t0) REVERT: B 320 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7369 (tm-30) REVERT: B 324 ASN cc_start: 0.9013 (t0) cc_final: 0.8529 (t0) REVERT: B 374 LYS cc_start: 0.8801 (tmtt) cc_final: 0.8494 (ttpp) REVERT: B 384 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8007 (tp30) REVERT: B 466 CYS cc_start: 0.8775 (m) cc_final: 0.8479 (p) REVERT: B 486 CYS cc_start: 0.9141 (t) cc_final: 0.8904 (t) REVERT: B 517 SER cc_start: 0.8528 (p) cc_final: 0.8306 (p) REVERT: B 537 LYS cc_start: 0.8955 (tptt) cc_final: 0.8488 (tptt) REVERT: B 549 ARG cc_start: 0.8449 (ttt180) cc_final: 0.8087 (ttt180) REVERT: B 583 LYS cc_start: 0.8999 (tmtt) cc_final: 0.8622 (tmtt) REVERT: B 687 ASP cc_start: 0.8807 (t0) cc_final: 0.8479 (t0) REVERT: B 698 ASP cc_start: 0.8459 (t70) cc_final: 0.8023 (t0) REVERT: B 704 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8440 (tm-30) outliers start: 40 outliers final: 31 residues processed: 275 average time/residue: 0.1283 time to fit residues: 46.7119 Evaluate side-chains 279 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 246 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 705 GLN Chi-restraints excluded: chain B residue 706 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 108 optimal weight: 0.4980 chunk 89 optimal weight: 0.0470 chunk 29 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 1 optimal weight: 0.0000 chunk 85 optimal weight: 0.0870 overall best weight: 0.2460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 HIS ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.113171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.096582 restraints weight = 20945.597| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.98 r_work: 0.3129 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10400 Z= 0.133 Angle : 0.686 15.935 14136 Z= 0.345 Chirality : 0.042 0.210 1718 Planarity : 0.004 0.049 1758 Dihedral : 5.534 82.447 1428 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.05 % Favored : 93.80 % Rotamer: Outliers : 2.94 % Allowed : 22.99 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.24), residues: 1322 helix: 0.89 (0.18), residues: 856 sheet: -0.04 (0.99), residues: 34 loop : -1.62 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 38 TYR 0.031 0.001 TYR B 377 PHE 0.027 0.001 PHE A 130 TRP 0.010 0.001 TRP A 83 HIS 0.016 0.001 HIS B 656 Details of bonding type rmsd covalent geometry : bond 0.00304 (10400) covalent geometry : angle 0.68560 (14136) hydrogen bonds : bond 0.03622 ( 569) hydrogen bonds : angle 3.95472 ( 1653) ********************** 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 285 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 252 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 SER cc_start: 0.8931 (m) cc_final: 0.8539 (p) REVERT: A 236 LEU cc_start: 0.8995 (tp) cc_final: 0.8756 (tt) REVERT: A 272 PHE cc_start: 0.8947 (t80) cc_final: 0.8434 (t80) REVERT: A 276 LEU cc_start: 0.9155 (mm) cc_final: 0.8533 (mm) REVERT: A 283 MET cc_start: 0.8813 (mmm) cc_final: 0.8460 (mmm) REVERT: A 293 LYS cc_start: 0.8424 (tppt) cc_final: 0.7879 (tppt) REVERT: A 318 ASN cc_start: 0.8411 (t0) cc_final: 0.8012 (t0) REVERT: A 440 ARG cc_start: 0.8062 (tmm-80) cc_final: 0.7386 (ttp80) REVERT: A 443 GLU cc_start: 0.8597 (pp20) cc_final: 0.8137 (mm-30) REVERT: A 463 MET cc_start: 0.8830 (mmm) cc_final: 0.8405 (mmm) REVERT: A 472 TRP cc_start: 0.9288 (t-100) cc_final: 0.8793 (t-100) REVERT: A 473 LYS cc_start: 0.9040 (mmmm) cc_final: 0.8679 (tppp) REVERT: A 496 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8769 (mt) REVERT: A 541 GLU cc_start: 0.8527 (mp0) cc_final: 0.8270 (mp0) REVERT: A 580 LYS cc_start: 0.7181 (tttt) cc_final: 0.6665 (tttt) REVERT: A 681 LYS cc_start: 0.9106 (tppp) cc_final: 0.8710 (tppp) REVERT: A 687 ASP cc_start: 0.8739 (t70) cc_final: 0.8416 (t0) REVERT: A 698 ASP cc_start: 0.8451 (t70) cc_final: 0.8113 (t0) REVERT: A 704 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8119 (tm-30) REVERT: A 712 ASN cc_start: 0.8632 (t0) cc_final: 0.8114 (t0) REVERT: A 714 ARG cc_start: 0.8453 (mtm180) cc_final: 0.8062 (mtm-85) REVERT: A 732 GLN cc_start: 0.7256 (tm-30) cc_final: 0.6783 (tm-30) REVERT: B 66 LYS cc_start: 0.8765 (tptt) cc_final: 0.8340 (tptp) REVERT: B 77 LYS cc_start: 0.8891 (ttmm) cc_final: 0.8536 (ttmm) REVERT: B 195 LEU cc_start: 0.8490 (tp) cc_final: 0.8268 (tt) REVERT: B 203 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8507 (m-80) REVERT: B 255 TYR cc_start: 0.9008 (m-10) cc_final: 0.8344 (m-10) REVERT: B 288 LEU cc_start: 0.8616 (tt) cc_final: 0.8204 (mm) REVERT: B 293 LYS cc_start: 0.8677 (tppt) cc_final: 0.8091 (tppt) REVERT: B 318 ASN cc_start: 0.8505 (t0) cc_final: 0.8198 (t0) REVERT: B 320 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7312 (tm-30) REVERT: B 324 ASN cc_start: 0.9011 (t0) cc_final: 0.8531 (t0) REVERT: B 374 LYS cc_start: 0.8807 (tmtt) cc_final: 0.8507 (ttpp) REVERT: B 376 ASP cc_start: 0.7894 (t0) cc_final: 0.7402 (t0) REVERT: B 384 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8091 (mm-30) REVERT: B 398 PHE cc_start: 0.8047 (m-10) cc_final: 0.7812 (m-10) REVERT: B 400 CYS cc_start: 0.8456 (m) cc_final: 0.8239 (m) REVERT: B 461 MET cc_start: 0.8833 (mmm) cc_final: 0.8544 (tpp) REVERT: B 470 ARG cc_start: 0.8487 (tpp80) cc_final: 0.8112 (tpp80) REVERT: B 486 CYS cc_start: 0.9141 (t) cc_final: 0.8899 (t) REVERT: B 495 ASP cc_start: 0.8697 (p0) cc_final: 0.8449 (p0) REVERT: B 517 SER cc_start: 0.8370 (p) cc_final: 0.8125 (p) REVERT: B 537 LYS cc_start: 0.8931 (tptt) cc_final: 0.8478 (tptt) REVERT: B 549 ARG cc_start: 0.8398 (ttt180) cc_final: 0.8052 (ttt180) REVERT: B 580 LYS cc_start: 0.7886 (tttt) cc_final: 0.7564 (tttp) REVERT: B 583 LYS cc_start: 0.8976 (tmtt) cc_final: 0.8624 (tmtt) REVERT: B 587 ARG cc_start: 0.7548 (mmm-85) cc_final: 0.7335 (mmt90) REVERT: B 687 ASP cc_start: 0.8729 (t0) cc_final: 0.8431 (t0) REVERT: B 696 GLN cc_start: 0.7690 (mm-40) cc_final: 0.7234 (mt0) REVERT: B 698 ASP cc_start: 0.8433 (t70) cc_final: 0.8023 (t0) REVERT: B 704 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8420 (tm-30) outliers start: 33 outliers final: 29 residues processed: 270 average time/residue: 0.1284 time to fit residues: 45.7930 Evaluate side-chains 277 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 246 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 656 HIS Chi-restraints excluded: chain B residue 705 GLN Chi-restraints excluded: chain B residue 706 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 125 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 55 optimal weight: 0.0030 chunk 54 optimal weight: 0.5980 chunk 129 optimal weight: 0.1980 chunk 70 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 HIS ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.112570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.096080 restraints weight = 21162.891| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.99 r_work: 0.3115 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10400 Z= 0.148 Angle : 0.700 16.213 14136 Z= 0.352 Chirality : 0.043 0.173 1718 Planarity : 0.004 0.041 1758 Dihedral : 5.475 81.601 1426 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.90 % Favored : 93.95 % Rotamer: Outliers : 3.12 % Allowed : 23.44 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.24), residues: 1322 helix: 0.90 (0.18), residues: 862 sheet: 0.07 (1.03), residues: 34 loop : -1.63 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 38 TYR 0.053 0.002 TYR A 361 PHE 0.029 0.001 PHE A 130 TRP 0.012 0.001 TRP B 518 HIS 0.012 0.001 HIS B 656 Details of bonding type rmsd covalent geometry : bond 0.00338 (10400) covalent geometry : angle 0.70020 (14136) hydrogen bonds : bond 0.03718 ( 569) hydrogen bonds : angle 3.93428 ( 1653) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2247.00 seconds wall clock time: 39 minutes 22.11 seconds (2362.11 seconds total)