Starting phenix.real_space_refine on Sat Aug 23 06:14:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hzn_35089/08_2025/8hzn_35089.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hzn_35089/08_2025/8hzn_35089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hzn_35089/08_2025/8hzn_35089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hzn_35089/08_2025/8hzn_35089.map" model { file = "/net/cci-nas-00/data/ceres_data/8hzn_35089/08_2025/8hzn_35089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hzn_35089/08_2025/8hzn_35089.cif" } resolution = 3.25 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 42 5.16 5 Cl 2 4.86 5 C 6656 2.51 5 N 1684 2.21 5 O 1816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10200 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.62, per 1000 atoms: 0.26 Number of scatterers: 10200 At special positions: 0 Unit cell: (86.818, 127.612, 117.152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 42 16.00 O 1816 8.00 N 1684 7.00 C 6656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 485.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 64 helices and 7 sheets defined 67.6% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.527A pdb=" N CYS A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.873A pdb=" N ALA A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 removed outlier: 4.028A pdb=" N TRP A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 75' Processing helix chain 'A' and resid 79 through 106 removed outlier: 4.870A pdb=" N LEU A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 120 removed outlier: 3.881A pdb=" N GLY A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.526A 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: 3.838A pdb=" N HIS A 160 " --> pdb=" O PRO A 157 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 161 " --> pdb=" O ASP A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 161' Processing helix chain 'A' and resid 179 through 206 removed outlier: 3.987A pdb=" N ALA A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.599A pdb=" N VAL A 212 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR A 214 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 241 Processing helix chain 'A' and resid 251 through 263 Processing helix chain 'A' and resid 268 through 292 Processing helix chain 'A' and resid 301 through 317 removed outlier: 3.635A pdb=" N ALA A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 374 Processing helix chain 'A' and resid 380 through 397 removed outlier: 3.765A pdb=" N GLU A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 416 removed outlier: 3.689A pdb=" N VAL A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 414 " --> pdb=" O THR A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 437 removed outlier: 3.518A pdb=" N VAL A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 430 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 446 through 458 removed outlier: 3.799A pdb=" N LEU A 450 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 3.989A 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: 3.547A pdb=" N ALA A 479 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A 490 " --> pdb=" O CYS A 486 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 515 removed outlier: 3.552A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 573 through 595 removed outlier: 3.814A pdb=" N TYR A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 686 removed outlier: 3.784A pdb=" N SER A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 706 removed outlier: 3.715A pdb=" N LYS A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 718 removed outlier: 3.557A pdb=" N ARG A 717 " --> pdb=" O ARG A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 removed outlier: 3.830A pdb=" N ALA A 725 " --> pdb=" O THR A 721 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 726 " --> pdb=" O VAL A 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.588A pdb=" N ALA B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 removed outlier: 3.757A pdb=" N ALA B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 4.021A pdb=" N TRP B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 105 removed outlier: 3.537A pdb=" N SER B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 110 Processing helix chain 'B' and resid 113 through 127 removed outlier: 3.984A pdb=" N LEU B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 141 through 156 removed outlier: 3.627A pdb=" N VAL B 151 " --> pdb=" O MET B 147 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.615A pdb=" N HIS B 160 " --> pdb=" O PRO B 157 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 161' Processing helix chain 'B' and resid 180 through 206 removed outlier: 3.896A pdb=" N ALA B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.630A pdb=" N VAL B 212 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR B 214 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 241 removed outlier: 3.728A pdb=" N ILE B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 268 through 292 removed outlier: 3.534A pdb=" N THR B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 317 removed outlier: 3.503A pdb=" N ALA B 317 " --> pdb=" O ILE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 376 removed outlier: 3.763A pdb=" N SER B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS B 375 " --> pdb=" O TYR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 397 removed outlier: 3.941A pdb=" N GLU B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 416 removed outlier: 3.651A pdb=" N VAL B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 437 removed outlier: 3.613A pdb=" N VAL B 436 " --> pdb=" O MET B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 446 through 458 removed outlier: 3.783A pdb=" N LEU B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 475 through 492 removed outlier: 3.554A pdb=" N ALA B 479 " --> pdb=" O ASN B 475 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE B 490 " --> pdb=" O CYS B 486 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 515 removed outlier: 3.546A pdb=" N LEU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 571 Processing helix chain 'B' and resid 573 through 595 removed outlier: 3.835A pdb=" N TYR B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG B 587 " --> pdb=" O LYS B 583 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS B 593 " --> pdb=" O GLN B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 685 removed outlier: 4.617A pdb=" N SER B 675 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 676 " --> pdb=" O GLY B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 706 removed outlier: 3.990A pdb=" N LYS B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 718 removed outlier: 3.556A pdb=" N ARG B 717 " --> pdb=" O ARG B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 736 removed outlier: 3.732A pdb=" N ALA B 725 " --> pdb=" O THR B 721 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 726 " --> pdb=" O VAL B 722 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 25 removed outlier: 3.618A pdb=" N VAL A 22 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 3.615A 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: 6.550A pdb=" N LYS A 546 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASP A 661 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU A 548 " --> pdb=" O ASP A 661 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AA6, first strand: chain 'B' and resid 522 through 523 Processing sheet with id=AA7, first strand: chain 'B' and resid 545 through 549 removed outlier: 6.604A pdb=" N LYS B 546 " --> pdb=" O VAL B 659 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASP B 661 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU B 548 " --> pdb=" O ASP B 661 " (cutoff:3.500A) 575 hydrogen bonds defined for protein. 1677 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: 1.67 Time building geometry restraints manager: 1.34 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: 2258 1.46 - 1.58: 4864 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 10400 Sorted by residual: bond pdb=" CA LEU B 162 " pdb=" CB LEU B 162 " ideal model delta sigma weight residual 1.526 1.537 -0.011 1.25e-02 6.40e+03 7.62e-01 bond pdb=" CA PHE A 121 " pdb=" C PHE A 121 " ideal model delta sigma weight residual 1.519 1.528 -0.009 1.01e-02 9.80e+03 7.28e-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 7.22e-01 bond pdb=" CA ASP B 669 " pdb=" C ASP B 669 " ideal model delta sigma weight residual 1.532 1.524 0.008 9.60e-03 1.09e+04 7.18e-01 bond pdb=" C VAL A 653 " pdb=" N PRO A 654 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.05e-01 ... (remaining 10395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 13857 1.42 - 2.84: 226 2.84 - 4.25: 37 4.25 - 5.67: 15 5.67 - 7.09: 1 Bond angle restraints: 14136 Sorted by residual: angle pdb=" N VAL A 699 " pdb=" CA VAL A 699 " pdb=" C VAL A 699 " ideal model delta sigma weight residual 111.81 108.71 3.10 8.60e-01 1.35e+00 1.30e+01 angle pdb=" N VAL B 699 " pdb=" CA VAL B 699 " pdb=" C VAL B 699 " ideal model delta sigma weight residual 111.81 108.83 2.98 8.60e-01 1.35e+00 1.20e+01 angle pdb=" N ILE B 686 " pdb=" CA ILE B 686 " pdb=" C ILE B 686 " ideal model delta sigma weight residual 111.91 109.18 2.73 8.90e-01 1.26e+00 9.39e+00 angle pdb=" N ILE A 686 " pdb=" CA ILE A 686 " pdb=" C ILE A 686 " ideal model delta sigma weight residual 111.91 109.22 2.69 8.90e-01 1.26e+00 9.11e+00 angle pdb=" C ASP A 669 " pdb=" N VAL A 670 " pdb=" CA VAL A 670 " ideal model delta sigma weight residual 121.97 126.31 -4.34 1.80e+00 3.09e-01 5.81e+00 ... (remaining 14131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 5982 16.84 - 33.68: 163 33.68 - 50.52: 28 50.52 - 67.36: 4 67.36 - 84.20: 5 Dihedral angle restraints: 6182 sinusoidal: 2346 harmonic: 3836 Sorted by residual: dihedral pdb=" N LYS A 681 " pdb=" CA LYS A 681 " pdb=" CB LYS A 681 " pdb=" CG LYS A 681 " ideal model delta sinusoidal sigma weight residual -180.00 -120.67 -59.33 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ASP A 669 " pdb=" C ASP A 669 " pdb=" N VAL A 670 " pdb=" CA VAL A 670 " ideal model delta harmonic sigma weight residual -180.00 -164.65 -15.35 0 5.00e+00 4.00e-02 9.43e+00 dihedral pdb=" N LEU A 668 " pdb=" CA LEU A 668 " pdb=" CB LEU A 668 " pdb=" CG LEU A 668 " ideal model delta sinusoidal sigma weight residual -180.00 -126.82 -53.18 3 1.50e+01 4.44e-03 9.18e+00 ... (remaining 6179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 919 0.023 - 0.047: 438 0.047 - 0.070: 241 0.070 - 0.093: 77 0.093 - 0.117: 43 Chirality restraints: 1718 Sorted by residual: chirality pdb=" CA ILE B 379 " pdb=" N ILE B 379 " pdb=" C ILE B 379 " pdb=" CB ILE B 379 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-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 3.31e-01 chirality pdb=" CA VAL A 688 " pdb=" N VAL A 688 " pdb=" C VAL A 688 " pdb=" CB VAL A 688 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.30e-01 ... (remaining 1715 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 552 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO B 553 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 553 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 553 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 552 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO A 553 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 553 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 553 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 111 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.90e+00 pdb=" N PRO A 112 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " 0.019 5.00e-02 4.00e+02 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 401 2.73 - 3.27: 11150 3.27 - 3.81: 16502 3.81 - 4.36: 20154 4.36 - 4.90: 33850 Nonbonded interactions: 82057 Sorted by model distance: nonbonded pdb=" OH TYR A 78 " pdb=" OD2 ASP A 87 " model vdw 2.182 3.040 nonbonded pdb=" O ASP A 669 " pdb=" N GLY A 672 " model vdw 2.242 3.120 nonbonded pdb=" OH TYR A 118 " pdb=" O GLY A 334 " model vdw 2.247 3.040 nonbonded pdb=" O THR A 485 " pdb=" OG SER A 489 " model vdw 2.261 3.040 nonbonded pdb=" OD1 ASN B 475 " pdb=" OG1 THR B 477 " model vdw 2.272 3.040 ... (remaining 82052 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: 0.02 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: 2.250 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.400 Find NCS groups from input model: 0.190 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 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= 0.106 Angle : 0.492 7.088 14136 Z= 0.300 Chirality : 0.037 0.117 1718 Planarity : 0.003 0.035 1758 Dihedral : 8.512 84.204 3710 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 3.12 % Allowed : 4.01 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.99 (0.19), residues: 1322 helix: -2.17 (0.14), residues: 876 sheet: -2.92 (0.77), residues: 34 loop : -3.36 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 512 TYR 0.008 0.001 TYR A 127 PHE 0.009 0.001 PHE A 555 TRP 0.004 0.000 TRP A 83 HIS 0.001 0.000 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00180 (10400) covalent geometry : angle 0.49168 (14136) hydrogen bonds : bond 0.23063 ( 575) hydrogen bonds : angle 7.10999 ( 1677) *********************** 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 411 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 376 time to evaluate : 0.415 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 38 ARG cc_start: 0.7730 (mtp-110) cc_final: 0.7165 (mtp-110) REVERT: A 66 LYS cc_start: 0.8511 (tppt) cc_final: 0.8077 (tptp) REVERT: A 160 HIS cc_start: 0.7819 (t-90) cc_final: 0.7602 (t-170) REVERT: A 258 ILE cc_start: 0.8499 (mm) cc_final: 0.8098 (mm) REVERT: A 273 ILE cc_start: 0.8310 (mt) cc_final: 0.8072 (tp) REVERT: A 318 ASN cc_start: 0.6901 (t0) cc_final: 0.6696 (t0) REVERT: A 350 LEU cc_start: 0.6272 (OUTLIER) cc_final: 0.5837 (tm) REVERT: A 369 LYS cc_start: 0.7845 (mmtt) cc_final: 0.7399 (mmtt) REVERT: A 385 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7460 (t80) REVERT: A 394 PHE cc_start: 0.8222 (t80) cc_final: 0.7248 (t80) REVERT: A 398 PHE cc_start: 0.6554 (m-80) cc_final: 0.6246 (m-80) REVERT: A 432 MET cc_start: 0.7964 (tpt) cc_final: 0.7697 (tpp) REVERT: A 464 GLN cc_start: 0.7704 (mt0) cc_final: 0.7046 (mt0) REVERT: A 475 ASN cc_start: 0.7767 (t0) cc_final: 0.6663 (t0) REVERT: A 478 ASP cc_start: 0.6770 (m-30) cc_final: 0.6337 (m-30) REVERT: A 486 CYS cc_start: 0.8410 (t) cc_final: 0.8181 (t) REVERT: A 569 THR cc_start: 0.8596 (t) cc_final: 0.8192 (m) REVERT: A 580 LYS cc_start: 0.7866 (mmtt) cc_final: 0.7422 (mmmm) REVERT: A 684 GLN cc_start: 0.7917 (tp40) cc_final: 0.7698 (tp40) REVERT: A 717 ARG cc_start: 0.8563 (ttm-80) cc_final: 0.8279 (ttm170) REVERT: B 66 LYS cc_start: 0.8505 (tppt) cc_final: 0.8123 (tppt) REVERT: B 78 TYR cc_start: 0.6781 (t80) cc_final: 0.6320 (t80) REVERT: B 87 ASP cc_start: 0.7044 (m-30) cc_final: 0.6580 (m-30) REVERT: B 114 GLN cc_start: 0.7744 (tt0) cc_final: 0.7510 (pt0) REVERT: B 246 ASN cc_start: 0.8239 (p0) cc_final: 0.8037 (p0) REVERT: B 268 ASN cc_start: 0.8327 (t0) cc_final: 0.7490 (t0) REVERT: B 271 ASP cc_start: 0.7882 (m-30) cc_final: 0.7245 (m-30) REVERT: B 287 GLU cc_start: 0.7275 (tp30) cc_final: 0.6919 (tp30) REVERT: B 290 ASP cc_start: 0.7559 (t0) cc_final: 0.7345 (t0) REVERT: B 303 GLU cc_start: 0.7401 (mp0) cc_final: 0.6897 (mp0) REVERT: B 305 ILE cc_start: 0.8590 (tp) cc_final: 0.8219 (pt) REVERT: B 318 ASN cc_start: 0.6926 (t0) cc_final: 0.6521 (t0) REVERT: B 320 GLU cc_start: 0.6331 (tp30) cc_final: 0.6119 (tp30) REVERT: B 350 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.6179 (tm) REVERT: B 355 SER cc_start: 0.8717 (m) cc_final: 0.8092 (p) REVERT: B 394 PHE cc_start: 0.8319 (t80) cc_final: 0.7527 (t80) REVERT: B 446 GLN cc_start: 0.8192 (mt0) cc_final: 0.7889 (mt0) REVERT: B 464 GLN cc_start: 0.8030 (mt0) cc_final: 0.7336 (mt0) REVERT: B 475 ASN cc_start: 0.7764 (t0) cc_final: 0.6830 (t0) REVERT: B 478 ASP cc_start: 0.6896 (m-30) cc_final: 0.6325 (m-30) REVERT: B 580 LYS cc_start: 0.7676 (mmtt) cc_final: 0.7274 (mmmm) REVERT: B 717 ARG cc_start: 0.8420 (ttm-80) cc_final: 0.7987 (ttm170) REVERT: B 727 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.7982 (mt) outliers start: 35 outliers final: 11 residues processed: 402 average time/residue: 0.1251 time to fit residues: 67.6850 Evaluate side-chains 315 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 300 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 727 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 413 GLN A 421 GLN A 474 GLN A 475 ASN A 514 GLN A 656 HIS A 705 GLN B 34 GLN B 160 HIS ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN B 475 ASN B 514 GLN B 656 HIS B 705 GLN B 728 HIS B 730 GLN B 731 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.127350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.108699 restraints weight = 16841.005| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.46 r_work: 0.3346 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10400 Z= 0.206 Angle : 0.660 8.081 14136 Z= 0.342 Chirality : 0.044 0.182 1718 Planarity : 0.005 0.048 1758 Dihedral : 5.906 79.920 1444 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.39 % Allowed : 12.75 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.22), residues: 1322 helix: -0.43 (0.17), residues: 866 sheet: -2.86 (0.82), residues: 36 loop : -2.95 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 38 TYR 0.026 0.002 TYR B 361 PHE 0.024 0.002 PHE A 130 TRP 0.008 0.001 TRP B 518 HIS 0.009 0.002 HIS B 656 Details of bonding type rmsd covalent geometry : bond 0.00461 (10400) covalent geometry : angle 0.66000 (14136) hydrogen bonds : bond 0.04816 ( 575) hydrogen bonds : angle 4.35210 ( 1677) *********************** 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 361 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 323 time to evaluate : 0.392 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: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8655 (tppt) cc_final: 0.8365 (tptp) REVERT: A 160 HIS cc_start: 0.8235 (t-90) cc_final: 0.8018 (t70) REVERT: A 258 ILE cc_start: 0.8674 (mm) cc_final: 0.8378 (mm) REVERT: A 259 GLU cc_start: 0.8324 (tt0) cc_final: 0.8111 (mt-10) REVERT: A 273 ILE cc_start: 0.8443 (mt) cc_final: 0.8211 (tp) REVERT: A 287 GLU cc_start: 0.7779 (tp30) cc_final: 0.7565 (tp30) REVERT: A 289 ASN cc_start: 0.8453 (t0) cc_final: 0.8129 (t0) REVERT: A 369 LYS cc_start: 0.8118 (mmtt) cc_final: 0.7651 (mmtt) REVERT: A 370 VAL cc_start: 0.8006 (t) cc_final: 0.7770 (p) REVERT: A 371 TYR cc_start: 0.8140 (m-80) cc_final: 0.7738 (m-80) REVERT: A 394 PHE cc_start: 0.8445 (t80) cc_final: 0.7650 (t80) REVERT: A 398 PHE cc_start: 0.7001 (m-80) cc_final: 0.6699 (m-80) REVERT: A 432 MET cc_start: 0.7990 (tpt) cc_final: 0.7653 (tpp) REVERT: A 436 VAL cc_start: 0.8484 (p) cc_final: 0.8186 (m) REVERT: A 470 ARG cc_start: 0.7235 (tpp80) cc_final: 0.6942 (tpp80) REVERT: A 473 LYS cc_start: 0.8467 (mtpt) cc_final: 0.8231 (mmmm) REVERT: A 475 ASN cc_start: 0.7967 (t0) cc_final: 0.7698 (t0) REVERT: A 486 CYS cc_start: 0.8839 (t) cc_final: 0.8489 (t) REVERT: A 495 ASP cc_start: 0.8460 (p0) cc_final: 0.8149 (p0) REVERT: A 496 LEU cc_start: 0.8898 (mm) cc_final: 0.8654 (mm) REVERT: A 560 ASP cc_start: 0.7819 (m-30) cc_final: 0.7537 (m-30) REVERT: A 569 THR cc_start: 0.8628 (t) cc_final: 0.8256 (m) REVERT: A 573 ASP cc_start: 0.7733 (t0) cc_final: 0.7448 (t0) REVERT: A 580 LYS cc_start: 0.7935 (mmtt) cc_final: 0.7450 (mmmm) REVERT: A 684 GLN cc_start: 0.8336 (tp40) cc_final: 0.8099 (tp-100) REVERT: A 687 ASP cc_start: 0.7889 (t0) cc_final: 0.7649 (t0) REVERT: A 714 ARG cc_start: 0.8072 (mtm-85) cc_final: 0.7866 (mtm-85) REVERT: B 27 TYR cc_start: 0.7916 (m-10) cc_final: 0.7711 (m-10) REVERT: B 66 LYS cc_start: 0.8779 (tppt) cc_final: 0.8548 (tppt) REVERT: B 78 TYR cc_start: 0.7256 (t80) cc_final: 0.6479 (t80) REVERT: B 87 ASP cc_start: 0.7588 (m-30) cc_final: 0.7175 (m-30) REVERT: B 114 GLN cc_start: 0.8206 (tt0) cc_final: 0.7905 (pt0) REVERT: B 246 ASN cc_start: 0.8444 (p0) cc_final: 0.8189 (p0) REVERT: B 250 ILE cc_start: 0.8446 (mm) cc_final: 0.8075 (tp) REVERT: B 268 ASN cc_start: 0.8491 (t0) cc_final: 0.7553 (t0) REVERT: B 271 ASP cc_start: 0.7898 (m-30) cc_final: 0.7545 (m-30) REVERT: B 289 ASN cc_start: 0.8284 (t0) cc_final: 0.7948 (t0) REVERT: B 303 GLU cc_start: 0.7729 (mp0) cc_final: 0.7487 (mp0) REVERT: B 305 ILE cc_start: 0.8622 (tp) cc_final: 0.8365 (pt) REVERT: B 318 ASN cc_start: 0.7784 (t0) cc_final: 0.7434 (t0) REVERT: B 350 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6431 (tm) REVERT: B 361 TYR cc_start: 0.8548 (t80) cc_final: 0.8098 (t80) REVERT: B 366 SER cc_start: 0.8658 (t) cc_final: 0.8311 (p) REVERT: B 369 LYS cc_start: 0.8398 (mmtt) cc_final: 0.8171 (mmtt) REVERT: B 377 TYR cc_start: 0.7485 (p90) cc_final: 0.7243 (p90) REVERT: B 385 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.8049 (m-80) REVERT: B 394 PHE cc_start: 0.8431 (t80) cc_final: 0.7831 (t80) REVERT: B 398 PHE cc_start: 0.7430 (m-80) cc_final: 0.6954 (m-80) REVERT: B 414 GLU cc_start: 0.7430 (tm-30) cc_final: 0.6954 (tm-30) REVERT: B 475 ASN cc_start: 0.8132 (t0) cc_final: 0.7744 (t0) REVERT: B 528 ASP cc_start: 0.8787 (p0) cc_final: 0.8564 (p0) REVERT: B 556 TYR cc_start: 0.8714 (p90) cc_final: 0.8041 (p90) REVERT: B 560 ASP cc_start: 0.7946 (m-30) cc_final: 0.7655 (m-30) REVERT: B 580 LYS cc_start: 0.7877 (mmtt) cc_final: 0.7460 (mmmm) REVERT: B 661 ASP cc_start: 0.8020 (t0) cc_final: 0.7772 (t0) REVERT: B 668 LEU cc_start: 0.6744 (mt) cc_final: 0.6502 (mt) REVERT: B 687 ASP cc_start: 0.8094 (t0) cc_final: 0.7844 (t0) REVERT: B 717 ARG cc_start: 0.8530 (ttm-80) cc_final: 0.8136 (ttm170) outliers start: 38 outliers final: 19 residues processed: 343 average time/residue: 0.1297 time to fit residues: 60.0623 Evaluate side-chains 314 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 293 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 541 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 32 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 96 optimal weight: 0.0570 chunk 42 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 0.0030 chunk 119 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 99 optimal weight: 0.0980 overall best weight: 0.2908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 135 HIS A 246 ASN A 656 HIS B 160 HIS ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 GLN B 464 GLN B 656 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.129417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.110676 restraints weight = 16621.974| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.43 r_work: 0.3370 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10400 Z= 0.129 Angle : 0.579 10.176 14136 Z= 0.297 Chirality : 0.041 0.157 1718 Planarity : 0.004 0.039 1758 Dihedral : 5.472 81.085 1437 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.74 % Allowed : 15.15 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.23), residues: 1322 helix: 0.20 (0.17), residues: 870 sheet: -2.51 (0.89), residues: 36 loop : -2.77 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 714 TYR 0.021 0.002 TYR B 377 PHE 0.016 0.001 PHE A 121 TRP 0.006 0.001 TRP B 482 HIS 0.009 0.001 HIS B 656 Details of bonding type rmsd covalent geometry : bond 0.00281 (10400) covalent geometry : angle 0.57854 (14136) hydrogen bonds : bond 0.04280 ( 575) hydrogen bonds : angle 4.09329 ( 1677) *********************** 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 350 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 308 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: symmetry clash revert: symmetry clash REVERT: A 21 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8222 (p) REVERT: A 66 LYS cc_start: 0.8653 (tppt) cc_final: 0.8374 (tptp) REVERT: A 250 ILE cc_start: 0.8237 (mm) cc_final: 0.7904 (tp) REVERT: A 258 ILE cc_start: 0.8660 (mm) cc_final: 0.8383 (mm) REVERT: A 268 ASN cc_start: 0.8374 (t0) cc_final: 0.8020 (t0) REVERT: A 273 ILE cc_start: 0.8442 (mt) cc_final: 0.8217 (tp) REVERT: A 289 ASN cc_start: 0.8388 (t0) cc_final: 0.8045 (t0) REVERT: A 369 LYS cc_start: 0.8080 (mmtt) cc_final: 0.7667 (mmpt) REVERT: A 370 VAL cc_start: 0.8049 (t) cc_final: 0.7800 (p) REVERT: A 371 TYR cc_start: 0.8058 (m-80) cc_final: 0.7677 (m-80) REVERT: A 394 PHE cc_start: 0.8459 (t80) cc_final: 0.7716 (t80) REVERT: A 398 PHE cc_start: 0.6889 (m-80) cc_final: 0.6620 (m-80) REVERT: A 405 THR cc_start: 0.8514 (p) cc_final: 0.8287 (t) REVERT: A 432 MET cc_start: 0.7967 (tpt) cc_final: 0.7601 (tpp) REVERT: A 436 VAL cc_start: 0.8486 (p) cc_final: 0.8200 (m) REVERT: A 470 ARG cc_start: 0.7220 (tpp80) cc_final: 0.6903 (tpp80) REVERT: A 473 LYS cc_start: 0.8444 (mtpt) cc_final: 0.8206 (mmmm) REVERT: A 475 ASN cc_start: 0.8085 (t0) cc_final: 0.7675 (t0) REVERT: A 486 CYS cc_start: 0.8800 (t) cc_final: 0.8464 (t) REVERT: A 495 ASP cc_start: 0.8388 (p0) cc_final: 0.8076 (p0) REVERT: A 496 LEU cc_start: 0.8829 (mm) cc_final: 0.8586 (mm) REVERT: A 560 ASP cc_start: 0.7771 (m-30) cc_final: 0.7424 (m-30) REVERT: A 569 THR cc_start: 0.8677 (t) cc_final: 0.8277 (m) REVERT: A 573 ASP cc_start: 0.7756 (t0) cc_final: 0.7396 (t0) REVERT: A 580 LYS cc_start: 0.8020 (mmtt) cc_final: 0.7523 (mmmm) REVERT: A 687 ASP cc_start: 0.7994 (t0) cc_final: 0.7660 (t0) REVERT: A 714 ARG cc_start: 0.8018 (mtm-85) cc_final: 0.7815 (mtm-85) REVERT: B 27 TYR cc_start: 0.7969 (m-10) cc_final: 0.7743 (m-10) REVERT: B 66 LYS cc_start: 0.8699 (tppt) cc_final: 0.8161 (tppt) REVERT: B 78 TYR cc_start: 0.7213 (t80) cc_final: 0.6565 (t80) REVERT: B 87 ASP cc_start: 0.7620 (m-30) cc_final: 0.7150 (m-30) REVERT: B 114 GLN cc_start: 0.8192 (tt0) cc_final: 0.7929 (pt0) REVERT: B 122 PHE cc_start: 0.8387 (m-80) cc_final: 0.8187 (m-10) REVERT: B 246 ASN cc_start: 0.8438 (p0) cc_final: 0.8219 (p0) REVERT: B 250 ILE cc_start: 0.8416 (mm) cc_final: 0.8032 (tp) REVERT: B 259 GLU cc_start: 0.8327 (tt0) cc_final: 0.8035 (mt-10) REVERT: B 268 ASN cc_start: 0.8426 (t0) cc_final: 0.7835 (t0) REVERT: B 271 ASP cc_start: 0.7789 (m-30) cc_final: 0.7547 (m-30) REVERT: B 289 ASN cc_start: 0.8313 (t0) cc_final: 0.7980 (t0) REVERT: B 303 GLU cc_start: 0.7736 (mp0) cc_final: 0.7493 (mp0) REVERT: B 305 ILE cc_start: 0.8605 (tp) cc_final: 0.8342 (pt) REVERT: B 318 ASN cc_start: 0.7782 (t0) cc_final: 0.7504 (t0) REVERT: B 350 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6590 (tm) REVERT: B 361 TYR cc_start: 0.8516 (t80) cc_final: 0.8028 (t80) REVERT: B 369 LYS cc_start: 0.8393 (mmtt) cc_final: 0.8147 (mmtt) REVERT: B 377 TYR cc_start: 0.7571 (p90) cc_final: 0.7295 (p90) REVERT: B 385 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: B 394 PHE cc_start: 0.8425 (t80) cc_final: 0.7777 (t80) REVERT: B 398 PHE cc_start: 0.7321 (m-80) cc_final: 0.6818 (m-80) REVERT: B 414 GLU cc_start: 0.7381 (tm-30) cc_final: 0.6983 (tm-30) REVERT: B 470 ARG cc_start: 0.7266 (tpp80) cc_final: 0.6871 (tpp80) REVERT: B 475 ASN cc_start: 0.8159 (t0) cc_final: 0.7226 (t0) REVERT: B 478 ASP cc_start: 0.7545 (m-30) cc_final: 0.7010 (m-30) REVERT: B 528 ASP cc_start: 0.8748 (p0) cc_final: 0.8460 (p0) REVERT: B 556 TYR cc_start: 0.8726 (p90) cc_final: 0.8110 (p90) REVERT: B 560 ASP cc_start: 0.7992 (m-30) cc_final: 0.7713 (m-30) REVERT: B 573 ASP cc_start: 0.7664 (t0) cc_final: 0.7322 (t0) REVERT: B 580 LYS cc_start: 0.7953 (mmtt) cc_final: 0.7497 (mmmm) REVERT: B 661 ASP cc_start: 0.7890 (t0) cc_final: 0.7622 (t0) REVERT: B 687 ASP cc_start: 0.8038 (t0) cc_final: 0.7727 (t0) REVERT: B 717 ARG cc_start: 0.8555 (ttm-80) cc_final: 0.8173 (ttm170) outliers start: 42 outliers final: 22 residues processed: 333 average time/residue: 0.1240 time to fit residues: 55.6437 Evaluate side-chains 322 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 297 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 541 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 84 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 55 optimal weight: 0.0770 chunk 117 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 114 GLN A 160 HIS A 246 ASN A 464 GLN A 656 HIS A 728 HIS B 160 HIS B 475 ASN B 656 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.126901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.108032 restraints weight = 16753.990| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.45 r_work: 0.3327 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10400 Z= 0.173 Angle : 0.606 10.078 14136 Z= 0.309 Chirality : 0.043 0.224 1718 Planarity : 0.004 0.045 1758 Dihedral : 5.086 54.773 1434 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.28 % Favored : 93.65 % Rotamer: Outliers : 4.19 % Allowed : 15.42 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.24), residues: 1322 helix: 0.54 (0.18), residues: 868 sheet: -2.21 (0.90), residues: 36 loop : -2.66 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 714 TYR 0.035 0.002 TYR A 361 PHE 0.022 0.001 PHE A 130 TRP 0.009 0.001 TRP A 74 HIS 0.009 0.001 HIS B 656 Details of bonding type rmsd covalent geometry : bond 0.00387 (10400) covalent geometry : angle 0.60589 (14136) hydrogen bonds : bond 0.04165 ( 575) hydrogen bonds : angle 3.99725 ( 1677) *********************** 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 353 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 306 time to evaluate : 0.409 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 21 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8343 (p) REVERT: A 66 LYS cc_start: 0.8686 (tppt) cc_final: 0.8392 (tptp) REVERT: A 188 LEU cc_start: 0.8010 (tp) cc_final: 0.7659 (tp) REVERT: A 247 TYR cc_start: 0.7947 (m-10) cc_final: 0.7418 (m-10) REVERT: A 258 ILE cc_start: 0.8707 (mm) cc_final: 0.8436 (mm) REVERT: A 259 GLU cc_start: 0.8109 (tt0) cc_final: 0.6784 (tt0) REVERT: A 273 ILE cc_start: 0.8457 (mt) cc_final: 0.8233 (tp) REVERT: A 303 GLU cc_start: 0.7773 (mp0) cc_final: 0.7484 (mp0) REVERT: A 348 ASP cc_start: 0.5825 (OUTLIER) cc_final: 0.4994 (p0) REVERT: A 369 LYS cc_start: 0.8101 (mmtt) cc_final: 0.7726 (mmpt) REVERT: A 370 VAL cc_start: 0.8064 (t) cc_final: 0.7836 (p) REVERT: A 371 TYR cc_start: 0.8127 (m-80) cc_final: 0.7732 (m-80) REVERT: A 394 PHE cc_start: 0.8465 (t80) cc_final: 0.7725 (t80) REVERT: A 398 PHE cc_start: 0.6994 (m-80) cc_final: 0.6695 (m-80) REVERT: A 405 THR cc_start: 0.8475 (p) cc_final: 0.8257 (t) REVERT: A 413 GLN cc_start: 0.6515 (pt0) cc_final: 0.6117 (pt0) REVERT: A 432 MET cc_start: 0.7969 (tpt) cc_final: 0.7603 (tpp) REVERT: A 436 VAL cc_start: 0.8555 (p) cc_final: 0.8283 (m) REVERT: A 470 ARG cc_start: 0.7257 (tpp80) cc_final: 0.7022 (tpp80) REVERT: A 473 LYS cc_start: 0.8412 (mtpt) cc_final: 0.8206 (mttm) REVERT: A 475 ASN cc_start: 0.8173 (t0) cc_final: 0.7432 (t0) REVERT: A 478 ASP cc_start: 0.7529 (m-30) cc_final: 0.6932 (m-30) REVERT: A 486 CYS cc_start: 0.8839 (t) cc_final: 0.8510 (t) REVERT: A 495 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8151 (p0) REVERT: A 496 LEU cc_start: 0.8841 (mm) cc_final: 0.8628 (mt) REVERT: A 560 ASP cc_start: 0.7923 (m-30) cc_final: 0.7622 (m-30) REVERT: A 569 THR cc_start: 0.8710 (t) cc_final: 0.8313 (m) REVERT: A 573 ASP cc_start: 0.7779 (t0) cc_final: 0.7399 (t0) REVERT: A 580 LYS cc_start: 0.7968 (mmtt) cc_final: 0.7492 (mmmm) REVERT: A 687 ASP cc_start: 0.8042 (t0) cc_final: 0.7717 (t0) REVERT: A 714 ARG cc_start: 0.8132 (mtm-85) cc_final: 0.7929 (mtm-85) REVERT: B 23 SER cc_start: 0.8845 (OUTLIER) cc_final: 0.8407 (p) REVERT: B 66 LYS cc_start: 0.8701 (tppt) cc_final: 0.8435 (tppt) REVERT: B 78 TYR cc_start: 0.7314 (t80) cc_final: 0.6592 (t80) REVERT: B 87 ASP cc_start: 0.7642 (m-30) cc_final: 0.7174 (m-30) REVERT: B 114 GLN cc_start: 0.8255 (tt0) cc_final: 0.7995 (pt0) REVERT: B 122 PHE cc_start: 0.8379 (m-80) cc_final: 0.8028 (m-80) REVERT: B 246 ASN cc_start: 0.8443 (p0) cc_final: 0.8219 (p0) REVERT: B 259 GLU cc_start: 0.8384 (tt0) cc_final: 0.8053 (mt-10) REVERT: B 289 ASN cc_start: 0.8390 (t0) cc_final: 0.8051 (t0) REVERT: B 303 GLU cc_start: 0.7731 (mp0) cc_final: 0.7472 (mp0) REVERT: B 305 ILE cc_start: 0.8623 (tp) cc_final: 0.8368 (pt) REVERT: B 318 ASN cc_start: 0.7943 (t0) cc_final: 0.7681 (t0) REVERT: B 361 TYR cc_start: 0.8604 (t80) cc_final: 0.7880 (t80) REVERT: B 369 LYS cc_start: 0.8495 (mmtt) cc_final: 0.8260 (mmtm) REVERT: B 385 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.7786 (m-80) REVERT: B 394 PHE cc_start: 0.8411 (t80) cc_final: 0.7789 (t80) REVERT: B 398 PHE cc_start: 0.7358 (m-80) cc_final: 0.6924 (m-80) REVERT: B 414 GLU cc_start: 0.7324 (tm-30) cc_final: 0.6932 (tm-30) REVERT: B 470 ARG cc_start: 0.7324 (tpp80) cc_final: 0.6938 (tpp80) REVERT: B 528 ASP cc_start: 0.8694 (p0) cc_final: 0.8455 (p0) REVERT: B 556 TYR cc_start: 0.8782 (p90) cc_final: 0.8219 (p90) REVERT: B 560 ASP cc_start: 0.7989 (m-30) cc_final: 0.7702 (m-30) REVERT: B 573 ASP cc_start: 0.7766 (t0) cc_final: 0.7193 (t0) REVERT: B 576 ARG cc_start: 0.7499 (mtm-85) cc_final: 0.7287 (mtm-85) REVERT: B 580 LYS cc_start: 0.7899 (mmtt) cc_final: 0.7461 (mmmm) REVERT: B 661 ASP cc_start: 0.7972 (t0) cc_final: 0.7763 (t0) REVERT: B 687 ASP cc_start: 0.8065 (t0) cc_final: 0.7750 (t0) REVERT: B 717 ARG cc_start: 0.8610 (ttm-80) cc_final: 0.8238 (ttm170) outliers start: 47 outliers final: 27 residues processed: 335 average time/residue: 0.1277 time to fit residues: 57.1295 Evaluate side-chains 328 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 296 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 78 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 95 optimal weight: 0.2980 chunk 119 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 112 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 246 ASN A 656 HIS B 160 HIS B 656 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.126114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.107235 restraints weight = 16610.698| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.43 r_work: 0.3311 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10400 Z= 0.174 Angle : 0.617 10.562 14136 Z= 0.313 Chirality : 0.043 0.224 1718 Planarity : 0.004 0.047 1758 Dihedral : 5.184 55.520 1434 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.43 % Favored : 93.49 % Rotamer: Outliers : 4.46 % Allowed : 16.31 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.24), residues: 1322 helix: 0.60 (0.18), residues: 880 sheet: -2.04 (0.90), residues: 36 loop : -2.53 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 714 TYR 0.038 0.002 TYR A 361 PHE 0.025 0.001 PHE B 130 TRP 0.004 0.001 TRP B 482 HIS 0.009 0.001 HIS B 656 Details of bonding type rmsd covalent geometry : bond 0.00392 (10400) covalent geometry : angle 0.61737 (14136) hydrogen bonds : bond 0.04165 ( 575) hydrogen bonds : angle 4.00254 ( 1677) *********************** 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 339 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 289 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8374 (p) REVERT: A 66 LYS cc_start: 0.8733 (tppt) cc_final: 0.8461 (tptp) REVERT: A 247 TYR cc_start: 0.8180 (m-10) cc_final: 0.7623 (m-10) REVERT: A 258 ILE cc_start: 0.8794 (mm) cc_final: 0.8526 (mm) REVERT: A 259 GLU cc_start: 0.8390 (tt0) cc_final: 0.7585 (tt0) REVERT: A 287 GLU cc_start: 0.7966 (tp30) cc_final: 0.7618 (tp30) REVERT: A 303 GLU cc_start: 0.8004 (mp0) cc_final: 0.7695 (mp0) REVERT: A 348 ASP cc_start: 0.6016 (OUTLIER) cc_final: 0.5007 (p0) REVERT: A 369 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7798 (mmpt) REVERT: A 370 VAL cc_start: 0.8215 (t) cc_final: 0.7878 (p) REVERT: A 371 TYR cc_start: 0.8198 (m-80) cc_final: 0.7803 (m-80) REVERT: A 394 PHE cc_start: 0.8591 (t80) cc_final: 0.7887 (t80) REVERT: A 398 PHE cc_start: 0.7282 (m-80) cc_final: 0.6925 (m-80) REVERT: A 413 GLN cc_start: 0.6676 (pt0) cc_final: 0.6289 (pt0) REVERT: A 432 MET cc_start: 0.8144 (tpt) cc_final: 0.7716 (tpp) REVERT: A 436 VAL cc_start: 0.8692 (p) cc_final: 0.8420 (m) REVERT: A 470 ARG cc_start: 0.7665 (tpp80) cc_final: 0.7417 (tpp80) REVERT: A 473 LYS cc_start: 0.8617 (mtpt) cc_final: 0.8368 (mtmm) REVERT: A 475 ASN cc_start: 0.8405 (t0) cc_final: 0.7457 (t0) REVERT: A 478 ASP cc_start: 0.7822 (m-30) cc_final: 0.7199 (m-30) REVERT: A 486 CYS cc_start: 0.8999 (t) cc_final: 0.8683 (t) REVERT: A 495 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8319 (p0) REVERT: A 496 LEU cc_start: 0.8935 (mm) cc_final: 0.8727 (mt) REVERT: A 560 ASP cc_start: 0.8191 (m-30) cc_final: 0.7824 (m-30) REVERT: A 569 THR cc_start: 0.8765 (t) cc_final: 0.8342 (m) REVERT: A 573 ASP cc_start: 0.7972 (t0) cc_final: 0.7590 (t0) REVERT: A 580 LYS cc_start: 0.8114 (mmtt) cc_final: 0.7652 (mmmm) REVERT: A 687 ASP cc_start: 0.8196 (t0) cc_final: 0.7890 (t0) REVERT: A 714 ARG cc_start: 0.8377 (mtm-85) cc_final: 0.8170 (mtm-85) REVERT: B 23 SER cc_start: 0.8923 (OUTLIER) cc_final: 0.8525 (p) REVERT: B 66 LYS cc_start: 0.8733 (tppt) cc_final: 0.8400 (tptp) REVERT: B 87 ASP cc_start: 0.7783 (m-30) cc_final: 0.7124 (m-30) REVERT: B 122 PHE cc_start: 0.8515 (m-80) cc_final: 0.8252 (m-80) REVERT: B 246 ASN cc_start: 0.8582 (p0) cc_final: 0.8348 (p0) REVERT: B 259 GLU cc_start: 0.8625 (tt0) cc_final: 0.8350 (mt-10) REVERT: B 268 ASN cc_start: 0.8503 (t0) cc_final: 0.8167 (t0) REVERT: B 289 ASN cc_start: 0.8531 (t0) cc_final: 0.8216 (t0) REVERT: B 303 GLU cc_start: 0.7995 (mp0) cc_final: 0.7729 (mp0) REVERT: B 305 ILE cc_start: 0.8704 (tp) cc_final: 0.8454 (pt) REVERT: B 318 ASN cc_start: 0.8249 (t0) cc_final: 0.7915 (t0) REVERT: B 361 TYR cc_start: 0.8728 (t80) cc_final: 0.7981 (t80) REVERT: B 369 LYS cc_start: 0.8498 (mmtt) cc_final: 0.8221 (mmtt) REVERT: B 384 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7608 (mm-30) REVERT: B 385 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: B 394 PHE cc_start: 0.8502 (t80) cc_final: 0.7960 (t80) REVERT: B 398 PHE cc_start: 0.7500 (m-80) cc_final: 0.7136 (m-80) REVERT: B 414 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7056 (tm-30) REVERT: B 470 ARG cc_start: 0.7809 (tpp80) cc_final: 0.7389 (tpp80) REVERT: B 528 ASP cc_start: 0.8899 (p0) cc_final: 0.8624 (p0) REVERT: B 560 ASP cc_start: 0.8255 (m-30) cc_final: 0.7987 (m-30) REVERT: B 573 ASP cc_start: 0.8006 (t0) cc_final: 0.7629 (t0) REVERT: B 580 LYS cc_start: 0.8084 (mmtt) cc_final: 0.7645 (mmmm) REVERT: B 661 ASP cc_start: 0.8172 (t0) cc_final: 0.7955 (t0) REVERT: B 687 ASP cc_start: 0.8299 (t0) cc_final: 0.7960 (t0) REVERT: B 717 ARG cc_start: 0.8660 (ttm-80) cc_final: 0.8266 (ttm170) outliers start: 50 outliers final: 32 residues processed: 319 average time/residue: 0.1272 time to fit residues: 54.1120 Evaluate side-chains 324 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 287 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.8980 chunk 90 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 44 optimal weight: 0.0870 chunk 23 optimal weight: 0.8980 chunk 121 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 246 ASN A 656 HIS B 160 HIS B 656 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.126619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.107853 restraints weight = 16701.073| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.42 r_work: 0.3322 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10400 Z= 0.151 Angle : 0.612 9.964 14136 Z= 0.308 Chirality : 0.043 0.220 1718 Planarity : 0.004 0.046 1758 Dihedral : 5.210 55.723 1434 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.28 % Favored : 93.65 % Rotamer: Outliers : 4.90 % Allowed : 16.49 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.24), residues: 1322 helix: 0.73 (0.18), residues: 874 sheet: -1.97 (0.90), residues: 36 loop : -2.36 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 714 TYR 0.046 0.002 TYR A 361 PHE 0.023 0.001 PHE A 130 TRP 0.005 0.001 TRP A 74 HIS 0.009 0.001 HIS B 656 Details of bonding type rmsd covalent geometry : bond 0.00337 (10400) covalent geometry : angle 0.61242 (14136) hydrogen bonds : bond 0.04050 ( 575) hydrogen bonds : angle 3.95880 ( 1677) *********************** 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 344 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 289 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8379 (p) REVERT: A 66 LYS cc_start: 0.8714 (tppt) cc_final: 0.8443 (tptp) REVERT: A 247 TYR cc_start: 0.8158 (m-10) cc_final: 0.7497 (m-10) REVERT: A 258 ILE cc_start: 0.8803 (mm) cc_final: 0.8528 (mm) REVERT: A 259 GLU cc_start: 0.8384 (tt0) cc_final: 0.7389 (tt0) REVERT: A 268 ASN cc_start: 0.8416 (t0) cc_final: 0.8008 (t0) REVERT: A 287 GLU cc_start: 0.7959 (tp30) cc_final: 0.7586 (tp30) REVERT: A 303 GLU cc_start: 0.8044 (mp0) cc_final: 0.7719 (mp0) REVERT: A 348 ASP cc_start: 0.5997 (OUTLIER) cc_final: 0.4964 (p0) REVERT: A 369 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7789 (mmpt) REVERT: A 370 VAL cc_start: 0.8201 (t) cc_final: 0.7872 (p) REVERT: A 371 TYR cc_start: 0.8196 (m-80) cc_final: 0.7795 (m-80) REVERT: A 377 TYR cc_start: 0.7242 (p90) cc_final: 0.6976 (p90) REVERT: A 394 PHE cc_start: 0.8579 (t80) cc_final: 0.7946 (t80) REVERT: A 398 PHE cc_start: 0.7284 (m-80) cc_final: 0.6926 (m-80) REVERT: A 413 GLN cc_start: 0.6598 (pt0) cc_final: 0.6232 (pt0) REVERT: A 432 MET cc_start: 0.8130 (tpt) cc_final: 0.7710 (tpp) REVERT: A 436 VAL cc_start: 0.8711 (p) cc_final: 0.8431 (m) REVERT: A 470 ARG cc_start: 0.7666 (tpp80) cc_final: 0.7422 (tpp80) REVERT: A 473 LYS cc_start: 0.8606 (mtpt) cc_final: 0.8358 (mtmm) REVERT: A 475 ASN cc_start: 0.8416 (t0) cc_final: 0.7700 (t0) REVERT: A 478 ASP cc_start: 0.7917 (m-30) cc_final: 0.7333 (m-30) REVERT: A 486 CYS cc_start: 0.8982 (t) cc_final: 0.8666 (t) REVERT: A 495 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8314 (p0) REVERT: A 496 LEU cc_start: 0.8912 (mm) cc_final: 0.8698 (mt) REVERT: A 569 THR cc_start: 0.8737 (t) cc_final: 0.8326 (m) REVERT: A 573 ASP cc_start: 0.7983 (t0) cc_final: 0.7606 (t0) REVERT: A 580 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7656 (mmmm) REVERT: A 687 ASP cc_start: 0.8230 (t0) cc_final: 0.7922 (t0) REVERT: A 714 ARG cc_start: 0.8379 (mtm-85) cc_final: 0.8174 (mtm-85) REVERT: B 23 SER cc_start: 0.8913 (OUTLIER) cc_final: 0.8511 (p) REVERT: B 66 LYS cc_start: 0.8724 (tppt) cc_final: 0.8172 (tppt) REVERT: B 87 ASP cc_start: 0.7793 (m-30) cc_final: 0.7367 (m-30) REVERT: B 122 PHE cc_start: 0.8471 (m-80) cc_final: 0.8201 (m-80) REVERT: B 246 ASN cc_start: 0.8574 (p0) cc_final: 0.8343 (p0) REVERT: B 258 ILE cc_start: 0.8836 (mm) cc_final: 0.8631 (mm) REVERT: B 259 GLU cc_start: 0.8642 (tt0) cc_final: 0.8416 (mt-10) REVERT: B 268 ASN cc_start: 0.8507 (t0) cc_final: 0.8182 (t0) REVERT: B 289 ASN cc_start: 0.8567 (t0) cc_final: 0.8233 (t0) REVERT: B 303 GLU cc_start: 0.7987 (mp0) cc_final: 0.7716 (mp0) REVERT: B 305 ILE cc_start: 0.8692 (tp) cc_final: 0.8439 (pt) REVERT: B 318 ASN cc_start: 0.8249 (t0) cc_final: 0.7895 (t0) REVERT: B 361 TYR cc_start: 0.8766 (t80) cc_final: 0.7983 (t80) REVERT: B 369 LYS cc_start: 0.8471 (mmtt) cc_final: 0.8182 (mmtt) REVERT: B 384 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7594 (mm-30) REVERT: B 385 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.7815 (m-80) REVERT: B 394 PHE cc_start: 0.8505 (t80) cc_final: 0.7933 (t80) REVERT: B 398 PHE cc_start: 0.7476 (m-80) cc_final: 0.7138 (m-80) REVERT: B 414 GLU cc_start: 0.7407 (tm-30) cc_final: 0.7017 (tm-30) REVERT: B 470 ARG cc_start: 0.7810 (tpp80) cc_final: 0.7393 (tpp80) REVERT: B 473 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8473 (mtmm) REVERT: B 492 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8891 (pp) REVERT: B 528 ASP cc_start: 0.8880 (p0) cc_final: 0.8602 (p0) REVERT: B 560 ASP cc_start: 0.8237 (m-30) cc_final: 0.7946 (m-30) REVERT: B 573 ASP cc_start: 0.8003 (t0) cc_final: 0.7618 (t0) REVERT: B 580 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7651 (mmmm) REVERT: B 661 ASP cc_start: 0.8175 (t0) cc_final: 0.7936 (t0) REVERT: B 687 ASP cc_start: 0.8284 (t0) cc_final: 0.7943 (t0) REVERT: B 717 ARG cc_start: 0.8694 (ttm-80) cc_final: 0.8260 (ttm170) outliers start: 55 outliers final: 31 residues processed: 321 average time/residue: 0.1264 time to fit residues: 54.1626 Evaluate side-chains 314 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 276 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 473 LYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 53 optimal weight: 0.0970 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 0.0980 chunk 90 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 110 optimal weight: 0.0870 chunk 71 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 58 optimal weight: 0.0000 overall best weight: 0.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 246 ASN A 656 HIS B 160 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.128339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.109553 restraints weight = 16528.712| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.41 r_work: 0.3347 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10400 Z= 0.118 Angle : 0.599 9.882 14136 Z= 0.299 Chirality : 0.042 0.248 1718 Planarity : 0.004 0.042 1758 Dihedral : 5.160 55.062 1434 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.90 % Favored : 94.02 % Rotamer: Outliers : 4.46 % Allowed : 17.29 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.24), residues: 1322 helix: 0.86 (0.18), residues: 874 sheet: -1.93 (0.89), residues: 36 loop : -2.28 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 714 TYR 0.050 0.002 TYR A 361 PHE 0.028 0.001 PHE B 130 TRP 0.005 0.001 TRP B 482 HIS 0.006 0.001 HIS B 656 Details of bonding type rmsd covalent geometry : bond 0.00254 (10400) covalent geometry : angle 0.59931 (14136) hydrogen bonds : bond 0.03832 ( 575) hydrogen bonds : angle 3.92377 ( 1677) *********************** 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 336 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 286 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8339 (p) REVERT: A 66 LYS cc_start: 0.8673 (tppt) cc_final: 0.8375 (tptp) REVERT: A 247 TYR cc_start: 0.8128 (m-10) cc_final: 0.7396 (m-10) REVERT: A 258 ILE cc_start: 0.8792 (mm) cc_final: 0.8511 (mm) REVERT: A 259 GLU cc_start: 0.8352 (tt0) cc_final: 0.7253 (tt0) REVERT: A 287 GLU cc_start: 0.7929 (tp30) cc_final: 0.7555 (tp30) REVERT: A 303 GLU cc_start: 0.8010 (mp0) cc_final: 0.7688 (mp0) REVERT: A 348 ASP cc_start: 0.5922 (OUTLIER) cc_final: 0.4871 (p0) REVERT: A 366 SER cc_start: 0.8774 (t) cc_final: 0.8427 (p) REVERT: A 369 LYS cc_start: 0.8175 (mmtt) cc_final: 0.7760 (mmpt) REVERT: A 371 TYR cc_start: 0.8107 (m-80) cc_final: 0.7737 (m-80) REVERT: A 384 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7435 (mm-30) REVERT: A 394 PHE cc_start: 0.8588 (t80) cc_final: 0.7984 (t80) REVERT: A 398 PHE cc_start: 0.7187 (m-80) cc_final: 0.6861 (m-80) REVERT: A 413 GLN cc_start: 0.6482 (pt0) cc_final: 0.6073 (pt0) REVERT: A 432 MET cc_start: 0.8113 (tpt) cc_final: 0.7697 (tpp) REVERT: A 436 VAL cc_start: 0.8694 (p) cc_final: 0.8415 (m) REVERT: A 470 ARG cc_start: 0.7617 (tpp80) cc_final: 0.7357 (tpp80) REVERT: A 473 LYS cc_start: 0.8596 (mtpt) cc_final: 0.8347 (mtmm) REVERT: A 475 ASN cc_start: 0.8438 (t0) cc_final: 0.7493 (t0) REVERT: A 478 ASP cc_start: 0.7908 (m-30) cc_final: 0.7257 (m-30) REVERT: A 486 CYS cc_start: 0.8952 (t) cc_final: 0.8641 (t) REVERT: A 495 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8299 (p0) REVERT: A 496 LEU cc_start: 0.8911 (mm) cc_final: 0.8698 (mt) REVERT: A 569 THR cc_start: 0.8721 (t) cc_final: 0.8302 (m) REVERT: A 573 ASP cc_start: 0.7942 (t0) cc_final: 0.7552 (t0) REVERT: A 580 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7631 (mmmm) REVERT: A 674 ARG cc_start: 0.8197 (mtm-85) cc_final: 0.7891 (mtm180) REVERT: A 687 ASP cc_start: 0.8237 (t0) cc_final: 0.7945 (t0) REVERT: A 714 ARG cc_start: 0.8362 (mtm-85) cc_final: 0.8154 (mtm-85) REVERT: B 23 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8490 (p) REVERT: B 66 LYS cc_start: 0.8657 (tppt) cc_final: 0.8209 (tppt) REVERT: B 87 ASP cc_start: 0.7809 (m-30) cc_final: 0.7440 (m-30) REVERT: B 122 PHE cc_start: 0.8439 (m-80) cc_final: 0.8168 (m-80) REVERT: B 246 ASN cc_start: 0.8558 (p0) cc_final: 0.8333 (p0) REVERT: B 258 ILE cc_start: 0.8827 (mm) cc_final: 0.8611 (mm) REVERT: B 259 GLU cc_start: 0.8619 (tt0) cc_final: 0.8400 (mt-10) REVERT: B 268 ASN cc_start: 0.8485 (t0) cc_final: 0.8201 (t0) REVERT: B 289 ASN cc_start: 0.8517 (t0) cc_final: 0.8173 (t0) REVERT: B 303 GLU cc_start: 0.7929 (mp0) cc_final: 0.7673 (mp0) REVERT: B 305 ILE cc_start: 0.8653 (tp) cc_final: 0.8409 (pt) REVERT: B 318 ASN cc_start: 0.8232 (t0) cc_final: 0.7895 (t0) REVERT: B 361 TYR cc_start: 0.8721 (t80) cc_final: 0.7934 (t80) REVERT: B 369 LYS cc_start: 0.8464 (mmtt) cc_final: 0.8249 (mmtt) REVERT: B 384 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7607 (mm-30) REVERT: B 385 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.7809 (m-80) REVERT: B 394 PHE cc_start: 0.8496 (t80) cc_final: 0.7942 (t80) REVERT: B 398 PHE cc_start: 0.7398 (m-80) cc_final: 0.7084 (m-80) REVERT: B 414 GLU cc_start: 0.7367 (tm-30) cc_final: 0.6980 (tm-30) REVERT: B 470 ARG cc_start: 0.7797 (tpp80) cc_final: 0.7381 (tpp80) REVERT: B 473 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8430 (mtmm) REVERT: B 492 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8897 (pp) REVERT: B 528 ASP cc_start: 0.8866 (p0) cc_final: 0.8586 (p0) REVERT: B 560 ASP cc_start: 0.8211 (m-30) cc_final: 0.7918 (m-30) REVERT: B 573 ASP cc_start: 0.7980 (t0) cc_final: 0.7581 (t0) REVERT: B 580 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7666 (mmmm) REVERT: B 661 ASP cc_start: 0.8109 (t0) cc_final: 0.7872 (t0) REVERT: B 687 ASP cc_start: 0.8286 (t0) cc_final: 0.7940 (t0) REVERT: B 717 ARG cc_start: 0.8688 (ttm-80) cc_final: 0.8179 (ttm170) outliers start: 50 outliers final: 32 residues processed: 312 average time/residue: 0.1260 time to fit residues: 52.6212 Evaluate side-chains 321 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 282 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 473 LYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 44 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 110 optimal weight: 0.0980 chunk 93 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 80 optimal weight: 0.0170 chunk 46 optimal weight: 0.9990 chunk 75 optimal weight: 0.0370 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 246 ASN A 656 HIS B 160 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.128017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.109190 restraints weight = 16654.224| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.43 r_work: 0.3347 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10400 Z= 0.132 Angle : 0.608 9.869 14136 Z= 0.305 Chirality : 0.042 0.236 1718 Planarity : 0.004 0.042 1758 Dihedral : 5.110 54.951 1434 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.20 % Favored : 93.72 % Rotamer: Outliers : 4.19 % Allowed : 18.00 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.25), residues: 1322 helix: 0.91 (0.18), residues: 874 sheet: -1.81 (0.88), residues: 36 loop : -2.23 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 714 TYR 0.046 0.002 TYR A 361 PHE 0.012 0.001 PHE B 121 TRP 0.006 0.001 TRP A 74 HIS 0.006 0.001 HIS B 656 Details of bonding type rmsd covalent geometry : bond 0.00293 (10400) covalent geometry : angle 0.60784 (14136) hydrogen bonds : bond 0.03809 ( 575) hydrogen bonds : angle 3.92541 ( 1677) *********************** 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 332 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 285 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8369 (p) REVERT: A 66 LYS cc_start: 0.8612 (tppt) cc_final: 0.8288 (tptp) REVERT: A 247 TYR cc_start: 0.7870 (m-10) cc_final: 0.7131 (m-10) REVERT: A 258 ILE cc_start: 0.8734 (mm) cc_final: 0.8473 (mm) REVERT: A 259 GLU cc_start: 0.8127 (tt0) cc_final: 0.6932 (tt0) REVERT: A 287 GLU cc_start: 0.7713 (tp30) cc_final: 0.7348 (tp30) REVERT: A 303 GLU cc_start: 0.7745 (mp0) cc_final: 0.7423 (mp0) REVERT: A 348 ASP cc_start: 0.5569 (OUTLIER) cc_final: 0.4464 (p0) REVERT: A 369 LYS cc_start: 0.8101 (mmtt) cc_final: 0.7649 (mmtt) REVERT: A 370 VAL cc_start: 0.8076 (t) cc_final: 0.7865 (p) REVERT: A 371 TYR cc_start: 0.8061 (m-80) cc_final: 0.7747 (m-80) REVERT: A 394 PHE cc_start: 0.8487 (t80) cc_final: 0.7859 (t80) REVERT: A 398 PHE cc_start: 0.6942 (m-80) cc_final: 0.6662 (m-80) REVERT: A 405 THR cc_start: 0.8626 (p) cc_final: 0.8406 (t) REVERT: A 413 GLN cc_start: 0.6266 (pt0) cc_final: 0.5861 (pt0) REVERT: A 432 MET cc_start: 0.7960 (tpt) cc_final: 0.7553 (tpp) REVERT: A 436 VAL cc_start: 0.8638 (p) cc_final: 0.8376 (m) REVERT: A 470 ARG cc_start: 0.7258 (tpp80) cc_final: 0.6991 (tpp80) REVERT: A 473 LYS cc_start: 0.8472 (mtpt) cc_final: 0.8257 (mtmm) REVERT: A 475 ASN cc_start: 0.8183 (t0) cc_final: 0.7110 (t0) REVERT: A 478 ASP cc_start: 0.7646 (m-30) cc_final: 0.6926 (m-30) REVERT: A 486 CYS cc_start: 0.8816 (t) cc_final: 0.8500 (t) REVERT: A 495 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.8116 (p0) REVERT: A 496 LEU cc_start: 0.8843 (mm) cc_final: 0.8609 (mt) REVERT: A 569 THR cc_start: 0.8710 (t) cc_final: 0.8304 (m) REVERT: A 573 ASP cc_start: 0.7754 (t0) cc_final: 0.7370 (t0) REVERT: A 580 LYS cc_start: 0.7954 (mmtt) cc_final: 0.7490 (mmmm) REVERT: A 674 ARG cc_start: 0.8028 (mtm-85) cc_final: 0.7710 (mtm180) REVERT: A 687 ASP cc_start: 0.8032 (t0) cc_final: 0.7760 (t0) REVERT: A 714 ARG cc_start: 0.8084 (mtm-85) cc_final: 0.7868 (mtm-85) REVERT: B 66 LYS cc_start: 0.8606 (tppt) cc_final: 0.8328 (tppt) REVERT: B 87 ASP cc_start: 0.7708 (m-30) cc_final: 0.7368 (m-30) REVERT: B 122 PHE cc_start: 0.8268 (m-80) cc_final: 0.8044 (m-80) REVERT: B 246 ASN cc_start: 0.8432 (p0) cc_final: 0.8217 (p0) REVERT: B 258 ILE cc_start: 0.8756 (mm) cc_final: 0.8547 (mm) REVERT: B 259 GLU cc_start: 0.8395 (tt0) cc_final: 0.8188 (mt-10) REVERT: B 268 ASN cc_start: 0.8398 (t0) cc_final: 0.8095 (t0) REVERT: B 289 ASN cc_start: 0.8391 (t0) cc_final: 0.8004 (t0) REVERT: B 303 GLU cc_start: 0.7690 (mp0) cc_final: 0.7441 (mp0) REVERT: B 305 ILE cc_start: 0.8558 (tp) cc_final: 0.8325 (pt) REVERT: B 318 ASN cc_start: 0.8044 (t0) cc_final: 0.7699 (t0) REVERT: B 361 TYR cc_start: 0.8642 (t80) cc_final: 0.7826 (t80) REVERT: B 384 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7421 (mm-30) REVERT: B 385 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.7749 (m-80) REVERT: B 394 PHE cc_start: 0.8390 (t80) cc_final: 0.7798 (t80) REVERT: B 398 PHE cc_start: 0.7236 (m-80) cc_final: 0.6905 (m-80) REVERT: B 414 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6780 (tm-30) REVERT: B 470 ARG cc_start: 0.7456 (tpp80) cc_final: 0.7120 (tpp80) REVERT: B 473 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8321 (mtmm) REVERT: B 492 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8864 (pt) REVERT: B 528 ASP cc_start: 0.8689 (p0) cc_final: 0.8401 (p0) REVERT: B 560 ASP cc_start: 0.7952 (m-30) cc_final: 0.7642 (m-30) REVERT: B 573 ASP cc_start: 0.7771 (t0) cc_final: 0.7143 (t0) REVERT: B 580 LYS cc_start: 0.7973 (mmtt) cc_final: 0.7508 (mmmm) REVERT: B 661 ASP cc_start: 0.7971 (t0) cc_final: 0.7730 (t0) REVERT: B 687 ASP cc_start: 0.8071 (t0) cc_final: 0.7722 (t0) REVERT: B 717 ARG cc_start: 0.8630 (ttm-80) cc_final: 0.8147 (ttm170) outliers start: 47 outliers final: 33 residues processed: 308 average time/residue: 0.1235 time to fit residues: 50.8700 Evaluate side-chains 321 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 282 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 473 LYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 88 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 95 optimal weight: 0.2980 chunk 8 optimal weight: 0.2980 chunk 120 optimal weight: 0.0970 chunk 71 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 0.0470 chunk 49 optimal weight: 0.0670 overall best weight: 0.1614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 246 ASN A 656 HIS B 135 HIS B 160 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.129364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.110793 restraints weight = 16660.438| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.42 r_work: 0.3370 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10400 Z= 0.118 Angle : 0.601 10.218 14136 Z= 0.300 Chirality : 0.042 0.226 1718 Planarity : 0.004 0.041 1758 Dihedral : 5.083 54.437 1434 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.01 % Allowed : 18.36 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.25), residues: 1322 helix: 1.02 (0.18), residues: 870 sheet: -1.77 (0.88), residues: 36 loop : -2.18 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 38 TYR 0.019 0.001 TYR A 361 PHE 0.015 0.001 PHE A 121 TRP 0.005 0.001 TRP B 74 HIS 0.007 0.001 HIS B 656 Details of bonding type rmsd covalent geometry : bond 0.00255 (10400) covalent geometry : angle 0.60146 (14136) hydrogen bonds : bond 0.03706 ( 575) hydrogen bonds : angle 3.91194 ( 1677) *********************** 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 325 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 280 time to evaluate : 0.313 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 21 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8348 (p) REVERT: A 66 LYS cc_start: 0.8591 (tppt) cc_final: 0.8269 (tptp) REVERT: A 247 TYR cc_start: 0.7830 (m-10) cc_final: 0.7509 (m-10) REVERT: A 258 ILE cc_start: 0.8731 (mm) cc_final: 0.8458 (mm) REVERT: A 268 ASN cc_start: 0.8267 (t0) cc_final: 0.7822 (t0) REVERT: A 287 GLU cc_start: 0.7705 (tp30) cc_final: 0.7335 (tp30) REVERT: A 303 GLU cc_start: 0.7733 (mp0) cc_final: 0.7414 (mp0) REVERT: A 329 LYS cc_start: 0.8519 (pttt) cc_final: 0.8205 (pttm) REVERT: A 348 ASP cc_start: 0.5557 (OUTLIER) cc_final: 0.4438 (p0) REVERT: A 369 LYS cc_start: 0.8064 (mmtt) cc_final: 0.7611 (mmtt) REVERT: A 370 VAL cc_start: 0.8060 (t) cc_final: 0.7856 (p) REVERT: A 371 TYR cc_start: 0.7970 (m-80) cc_final: 0.7643 (m-80) REVERT: A 394 PHE cc_start: 0.8485 (t80) cc_final: 0.7835 (t80) REVERT: A 398 PHE cc_start: 0.6915 (m-80) cc_final: 0.6645 (m-80) REVERT: A 413 GLN cc_start: 0.6104 (pt0) cc_final: 0.5655 (pt0) REVERT: A 432 MET cc_start: 0.7951 (tpt) cc_final: 0.7544 (tpp) REVERT: A 436 VAL cc_start: 0.8619 (p) cc_final: 0.8361 (m) REVERT: A 470 ARG cc_start: 0.7258 (tpp80) cc_final: 0.6983 (tpp80) REVERT: A 473 LYS cc_start: 0.8473 (mtpt) cc_final: 0.8248 (mtmm) REVERT: A 475 ASN cc_start: 0.8210 (t0) cc_final: 0.7179 (t0) REVERT: A 478 ASP cc_start: 0.7644 (m-30) cc_final: 0.6927 (m-30) REVERT: A 486 CYS cc_start: 0.8783 (t) cc_final: 0.8445 (t) REVERT: A 496 LEU cc_start: 0.8821 (mm) cc_final: 0.8597 (mt) REVERT: A 569 THR cc_start: 0.8702 (t) cc_final: 0.8306 (m) REVERT: A 573 ASP cc_start: 0.7723 (t0) cc_final: 0.7340 (t0) REVERT: A 580 LYS cc_start: 0.8016 (mmtt) cc_final: 0.7540 (mmmm) REVERT: A 674 ARG cc_start: 0.8003 (mtm-85) cc_final: 0.7482 (mtm180) REVERT: A 678 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7441 (mpp) REVERT: A 687 ASP cc_start: 0.8020 (t0) cc_final: 0.7758 (t0) REVERT: A 714 ARG cc_start: 0.8104 (mtm-85) cc_final: 0.7882 (mtm-85) REVERT: B 66 LYS cc_start: 0.8581 (tppt) cc_final: 0.8298 (tppt) REVERT: B 87 ASP cc_start: 0.7697 (m-30) cc_final: 0.7329 (m-30) REVERT: B 122 PHE cc_start: 0.8227 (m-80) cc_final: 0.8026 (m-10) REVERT: B 246 ASN cc_start: 0.8402 (p0) cc_final: 0.8193 (p0) REVERT: B 258 ILE cc_start: 0.8746 (mm) cc_final: 0.8513 (mm) REVERT: B 259 GLU cc_start: 0.8406 (tt0) cc_final: 0.8176 (mt-10) REVERT: B 303 GLU cc_start: 0.7624 (mp0) cc_final: 0.7400 (mp0) REVERT: B 305 ILE cc_start: 0.8558 (tp) cc_final: 0.8311 (pt) REVERT: B 318 ASN cc_start: 0.8021 (t0) cc_final: 0.7680 (t0) REVERT: B 361 TYR cc_start: 0.8602 (t80) cc_final: 0.7827 (t80) REVERT: B 385 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.7757 (m-80) REVERT: B 394 PHE cc_start: 0.8380 (t80) cc_final: 0.7874 (t80) REVERT: B 398 PHE cc_start: 0.7175 (m-80) cc_final: 0.6937 (m-80) REVERT: B 414 GLU cc_start: 0.7080 (tm-30) cc_final: 0.6709 (tm-30) REVERT: B 470 ARG cc_start: 0.7461 (tpp80) cc_final: 0.7098 (tpp80) REVERT: B 492 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8866 (pt) REVERT: B 528 ASP cc_start: 0.8692 (p0) cc_final: 0.8403 (p0) REVERT: B 560 ASP cc_start: 0.7952 (m-30) cc_final: 0.7656 (m-30) REVERT: B 573 ASP cc_start: 0.7650 (t0) cc_final: 0.7264 (t0) REVERT: B 580 LYS cc_start: 0.7972 (mmtt) cc_final: 0.7491 (mmmm) REVERT: B 661 ASP cc_start: 0.7950 (t0) cc_final: 0.7699 (t0) REVERT: B 674 ARG cc_start: 0.7881 (mtm-85) cc_final: 0.7635 (mtm-85) REVERT: B 687 ASP cc_start: 0.8061 (t0) cc_final: 0.7723 (t0) REVERT: B 717 ARG cc_start: 0.8626 (ttm-80) cc_final: 0.8128 (ttm170) outliers start: 45 outliers final: 30 residues processed: 303 average time/residue: 0.1178 time to fit residues: 47.5610 Evaluate side-chains 313 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 278 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 22 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 125 optimal weight: 0.0770 chunk 91 optimal weight: 0.0050 chunk 44 optimal weight: 0.9990 chunk 88 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 overall best weight: 0.2752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 246 ASN A 656 HIS B 160 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.129064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.110395 restraints weight = 16520.215| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.43 r_work: 0.3366 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10400 Z= 0.126 Angle : 0.610 9.863 14136 Z= 0.305 Chirality : 0.042 0.223 1718 Planarity : 0.004 0.045 1758 Dihedral : 4.874 48.198 1432 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.75 % Favored : 94.18 % Rotamer: Outliers : 3.39 % Allowed : 19.16 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.25), residues: 1322 helix: 1.02 (0.18), residues: 870 sheet: -1.65 (0.88), residues: 36 loop : -2.14 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 714 TYR 0.025 0.001 TYR A 361 PHE 0.027 0.001 PHE B 130 TRP 0.005 0.001 TRP A 74 HIS 0.006 0.001 HIS B 656 Details of bonding type rmsd covalent geometry : bond 0.00281 (10400) covalent geometry : angle 0.60983 (14136) hydrogen bonds : bond 0.03697 ( 575) hydrogen bonds : angle 3.92110 ( 1677) ********************** 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 321 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 283 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8362 (p) REVERT: A 66 LYS cc_start: 0.8594 (tppt) cc_final: 0.8280 (tptp) REVERT: A 247 TYR cc_start: 0.7761 (m-10) cc_final: 0.7419 (m-10) REVERT: A 258 ILE cc_start: 0.8730 (mm) cc_final: 0.8461 (mm) REVERT: A 268 ASN cc_start: 0.8271 (t0) cc_final: 0.7879 (t0) REVERT: A 287 GLU cc_start: 0.7745 (tp30) cc_final: 0.7350 (tp30) REVERT: A 303 GLU cc_start: 0.7725 (mp0) cc_final: 0.7398 (mp0) REVERT: A 348 ASP cc_start: 0.5593 (OUTLIER) cc_final: 0.4124 (p0) REVERT: A 366 SER cc_start: 0.8766 (t) cc_final: 0.8376 (p) REVERT: A 369 LYS cc_start: 0.8111 (mmtt) cc_final: 0.7676 (mmtt) REVERT: A 370 VAL cc_start: 0.8083 (t) cc_final: 0.7880 (p) REVERT: A 371 TYR cc_start: 0.7960 (m-80) cc_final: 0.7679 (m-80) REVERT: A 394 PHE cc_start: 0.8487 (t80) cc_final: 0.7837 (t80) REVERT: A 398 PHE cc_start: 0.6950 (m-80) cc_final: 0.6673 (m-80) REVERT: A 413 GLN cc_start: 0.6115 (pt0) cc_final: 0.5681 (pt0) REVERT: A 432 MET cc_start: 0.7960 (tpt) cc_final: 0.7540 (tpp) REVERT: A 436 VAL cc_start: 0.8632 (p) cc_final: 0.8365 (m) REVERT: A 470 ARG cc_start: 0.7290 (tpp80) cc_final: 0.7015 (tpp80) REVERT: A 473 LYS cc_start: 0.8486 (mtpt) cc_final: 0.8253 (mtmm) REVERT: A 475 ASN cc_start: 0.8231 (t0) cc_final: 0.7264 (t0) REVERT: A 478 ASP cc_start: 0.7647 (m-30) cc_final: 0.6950 (m-30) REVERT: A 486 CYS cc_start: 0.8787 (t) cc_final: 0.8465 (t) REVERT: A 569 THR cc_start: 0.8714 (t) cc_final: 0.8319 (m) REVERT: A 573 ASP cc_start: 0.7724 (t0) cc_final: 0.7341 (t0) REVERT: A 580 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7560 (mmmm) REVERT: A 674 ARG cc_start: 0.7988 (mtm-85) cc_final: 0.7470 (mtm180) REVERT: A 678 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7443 (mpp) REVERT: A 687 ASP cc_start: 0.8004 (t0) cc_final: 0.7770 (t0) REVERT: A 714 ARG cc_start: 0.8132 (mtm-85) cc_final: 0.7912 (mtm-85) REVERT: B 66 LYS cc_start: 0.8572 (tppt) cc_final: 0.8074 (tppt) REVERT: B 87 ASP cc_start: 0.7688 (m-30) cc_final: 0.7338 (m-30) REVERT: B 246 ASN cc_start: 0.8407 (p0) cc_final: 0.8191 (p0) REVERT: B 258 ILE cc_start: 0.8752 (mm) cc_final: 0.8519 (mm) REVERT: B 259 GLU cc_start: 0.8417 (tt0) cc_final: 0.8186 (mt-10) REVERT: B 268 ASN cc_start: 0.8434 (t0) cc_final: 0.8176 (t0) REVERT: B 305 ILE cc_start: 0.8560 (tp) cc_final: 0.8314 (pt) REVERT: B 318 ASN cc_start: 0.8033 (t0) cc_final: 0.7695 (t0) REVERT: B 361 TYR cc_start: 0.8609 (t80) cc_final: 0.7825 (t80) REVERT: B 385 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7732 (m-80) REVERT: B 394 PHE cc_start: 0.8373 (t80) cc_final: 0.7851 (t80) REVERT: B 398 PHE cc_start: 0.7206 (m-80) cc_final: 0.6967 (m-80) REVERT: B 414 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6687 (tm-30) REVERT: B 470 ARG cc_start: 0.7455 (tpp80) cc_final: 0.7113 (tpp80) REVERT: B 492 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8881 (pt) REVERT: B 528 ASP cc_start: 0.8691 (p0) cc_final: 0.8400 (p0) REVERT: B 560 ASP cc_start: 0.7937 (m-30) cc_final: 0.7639 (m-30) REVERT: B 573 ASP cc_start: 0.7667 (t0) cc_final: 0.7293 (t0) REVERT: B 580 LYS cc_start: 0.7986 (mmtt) cc_final: 0.7507 (mmmm) REVERT: B 661 ASP cc_start: 0.7958 (t0) cc_final: 0.7705 (t0) REVERT: B 674 ARG cc_start: 0.7881 (mtm-85) cc_final: 0.7634 (mtm-85) REVERT: B 687 ASP cc_start: 0.8070 (t0) cc_final: 0.7738 (t0) REVERT: B 717 ARG cc_start: 0.8617 (ttm-80) cc_final: 0.8122 (ttm170) outliers start: 38 outliers final: 29 residues processed: 305 average time/residue: 0.1088 time to fit residues: 44.6708 Evaluate side-chains 315 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 281 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 20 optimal weight: 0.2980 chunk 106 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 119 optimal weight: 0.4980 chunk 96 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 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 160 HIS A 656 HIS B 160 HIS B 656 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.127259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.108551 restraints weight = 16688.138| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.44 r_work: 0.3335 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10400 Z= 0.166 Angle : 0.633 9.522 14136 Z= 0.318 Chirality : 0.044 0.226 1718 Planarity : 0.004 0.048 1758 Dihedral : 4.937 47.408 1432 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.67 % Favored : 94.25 % Rotamer: Outliers : 3.12 % Allowed : 19.61 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.25), residues: 1322 helix: 0.96 (0.18), residues: 870 sheet: -1.57 (0.88), residues: 36 loop : -2.12 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 38 TYR 0.023 0.002 TYR A 361 PHE 0.034 0.001 PHE B 122 TRP 0.005 0.001 TRP A 74 HIS 0.006 0.001 HIS B 656 Details of bonding type rmsd covalent geometry : bond 0.00376 (10400) covalent geometry : angle 0.63306 (14136) hydrogen bonds : bond 0.03871 ( 575) hydrogen bonds : angle 3.96122 ( 1677) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2437.83 seconds wall clock time: 42 minutes 42.00 seconds (2562.00 seconds total)