Starting phenix.real_space_refine on Sat Nov 16 02:55:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzn_35089/11_2024/8hzn_35089.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzn_35089/11_2024/8hzn_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzn_35089/11_2024/8hzn_35089.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzn_35089/11_2024/8hzn_35089.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzn_35089/11_2024/8hzn_35089.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzn_35089/11_2024/8hzn_35089.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10200 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.80, per 1000 atoms: 0.67 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: 2.79 Conformation dependent library (CDL) restraints added in 1.3 seconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 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: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.527A 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: 3.19 Time building geometry restraints manager: 3.14 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: 0.00 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.760 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.830 ------------------------------------------------------------------------------- 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= 0.116 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (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 TRP 0.004 0.000 TRP A 83 HIS 0.001 0.000 HIS A 723 PHE 0.009 0.001 PHE A 555 TYR 0.008 0.001 TYR A 127 ARG 0.001 0.000 ARG B 512 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 376 time to evaluate : 1.141 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: 0.2630 time to fit residues: 141.0088 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 : 1.207 ------------------------------------------------------------------------------- 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 111 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10400 Z= 0.324 Angle : 0.669 8.171 14136 Z= 0.347 Chirality : 0.045 0.187 1718 Planarity : 0.005 0.049 1758 Dihedral : 5.930 80.092 1444 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.57 % Allowed : 12.75 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.22), residues: 1322 helix: -0.44 (0.17), residues: 866 sheet: -2.86 (0.82), residues: 36 loop : -2.96 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 518 HIS 0.009 0.002 HIS B 656 PHE 0.024 0.002 PHE A 130 TYR 0.025 0.002 TYR B 361 ARG 0.006 0.001 ARG B 38 *********************** 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 362 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 322 time to evaluate : 1.175 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 66 LYS cc_start: 0.8580 (tppt) cc_final: 0.8255 (tptp) REVERT: A 160 HIS cc_start: 0.8022 (t-90) cc_final: 0.7789 (t70) REVERT: A 258 ILE cc_start: 0.8564 (mm) cc_final: 0.8272 (mm) REVERT: A 273 ILE cc_start: 0.8361 (mt) cc_final: 0.8105 (tp) REVERT: A 289 ASN cc_start: 0.8247 (t0) cc_final: 0.7902 (t0) REVERT: A 318 ASN cc_start: 0.7465 (t0) cc_final: 0.7155 (t0) REVERT: A 369 LYS cc_start: 0.7972 (mmtt) cc_final: 0.7479 (mmtt) REVERT: A 371 TYR cc_start: 0.8143 (m-80) cc_final: 0.7761 (m-80) REVERT: A 394 PHE cc_start: 0.8297 (t80) cc_final: 0.7423 (t80) REVERT: A 398 PHE cc_start: 0.6762 (m-80) cc_final: 0.6437 (m-80) REVERT: A 432 MET cc_start: 0.7711 (tpt) cc_final: 0.7367 (tpp) REVERT: A 436 VAL cc_start: 0.8430 (p) cc_final: 0.8142 (m) REVERT: A 475 ASN cc_start: 0.7617 (t0) cc_final: 0.6657 (t0) REVERT: A 486 CYS cc_start: 0.8440 (t) cc_final: 0.8111 (t) REVERT: A 496 LEU cc_start: 0.8861 (mm) cc_final: 0.8611 (mm) REVERT: A 569 THR cc_start: 0.8738 (t) cc_final: 0.8336 (m) REVERT: A 573 ASP cc_start: 0.7343 (t0) cc_final: 0.7142 (t0) REVERT: A 580 LYS cc_start: 0.7795 (mmtt) cc_final: 0.7323 (mmmm) REVERT: A 684 GLN cc_start: 0.7927 (tp40) cc_final: 0.7699 (tp-100) REVERT: B 27 TYR cc_start: 0.7713 (m-10) cc_final: 0.7461 (m-10) REVERT: B 66 LYS cc_start: 0.8738 (tppt) cc_final: 0.8495 (tppt) REVERT: B 78 TYR cc_start: 0.7152 (t80) cc_final: 0.6395 (t80) REVERT: B 87 ASP cc_start: 0.7482 (m-30) cc_final: 0.7056 (m-30) REVERT: B 114 GLN cc_start: 0.7871 (tt0) cc_final: 0.7579 (pt0) REVERT: B 246 ASN cc_start: 0.8253 (p0) cc_final: 0.8014 (p0) REVERT: B 250 ILE cc_start: 0.8370 (mm) cc_final: 0.8006 (tp) REVERT: B 268 ASN cc_start: 0.8450 (t0) cc_final: 0.7362 (t0) REVERT: B 271 ASP cc_start: 0.7753 (m-30) cc_final: 0.7311 (m-30) REVERT: B 289 ASN cc_start: 0.8132 (t0) cc_final: 0.7782 (t0) REVERT: B 303 GLU cc_start: 0.7343 (mp0) cc_final: 0.7093 (mp0) REVERT: B 305 ILE cc_start: 0.8430 (tp) cc_final: 0.8171 (pt) REVERT: B 318 ASN cc_start: 0.7582 (t0) cc_final: 0.7155 (t0) REVERT: B 350 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6389 (tm) REVERT: B 361 TYR cc_start: 0.8369 (t80) cc_final: 0.7815 (t80) REVERT: B 366 SER cc_start: 0.8665 (t) cc_final: 0.8353 (p) REVERT: B 369 LYS cc_start: 0.8302 (mmtt) cc_final: 0.8082 (mmtt) REVERT: B 377 TYR cc_start: 0.7538 (p90) cc_final: 0.7329 (p90) REVERT: B 385 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.8008 (m-80) REVERT: B 394 PHE cc_start: 0.8327 (t80) cc_final: 0.7689 (t80) REVERT: B 398 PHE cc_start: 0.7193 (m-80) cc_final: 0.6693 (m-80) REVERT: B 414 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6795 (tm-30) REVERT: B 464 GLN cc_start: 0.7949 (mt0) cc_final: 0.7724 (mt0) REVERT: B 475 ASN cc_start: 0.7720 (t0) cc_final: 0.7439 (t0) REVERT: B 556 TYR cc_start: 0.8645 (p90) cc_final: 0.8039 (p90) REVERT: B 580 LYS cc_start: 0.7706 (mmtt) cc_final: 0.7300 (mmmm) REVERT: B 668 LEU cc_start: 0.6545 (mt) cc_final: 0.6307 (mt) REVERT: B 687 ASP cc_start: 0.7690 (t0) cc_final: 0.7489 (t0) REVERT: B 717 ARG cc_start: 0.8436 (ttm-80) cc_final: 0.8011 (ttm170) outliers start: 40 outliers final: 21 residues processed: 344 average time/residue: 0.2764 time to fit residues: 126.6971 Evaluate side-chains 320 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 297 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 86 SER 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 308 ILE 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 66 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 129 optimal weight: 0.2980 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 135 HIS ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS B 160 HIS ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10400 Z= 0.313 Angle : 0.637 10.773 14136 Z= 0.330 Chirality : 0.044 0.179 1718 Planarity : 0.005 0.050 1758 Dihedral : 5.660 81.389 1437 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.28 % Favored : 93.65 % Rotamer: Outliers : 4.01 % Allowed : 14.97 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.23), residues: 1322 helix: 0.01 (0.17), residues: 886 sheet: -2.40 (0.90), residues: 36 loop : -2.76 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 74 HIS 0.009 0.001 HIS B 656 PHE 0.018 0.002 PHE A 121 TYR 0.020 0.002 TYR B 377 ARG 0.008 0.001 ARG B 213 *********************** 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 357 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 312 time to evaluate : 1.157 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: 0.8590 (OUTLIER) cc_final: 0.8338 (p) REVERT: A 66 LYS cc_start: 0.8615 (tppt) cc_final: 0.8308 (tptp) REVERT: A 258 ILE cc_start: 0.8592 (mm) cc_final: 0.8308 (mm) REVERT: A 314 SER cc_start: 0.8833 (t) cc_final: 0.8528 (p) REVERT: A 318 ASN cc_start: 0.7654 (t0) cc_final: 0.7359 (t0) REVERT: A 348 ASP cc_start: 0.5674 (OUTLIER) cc_final: 0.4401 (p0) REVERT: A 369 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7535 (mmtt) REVERT: A 371 TYR cc_start: 0.8118 (m-80) cc_final: 0.7703 (m-80) REVERT: A 394 PHE cc_start: 0.8325 (t80) cc_final: 0.7497 (t80) REVERT: A 398 PHE cc_start: 0.6818 (m-80) cc_final: 0.6454 (m-80) REVERT: A 432 MET cc_start: 0.7754 (tpt) cc_final: 0.7367 (tpp) REVERT: A 436 VAL cc_start: 0.8521 (p) cc_final: 0.8230 (m) REVERT: A 486 CYS cc_start: 0.8415 (t) cc_final: 0.8117 (t) REVERT: A 569 THR cc_start: 0.8777 (t) cc_final: 0.8376 (m) REVERT: A 580 LYS cc_start: 0.7807 (mmtt) cc_final: 0.7369 (mmmm) REVERT: B 20 TYR cc_start: 0.7873 (t80) cc_final: 0.7640 (t80) REVERT: B 21 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8257 (p) REVERT: B 23 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8290 (p) REVERT: B 66 LYS cc_start: 0.8700 (tppt) cc_final: 0.8469 (tppt) REVERT: B 87 ASP cc_start: 0.7592 (m-30) cc_final: 0.6948 (m-30) REVERT: B 114 GLN cc_start: 0.7949 (tt0) cc_final: 0.7635 (pt0) REVERT: B 153 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8310 (mt) REVERT: B 246 ASN cc_start: 0.8284 (p0) cc_final: 0.8062 (p0) REVERT: B 250 ILE cc_start: 0.8619 (mm) cc_final: 0.8175 (tp) REVERT: B 268 ASN cc_start: 0.8420 (t0) cc_final: 0.7242 (t0) REVERT: B 271 ASP cc_start: 0.7719 (m-30) cc_final: 0.7245 (m-30) REVERT: B 289 ASN cc_start: 0.8219 (t0) cc_final: 0.7869 (t0) REVERT: B 303 GLU cc_start: 0.7389 (mp0) cc_final: 0.7087 (mp0) REVERT: B 305 ILE cc_start: 0.8429 (tp) cc_final: 0.8168 (pt) REVERT: B 318 ASN cc_start: 0.7757 (t0) cc_final: 0.7425 (t0) REVERT: B 350 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6606 (tm) REVERT: B 355 SER cc_start: 0.8407 (m) cc_final: 0.8004 (p) REVERT: B 361 TYR cc_start: 0.8450 (t80) cc_final: 0.7611 (t80) REVERT: B 385 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.7792 (m-80) REVERT: B 394 PHE cc_start: 0.8304 (t80) cc_final: 0.7650 (t80) REVERT: B 398 PHE cc_start: 0.7222 (m-80) cc_final: 0.6716 (m-80) REVERT: B 414 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6808 (tm-30) REVERT: B 475 ASN cc_start: 0.7708 (t0) cc_final: 0.6939 (t0) REVERT: B 478 ASP cc_start: 0.6858 (m-30) cc_final: 0.6638 (m-30) REVERT: B 556 TYR cc_start: 0.8702 (p90) cc_final: 0.8219 (p90) REVERT: B 573 ASP cc_start: 0.7340 (t0) cc_final: 0.6941 (t0) REVERT: B 580 LYS cc_start: 0.7711 (mmtt) cc_final: 0.7298 (mmmm) REVERT: B 668 LEU cc_start: 0.6544 (mt) cc_final: 0.6333 (mt) REVERT: B 687 ASP cc_start: 0.7666 (t0) cc_final: 0.7371 (t0) REVERT: B 717 ARG cc_start: 0.8464 (ttm-80) cc_final: 0.8071 (ttm170) outliers start: 45 outliers final: 23 residues processed: 339 average time/residue: 0.2714 time to fit residues: 122.5045 Evaluate side-chains 319 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 289 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 46 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 280 ILE 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 390 ILE 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 21 THR 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 153 LEU Chi-restraints excluded: chain B residue 198 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 405 THR Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 160 HIS A 413 GLN A 514 GLN 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10400 Z= 0.263 Angle : 0.623 9.347 14136 Z= 0.320 Chirality : 0.043 0.174 1718 Planarity : 0.004 0.051 1758 Dihedral : 5.278 55.419 1434 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.20 % Favored : 93.72 % Rotamer: Outliers : 4.10 % Allowed : 16.49 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.24), residues: 1322 helix: 0.33 (0.18), residues: 886 sheet: -2.15 (0.91), residues: 36 loop : -2.65 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 482 HIS 0.009 0.001 HIS B 656 PHE 0.021 0.001 PHE A 130 TYR 0.024 0.002 TYR A 361 ARG 0.007 0.001 ARG B 38 *********************** 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 334 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 288 time to evaluate : 1.230 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: 0.8699 (OUTLIER) cc_final: 0.8425 (p) REVERT: A 66 LYS cc_start: 0.8614 (tppt) cc_final: 0.8295 (tptp) REVERT: A 258 ILE cc_start: 0.8623 (mm) cc_final: 0.8348 (mm) REVERT: A 303 GLU cc_start: 0.7420 (mp0) cc_final: 0.7092 (mp0) REVERT: A 314 SER cc_start: 0.8845 (t) cc_final: 0.8536 (p) REVERT: A 318 ASN cc_start: 0.7768 (t0) cc_final: 0.7383 (t0) REVERT: A 361 TYR cc_start: 0.8177 (t80) cc_final: 0.7653 (t80) REVERT: A 369 LYS cc_start: 0.7899 (mmtt) cc_final: 0.7520 (mmpt) REVERT: A 371 TYR cc_start: 0.8091 (m-80) cc_final: 0.7671 (m-80) REVERT: A 377 TYR cc_start: 0.7222 (p90) cc_final: 0.6988 (p90) REVERT: A 394 PHE cc_start: 0.8329 (t80) cc_final: 0.7527 (t80) REVERT: A 398 PHE cc_start: 0.6790 (m-80) cc_final: 0.6404 (m-80) REVERT: A 413 GLN cc_start: 0.6160 (pt0) cc_final: 0.5938 (pt0) REVERT: A 432 MET cc_start: 0.7758 (tpt) cc_final: 0.7368 (tpp) REVERT: A 436 VAL cc_start: 0.8573 (p) cc_final: 0.8297 (m) REVERT: A 486 CYS cc_start: 0.8411 (t) cc_final: 0.8112 (t) REVERT: A 569 THR cc_start: 0.8771 (t) cc_final: 0.8373 (m) REVERT: A 573 ASP cc_start: 0.7329 (t0) cc_final: 0.7118 (t0) REVERT: A 580 LYS cc_start: 0.7799 (mmtt) cc_final: 0.7365 (mmmm) REVERT: B 21 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8354 (p) REVERT: B 23 SER cc_start: 0.8692 (OUTLIER) cc_final: 0.8321 (p) REVERT: B 38 ARG cc_start: 0.7958 (mtp-110) cc_final: 0.7757 (mtp85) REVERT: B 66 LYS cc_start: 0.8676 (tppt) cc_final: 0.8385 (tppt) REVERT: B 87 ASP cc_start: 0.7619 (m-30) cc_final: 0.7009 (m-30) REVERT: B 122 PHE cc_start: 0.8192 (m-80) cc_final: 0.7976 (m-80) REVERT: B 153 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8314 (mt) REVERT: B 246 ASN cc_start: 0.8298 (p0) cc_final: 0.8069 (p0) REVERT: B 259 GLU cc_start: 0.8052 (tt0) cc_final: 0.7775 (mt-10) REVERT: B 268 ASN cc_start: 0.8411 (t0) cc_final: 0.7857 (t0) REVERT: B 271 ASP cc_start: 0.7690 (m-30) cc_final: 0.7472 (m-30) REVERT: B 289 ASN cc_start: 0.8257 (t0) cc_final: 0.7901 (t0) REVERT: B 303 GLU cc_start: 0.7354 (mp0) cc_final: 0.7069 (mp0) REVERT: B 305 ILE cc_start: 0.8425 (tp) cc_final: 0.8153 (pt) REVERT: B 318 ASN cc_start: 0.7867 (t0) cc_final: 0.7455 (t0) REVERT: B 361 TYR cc_start: 0.8431 (t80) cc_final: 0.7569 (t80) REVERT: B 369 LYS cc_start: 0.8357 (mmtt) cc_final: 0.8030 (mmtt) REVERT: B 384 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7246 (mm-30) REVERT: B 385 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7744 (m-80) REVERT: B 394 PHE cc_start: 0.8297 (t80) cc_final: 0.7584 (t80) REVERT: B 398 PHE cc_start: 0.7169 (m-80) cc_final: 0.6684 (m-80) REVERT: B 414 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6783 (tm-30) REVERT: B 573 ASP cc_start: 0.7339 (t0) cc_final: 0.7032 (t0) REVERT: B 580 LYS cc_start: 0.7721 (mmtt) cc_final: 0.7303 (mmmm) REVERT: B 668 LEU cc_start: 0.6269 (mt) cc_final: 0.6050 (mt) REVERT: B 687 ASP cc_start: 0.7666 (t0) cc_final: 0.7379 (t0) REVERT: B 717 ARG cc_start: 0.8467 (ttm-80) cc_final: 0.8024 (ttm170) outliers start: 46 outliers final: 30 residues processed: 313 average time/residue: 0.2752 time to fit residues: 113.9592 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 : 1.200 ------------------------------------------------------------------------------- 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 103 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 350 LEU 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 703 MET Chi-restraints excluded: chain B residue 21 THR 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 153 LEU Chi-restraints excluded: chain B residue 198 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 399 SER 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 678 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 95 optimal weight: 0.0970 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 0.0970 chunk 88 optimal weight: 0.0270 chunk 0 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 0.3834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS B 160 HIS B 656 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10400 Z= 0.196 Angle : 0.590 8.720 14136 Z= 0.303 Chirality : 0.042 0.160 1718 Planarity : 0.004 0.047 1758 Dihedral : 5.054 55.393 1432 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.05 % Favored : 93.87 % Rotamer: Outliers : 4.37 % Allowed : 16.76 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.24), residues: 1322 helix: 0.56 (0.18), residues: 886 sheet: -2.07 (0.90), residues: 36 loop : -2.52 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 482 HIS 0.009 0.001 HIS B 656 PHE 0.025 0.001 PHE A 385 TYR 0.023 0.002 TYR A 361 ARG 0.008 0.000 ARG B 714 *********************** 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 341 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 292 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8411 (p) REVERT: A 66 LYS cc_start: 0.8554 (tppt) cc_final: 0.8239 (tptp) REVERT: A 268 ASN cc_start: 0.8188 (t0) cc_final: 0.7720 (t0) REVERT: A 303 GLU cc_start: 0.7379 (mp0) cc_final: 0.7030 (mp0) REVERT: A 314 SER cc_start: 0.8823 (t) cc_final: 0.8519 (p) REVERT: A 318 ASN cc_start: 0.7785 (t0) cc_final: 0.7310 (t0) REVERT: A 321 LYS cc_start: 0.7827 (ttpp) cc_final: 0.7471 (ttpp) REVERT: A 348 ASP cc_start: 0.5505 (OUTLIER) cc_final: 0.4395 (p0) REVERT: A 369 LYS cc_start: 0.7932 (mmtt) cc_final: 0.7562 (mmpt) REVERT: A 371 TYR cc_start: 0.7988 (m-80) cc_final: 0.7640 (m-80) REVERT: A 377 TYR cc_start: 0.7184 (p90) cc_final: 0.6864 (p90) REVERT: A 394 PHE cc_start: 0.8322 (t80) cc_final: 0.7601 (t80) REVERT: A 398 PHE cc_start: 0.6695 (m-80) cc_final: 0.6325 (m-80) REVERT: A 413 GLN cc_start: 0.6002 (pt0) cc_final: 0.5680 (pt0) REVERT: A 432 MET cc_start: 0.7764 (tpt) cc_final: 0.7376 (tpp) REVERT: A 436 VAL cc_start: 0.8580 (p) cc_final: 0.8312 (m) REVERT: A 486 CYS cc_start: 0.8399 (t) cc_final: 0.8077 (t) REVERT: A 569 THR cc_start: 0.8752 (t) cc_final: 0.8360 (m) REVERT: A 573 ASP cc_start: 0.7341 (t0) cc_final: 0.7051 (t0) REVERT: A 580 LYS cc_start: 0.7802 (mmtt) cc_final: 0.7353 (mmmm) REVERT: A 717 ARG cc_start: 0.8640 (ttm-80) cc_final: 0.8209 (ttm170) REVERT: B 21 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8262 (p) REVERT: B 23 SER cc_start: 0.8637 (OUTLIER) cc_final: 0.8281 (p) REVERT: B 87 ASP cc_start: 0.7560 (m-30) cc_final: 0.7127 (m-30) REVERT: B 122 PHE cc_start: 0.8191 (m-80) cc_final: 0.7986 (m-80) REVERT: B 153 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8291 (mt) REVERT: B 188 LEU cc_start: 0.7652 (tp) cc_final: 0.7367 (tp) REVERT: B 246 ASN cc_start: 0.8305 (p0) cc_final: 0.8075 (p0) REVERT: B 259 GLU cc_start: 0.8041 (tt0) cc_final: 0.7727 (mt-10) REVERT: B 268 ASN cc_start: 0.8390 (t0) cc_final: 0.7969 (t0) REVERT: B 289 ASN cc_start: 0.8264 (t0) cc_final: 0.7898 (t0) REVERT: B 303 GLU cc_start: 0.7322 (mp0) cc_final: 0.7046 (mp0) REVERT: B 305 ILE cc_start: 0.8389 (tp) cc_final: 0.8122 (pt) REVERT: B 318 ASN cc_start: 0.7841 (t0) cc_final: 0.7362 (t0) REVERT: B 361 TYR cc_start: 0.8442 (t80) cc_final: 0.7633 (t80) REVERT: B 384 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7223 (mm-30) REVERT: B 385 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7744 (m-80) REVERT: B 394 PHE cc_start: 0.8286 (t80) cc_final: 0.7686 (t80) REVERT: B 398 PHE cc_start: 0.7050 (m-80) cc_final: 0.6721 (m-80) REVERT: B 414 GLU cc_start: 0.7066 (tm-30) cc_final: 0.6718 (tm-30) REVERT: B 492 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8715 (pp) REVERT: B 573 ASP cc_start: 0.7325 (t0) cc_final: 0.7073 (t0) REVERT: B 580 LYS cc_start: 0.7708 (mmtt) cc_final: 0.7296 (mmmm) REVERT: B 668 LEU cc_start: 0.6092 (mt) cc_final: 0.5581 (mm) REVERT: B 687 ASP cc_start: 0.7659 (t0) cc_final: 0.7342 (t0) REVERT: B 717 ARG cc_start: 0.8490 (ttm-80) cc_final: 0.8009 (ttm170) outliers start: 49 outliers final: 30 residues processed: 319 average time/residue: 0.2935 time to fit residues: 122.1495 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 : 1.254 ------------------------------------------------------------------------------- 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 103 MET Chi-restraints excluded: chain A residue 138 VAL 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 386 ILE Chi-restraints excluded: chain A residue 473 LYS 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 21 THR 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 153 LEU Chi-restraints excluded: chain B residue 198 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 405 THR Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 541 GLU 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 114 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 127 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 728 HIS B 135 HIS B 160 HIS B 656 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3616 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= 0.264 Angle : 0.623 8.132 14136 Z= 0.320 Chirality : 0.043 0.166 1718 Planarity : 0.004 0.051 1758 Dihedral : 5.107 55.915 1432 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.43 % Favored : 93.49 % Rotamer: Outliers : 4.99 % Allowed : 17.65 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.24), residues: 1322 helix: 0.58 (0.18), residues: 890 sheet: -1.98 (0.90), residues: 36 loop : -2.47 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 518 HIS 0.006 0.001 HIS B 656 PHE 0.021 0.001 PHE A 385 TYR 0.045 0.002 TYR A 361 ARG 0.008 0.001 ARG A 38 *********************** 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 345 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 289 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8455 (p) REVERT: A 66 LYS cc_start: 0.8578 (tppt) cc_final: 0.8257 (tptp) REVERT: A 268 ASN cc_start: 0.8221 (t0) cc_final: 0.7624 (t0) REVERT: A 271 ASP cc_start: 0.7651 (m-30) cc_final: 0.7366 (m-30) REVERT: A 303 GLU cc_start: 0.7379 (mp0) cc_final: 0.7032 (mp0) REVERT: A 314 SER cc_start: 0.8842 (t) cc_final: 0.8530 (p) REVERT: A 318 ASN cc_start: 0.7879 (t0) cc_final: 0.7426 (t0) REVERT: A 348 ASP cc_start: 0.5580 (OUTLIER) cc_final: 0.4175 (p0) REVERT: A 369 LYS cc_start: 0.8014 (mmtt) cc_final: 0.7582 (mmtt) REVERT: A 371 TYR cc_start: 0.8040 (m-80) cc_final: 0.7687 (m-80) REVERT: A 377 TYR cc_start: 0.7284 (p90) cc_final: 0.6983 (p90) REVERT: A 394 PHE cc_start: 0.8312 (t80) cc_final: 0.7588 (t80) REVERT: A 398 PHE cc_start: 0.6787 (m-80) cc_final: 0.6404 (m-80) REVERT: A 432 MET cc_start: 0.7781 (tpt) cc_final: 0.7332 (tpp) REVERT: A 436 VAL cc_start: 0.8609 (p) cc_final: 0.8328 (m) REVERT: A 486 CYS cc_start: 0.8415 (t) cc_final: 0.8096 (t) REVERT: A 569 THR cc_start: 0.8776 (t) cc_final: 0.8388 (m) REVERT: A 573 ASP cc_start: 0.7369 (t0) cc_final: 0.7134 (t0) REVERT: A 580 LYS cc_start: 0.7828 (mmtt) cc_final: 0.7387 (mmmm) REVERT: A 717 ARG cc_start: 0.8628 (ttm-80) cc_final: 0.8202 (ttm170) REVERT: B 21 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8355 (p) REVERT: B 87 ASP cc_start: 0.7594 (m-30) cc_final: 0.7245 (m-30) REVERT: B 122 PHE cc_start: 0.8194 (m-80) cc_final: 0.7976 (m-80) REVERT: B 246 ASN cc_start: 0.8295 (p0) cc_final: 0.8056 (p0) REVERT: B 259 GLU cc_start: 0.8094 (tt0) cc_final: 0.7747 (mt-10) REVERT: B 289 ASN cc_start: 0.8286 (t0) cc_final: 0.7889 (t0) REVERT: B 303 GLU cc_start: 0.7336 (mp0) cc_final: 0.7035 (mp0) REVERT: B 305 ILE cc_start: 0.8409 (tp) cc_final: 0.8153 (pt) REVERT: B 318 ASN cc_start: 0.7920 (t0) cc_final: 0.7424 (t0) REVERT: B 361 TYR cc_start: 0.8480 (t80) cc_final: 0.7588 (t80) REVERT: B 369 LYS cc_start: 0.8327 (mmtt) cc_final: 0.8022 (mmtt) REVERT: B 384 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7196 (mm-30) REVERT: B 385 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7729 (m-80) REVERT: B 394 PHE cc_start: 0.8271 (t80) cc_final: 0.7640 (t80) REVERT: B 398 PHE cc_start: 0.7108 (m-80) cc_final: 0.6748 (m-80) REVERT: B 414 GLU cc_start: 0.6968 (tm-30) cc_final: 0.6596 (tm-30) REVERT: B 492 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8776 (pp) REVERT: B 573 ASP cc_start: 0.7321 (t0) cc_final: 0.6994 (t0) REVERT: B 580 LYS cc_start: 0.7728 (mmtt) cc_final: 0.7320 (mmmm) REVERT: B 687 ASP cc_start: 0.7637 (t0) cc_final: 0.7334 (t0) REVERT: B 717 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.8015 (ttm170) outliers start: 56 outliers final: 32 residues processed: 320 average time/residue: 0.2940 time to fit residues: 123.4510 Evaluate side-chains 328 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 291 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 68 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 162 LEU 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 473 LYS Chi-restraints excluded: chain A residue 496 LEU 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 21 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 198 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 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 529 ILE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 695 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 78 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS B 160 HIS B 656 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10400 Z= 0.288 Angle : 0.647 8.613 14136 Z= 0.331 Chirality : 0.044 0.161 1718 Planarity : 0.005 0.053 1758 Dihedral : 5.210 56.674 1432 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.35 % Favored : 93.57 % Rotamer: Outliers : 4.46 % Allowed : 18.36 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.24), residues: 1322 helix: 0.60 (0.18), residues: 890 sheet: -1.92 (0.89), residues: 36 loop : -2.40 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 74 HIS 0.007 0.001 HIS B 656 PHE 0.026 0.001 PHE B 130 TYR 0.049 0.002 TYR A 361 ARG 0.009 0.001 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 283 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8570 (t) REVERT: A 66 LYS cc_start: 0.8617 (tppt) cc_final: 0.8260 (tptp) REVERT: A 268 ASN cc_start: 0.8236 (t0) cc_final: 0.7573 (t0) REVERT: A 271 ASP cc_start: 0.7678 (m-30) cc_final: 0.7341 (m-30) REVERT: A 303 GLU cc_start: 0.7402 (mp0) cc_final: 0.7037 (mp0) REVERT: A 314 SER cc_start: 0.8849 (t) cc_final: 0.8521 (p) REVERT: A 318 ASN cc_start: 0.7947 (t0) cc_final: 0.7563 (t0) REVERT: A 348 ASP cc_start: 0.5643 (OUTLIER) cc_final: 0.4532 (p0) REVERT: A 369 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7595 (mmtt) REVERT: A 371 TYR cc_start: 0.8050 (m-80) cc_final: 0.7742 (m-80) REVERT: A 377 TYR cc_start: 0.7367 (p90) cc_final: 0.7143 (p90) REVERT: A 394 PHE cc_start: 0.8305 (t80) cc_final: 0.7602 (t80) REVERT: A 398 PHE cc_start: 0.6798 (m-80) cc_final: 0.6394 (m-80) REVERT: A 432 MET cc_start: 0.7859 (tpt) cc_final: 0.7405 (tpp) REVERT: A 436 VAL cc_start: 0.8636 (p) cc_final: 0.8364 (m) REVERT: A 441 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.6388 (tp) REVERT: A 486 CYS cc_start: 0.8422 (t) cc_final: 0.8107 (t) REVERT: A 569 THR cc_start: 0.8760 (t) cc_final: 0.8367 (m) REVERT: A 573 ASP cc_start: 0.7411 (t0) cc_final: 0.7168 (t0) REVERT: A 580 LYS cc_start: 0.7847 (mmtt) cc_final: 0.7424 (mmmm) REVERT: A 674 ARG cc_start: 0.7711 (mtm-85) cc_final: 0.7435 (mtm180) REVERT: B 21 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8526 (t) REVERT: B 66 LYS cc_start: 0.8661 (tppt) cc_final: 0.8429 (tppt) REVERT: B 71 ILE cc_start: 0.8499 (tt) cc_final: 0.8254 (tp) REVERT: B 87 ASP cc_start: 0.7685 (m-30) cc_final: 0.7393 (m-30) REVERT: B 122 PHE cc_start: 0.8203 (m-80) cc_final: 0.7991 (m-80) REVERT: B 246 ASN cc_start: 0.8301 (p0) cc_final: 0.8051 (p0) REVERT: B 259 GLU cc_start: 0.8116 (tt0) cc_final: 0.7762 (mt-10) REVERT: B 268 ASN cc_start: 0.8371 (t0) cc_final: 0.7956 (t0) REVERT: B 289 ASN cc_start: 0.8282 (t0) cc_final: 0.7882 (t0) REVERT: B 303 GLU cc_start: 0.7345 (mp0) cc_final: 0.7049 (mp0) REVERT: B 305 ILE cc_start: 0.8424 (tp) cc_final: 0.8175 (pt) REVERT: B 318 ASN cc_start: 0.7942 (t0) cc_final: 0.7419 (t0) REVERT: B 336 LEU cc_start: 0.8005 (pt) cc_final: 0.7798 (pp) REVERT: B 355 SER cc_start: 0.8273 (m) cc_final: 0.7920 (p) REVERT: B 361 TYR cc_start: 0.8503 (t80) cc_final: 0.7998 (t80) REVERT: B 369 LYS cc_start: 0.8349 (mmtt) cc_final: 0.8043 (mmtt) REVERT: B 384 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7159 (mm-30) REVERT: B 394 PHE cc_start: 0.8259 (t80) cc_final: 0.7624 (t80) REVERT: B 398 PHE cc_start: 0.7094 (m-80) cc_final: 0.6711 (m-80) REVERT: B 414 GLU cc_start: 0.6947 (tm-30) cc_final: 0.6581 (tm-30) REVERT: B 492 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8767 (pp) REVERT: B 573 ASP cc_start: 0.7388 (t0) cc_final: 0.7161 (t0) REVERT: B 580 LYS cc_start: 0.7738 (mmtt) cc_final: 0.7329 (mmmm) REVERT: B 687 ASP cc_start: 0.7655 (t0) cc_final: 0.7332 (t0) REVERT: B 717 ARG cc_start: 0.8478 (ttm-80) cc_final: 0.7979 (ttm170) outliers start: 50 outliers final: 32 residues processed: 309 average time/residue: 0.2978 time to fit residues: 124.5058 Evaluate side-chains 325 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 288 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 68 LEU Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 162 LEU 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 441 LEU Chi-restraints excluded: chain A residue 473 LYS 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 21 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 114 GLN 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 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 399 SER 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 529 ILE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 695 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.0670 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 80 optimal weight: 0.4980 chunk 86 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 115 optimal weight: 0.3980 chunk 121 optimal weight: 0.9980 chunk 111 optimal weight: 0.2980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS B 160 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10400 Z= 0.199 Angle : 0.617 10.028 14136 Z= 0.314 Chirality : 0.042 0.148 1718 Planarity : 0.004 0.048 1758 Dihedral : 5.168 56.882 1432 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.43 % Favored : 93.49 % Rotamer: Outliers : 4.37 % Allowed : 19.25 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.24), residues: 1322 helix: 0.79 (0.18), residues: 874 sheet: -1.92 (0.89), residues: 36 loop : -2.25 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 482 HIS 0.004 0.001 HIS A 656 PHE 0.017 0.001 PHE A 385 TYR 0.055 0.002 TYR A 361 ARG 0.009 0.001 ARG B 38 *********************** 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 349 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 300 time to evaluate : 1.267 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: 0.8823 (OUTLIER) cc_final: 0.8431 (p) REVERT: A 66 LYS cc_start: 0.8559 (tppt) cc_final: 0.8204 (tptp) REVERT: A 268 ASN cc_start: 0.8217 (t0) cc_final: 0.7599 (t0) REVERT: A 271 ASP cc_start: 0.7652 (m-30) cc_final: 0.7323 (m-30) REVERT: A 303 GLU cc_start: 0.7396 (mp0) cc_final: 0.7026 (mp0) REVERT: A 314 SER cc_start: 0.8833 (t) cc_final: 0.8509 (p) REVERT: A 318 ASN cc_start: 0.7940 (t0) cc_final: 0.7573 (t0) REVERT: A 348 ASP cc_start: 0.5554 (OUTLIER) cc_final: 0.4102 (p0) REVERT: A 369 LYS cc_start: 0.8039 (mmtt) cc_final: 0.7484 (mmtt) REVERT: A 371 TYR cc_start: 0.7952 (m-80) cc_final: 0.7660 (m-80) REVERT: A 377 TYR cc_start: 0.7249 (p90) cc_final: 0.7002 (p90) REVERT: A 394 PHE cc_start: 0.8321 (t80) cc_final: 0.7627 (t80) REVERT: A 398 PHE cc_start: 0.6715 (m-80) cc_final: 0.6332 (m-80) REVERT: A 413 GLN cc_start: 0.6065 (pt0) cc_final: 0.5773 (pt0) REVERT: A 432 MET cc_start: 0.7798 (tpt) cc_final: 0.7332 (tpp) REVERT: A 436 VAL cc_start: 0.8642 (p) cc_final: 0.8363 (m) REVERT: A 486 CYS cc_start: 0.8412 (t) cc_final: 0.8103 (t) REVERT: A 569 THR cc_start: 0.8728 (t) cc_final: 0.8354 (m) REVERT: A 573 ASP cc_start: 0.7366 (t0) cc_final: 0.7112 (t0) REVERT: A 580 LYS cc_start: 0.7848 (mmtt) cc_final: 0.7415 (mmmm) REVERT: A 717 ARG cc_start: 0.8598 (ttm-80) cc_final: 0.8192 (ttm170) REVERT: B 21 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8313 (p) REVERT: B 66 LYS cc_start: 0.8646 (tppt) cc_final: 0.8386 (tppt) REVERT: B 71 ILE cc_start: 0.8474 (tt) cc_final: 0.8246 (tp) REVERT: B 87 ASP cc_start: 0.7667 (m-30) cc_final: 0.7392 (m-30) REVERT: B 122 PHE cc_start: 0.8187 (m-80) cc_final: 0.7978 (m-80) REVERT: B 246 ASN cc_start: 0.8288 (p0) cc_final: 0.8047 (p0) REVERT: B 259 GLU cc_start: 0.8099 (tt0) cc_final: 0.7834 (mt-10) REVERT: B 289 ASN cc_start: 0.8222 (t0) cc_final: 0.7818 (t0) REVERT: B 303 GLU cc_start: 0.7302 (mp0) cc_final: 0.7095 (mp0) REVERT: B 305 ILE cc_start: 0.8383 (tp) cc_final: 0.8132 (pt) REVERT: B 318 ASN cc_start: 0.7942 (t0) cc_final: 0.7452 (t0) REVERT: B 361 TYR cc_start: 0.8450 (t80) cc_final: 0.7604 (t80) REVERT: B 369 LYS cc_start: 0.8285 (mmtt) cc_final: 0.7984 (mmtt) REVERT: B 384 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7373 (mm-30) REVERT: B 385 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.7752 (m-80) REVERT: B 394 PHE cc_start: 0.8239 (t80) cc_final: 0.7716 (t80) REVERT: B 398 PHE cc_start: 0.7037 (m-80) cc_final: 0.6796 (m-80) REVERT: B 414 GLU cc_start: 0.6902 (tm-30) cc_final: 0.6563 (tm-30) REVERT: B 492 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8768 (pp) REVERT: B 573 ASP cc_start: 0.7354 (t0) cc_final: 0.7129 (t0) REVERT: B 580 LYS cc_start: 0.7729 (mmtt) cc_final: 0.7313 (mmmm) REVERT: B 687 ASP cc_start: 0.7647 (t0) cc_final: 0.7331 (t0) REVERT: B 717 ARG cc_start: 0.8451 (ttm-80) cc_final: 0.7942 (ttm170) outliers start: 49 outliers final: 32 residues processed: 325 average time/residue: 0.2997 time to fit residues: 128.3600 Evaluate side-chains 325 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 288 time to evaluate : 2.043 ------------------------------------------------------------------------------- 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 103 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 287 GLU 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 473 LYS Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 21 THR 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 114 GLN 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 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 463 MET 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 678 MET Chi-restraints excluded: chain B residue 695 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 51 optimal weight: 0.0050 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS B 160 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10400 Z= 0.250 Angle : 0.651 9.690 14136 Z= 0.332 Chirality : 0.044 0.182 1718 Planarity : 0.005 0.051 1758 Dihedral : 4.964 52.214 1430 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.81 % Favored : 93.12 % Rotamer: Outliers : 4.28 % Allowed : 20.14 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.24), residues: 1322 helix: 0.81 (0.18), residues: 870 sheet: -1.81 (0.88), residues: 36 loop : -2.23 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 74 HIS 0.005 0.001 HIS B 723 PHE 0.026 0.001 PHE B 130 TYR 0.054 0.002 TYR A 361 ARG 0.012 0.001 ARG A 586 *********************** 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 343 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 295 time to evaluate : 1.571 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: 0.8850 (OUTLIER) cc_final: 0.8580 (t) REVERT: A 66 LYS cc_start: 0.8569 (tppt) cc_final: 0.8214 (tptp) REVERT: A 268 ASN cc_start: 0.8208 (t0) cc_final: 0.7534 (t0) REVERT: A 271 ASP cc_start: 0.7667 (m-30) cc_final: 0.7315 (m-30) REVERT: A 303 GLU cc_start: 0.7414 (mp0) cc_final: 0.7038 (mp0) REVERT: A 314 SER cc_start: 0.8843 (t) cc_final: 0.8520 (p) REVERT: A 318 ASN cc_start: 0.7967 (t0) cc_final: 0.7602 (t0) REVERT: A 348 ASP cc_start: 0.5622 (OUTLIER) cc_final: 0.4163 (p0) REVERT: A 366 SER cc_start: 0.8722 (t) cc_final: 0.8360 (p) REVERT: A 369 LYS cc_start: 0.8064 (mmtt) cc_final: 0.7516 (mmtt) REVERT: A 371 TYR cc_start: 0.7972 (m-80) cc_final: 0.7701 (m-80) REVERT: A 377 TYR cc_start: 0.7323 (p90) cc_final: 0.7051 (p90) REVERT: A 413 GLN cc_start: 0.5951 (pt0) cc_final: 0.5629 (pt0) REVERT: A 432 MET cc_start: 0.7813 (tpt) cc_final: 0.7352 (tpp) REVERT: A 436 VAL cc_start: 0.8657 (p) cc_final: 0.8379 (m) REVERT: A 486 CYS cc_start: 0.8408 (t) cc_final: 0.8117 (t) REVERT: A 569 THR cc_start: 0.8737 (t) cc_final: 0.8362 (m) REVERT: A 573 ASP cc_start: 0.7373 (t0) cc_final: 0.7122 (t0) REVERT: A 580 LYS cc_start: 0.7841 (mmtt) cc_final: 0.7402 (mmmm) REVERT: A 587 ARG cc_start: 0.8122 (tpp80) cc_final: 0.7873 (tpp80) REVERT: A 695 LEU cc_start: 0.8005 (mm) cc_final: 0.7673 (mm) REVERT: A 717 ARG cc_start: 0.8554 (ttm-80) cc_final: 0.8115 (ttm170) REVERT: B 21 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8362 (p) REVERT: B 66 LYS cc_start: 0.8666 (tppt) cc_final: 0.8432 (tppt) REVERT: B 71 ILE cc_start: 0.8468 (tt) cc_final: 0.8251 (tp) REVERT: B 87 ASP cc_start: 0.7681 (m-30) cc_final: 0.7425 (m-30) REVERT: B 122 PHE cc_start: 0.8195 (m-80) cc_final: 0.7979 (m-80) REVERT: B 246 ASN cc_start: 0.8290 (p0) cc_final: 0.8047 (p0) REVERT: B 259 GLU cc_start: 0.8123 (tt0) cc_final: 0.7841 (mt-10) REVERT: B 289 ASN cc_start: 0.8221 (t0) cc_final: 0.7801 (t0) REVERT: B 303 GLU cc_start: 0.7326 (mp0) cc_final: 0.7031 (mp0) REVERT: B 305 ILE cc_start: 0.8412 (tp) cc_final: 0.8159 (pt) REVERT: B 318 ASN cc_start: 0.7974 (t0) cc_final: 0.7460 (t0) REVERT: B 361 TYR cc_start: 0.8460 (t80) cc_final: 0.7592 (t80) REVERT: B 369 LYS cc_start: 0.8300 (mmtt) cc_final: 0.8022 (mmtt) REVERT: B 384 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7368 (mm-30) REVERT: B 385 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7699 (m-80) REVERT: B 394 PHE cc_start: 0.8246 (t80) cc_final: 0.7723 (t80) REVERT: B 398 PHE cc_start: 0.7049 (m-80) cc_final: 0.6806 (m-80) REVERT: B 414 GLU cc_start: 0.6891 (tm-30) cc_final: 0.6566 (tm-30) REVERT: B 573 ASP cc_start: 0.7360 (t0) cc_final: 0.7138 (t0) REVERT: B 580 LYS cc_start: 0.7735 (mmtt) cc_final: 0.7318 (mmmm) REVERT: B 687 ASP cc_start: 0.7654 (t0) cc_final: 0.7333 (t0) REVERT: B 717 ARG cc_start: 0.8471 (ttm-80) cc_final: 0.7958 (ttm170) outliers start: 48 outliers final: 36 residues processed: 322 average time/residue: 0.3143 time to fit residues: 133.2754 Evaluate side-chains 331 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 291 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 103 MET Chi-restraints excluded: chain A residue 138 VAL 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 473 LYS Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 114 GLN 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 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 399 SER Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 463 MET 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 678 MET Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 727 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 80 optimal weight: 0.2980 chunk 64 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS B 160 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4029 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= 0.269 Angle : 0.668 11.273 14136 Z= 0.341 Chirality : 0.044 0.178 1718 Planarity : 0.005 0.052 1758 Dihedral : 5.056 54.220 1430 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.81 % Favored : 93.12 % Rotamer: Outliers : 3.92 % Allowed : 20.77 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.25), residues: 1322 helix: 0.78 (0.18), residues: 874 sheet: -1.77 (0.88), residues: 36 loop : -2.19 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 518 HIS 0.005 0.001 HIS B 723 PHE 0.021 0.001 PHE A 385 TYR 0.057 0.002 TYR A 361 ARG 0.012 0.001 ARG B 38 ********************** 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 337 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 293 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8613 (t) REVERT: A 66 LYS cc_start: 0.8571 (tppt) cc_final: 0.8226 (tptp) REVERT: A 203 PHE cc_start: 0.7924 (m-10) cc_final: 0.7603 (m-80) REVERT: A 268 ASN cc_start: 0.8205 (t0) cc_final: 0.7651 (t0) REVERT: A 271 ASP cc_start: 0.7681 (m-30) cc_final: 0.7275 (m-30) REVERT: A 303 GLU cc_start: 0.7422 (mp0) cc_final: 0.7042 (mp0) REVERT: A 314 SER cc_start: 0.8840 (t) cc_final: 0.8506 (p) REVERT: A 318 ASN cc_start: 0.7972 (t0) cc_final: 0.7592 (t0) REVERT: A 348 ASP cc_start: 0.5675 (OUTLIER) cc_final: 0.4210 (p0) REVERT: A 366 SER cc_start: 0.8746 (t) cc_final: 0.8361 (p) REVERT: A 369 LYS cc_start: 0.8072 (mmtt) cc_final: 0.7531 (mmtt) REVERT: A 371 TYR cc_start: 0.7988 (m-80) cc_final: 0.7695 (m-80) REVERT: A 377 TYR cc_start: 0.7356 (p90) cc_final: 0.7098 (p90) REVERT: A 394 PHE cc_start: 0.8241 (t80) cc_final: 0.7690 (t80) REVERT: A 413 GLN cc_start: 0.5969 (pt0) cc_final: 0.5542 (pt0) REVERT: A 432 MET cc_start: 0.7854 (tpt) cc_final: 0.7474 (tpp) REVERT: A 486 CYS cc_start: 0.8391 (t) cc_final: 0.8081 (t) REVERT: A 569 THR cc_start: 0.8733 (t) cc_final: 0.8357 (m) REVERT: A 573 ASP cc_start: 0.7381 (t0) cc_final: 0.7134 (t0) REVERT: A 580 LYS cc_start: 0.7844 (mmtt) cc_final: 0.7410 (mmmm) REVERT: A 587 ARG cc_start: 0.8041 (tpp80) cc_final: 0.7768 (tpp80) REVERT: A 695 LEU cc_start: 0.8017 (mm) cc_final: 0.7699 (mm) REVERT: A 717 ARG cc_start: 0.8552 (ttm-80) cc_final: 0.8113 (ttm170) REVERT: B 21 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8511 (t) REVERT: B 71 ILE cc_start: 0.8469 (tt) cc_final: 0.8240 (tp) REVERT: B 96 LEU cc_start: 0.8266 (mt) cc_final: 0.8000 (mm) REVERT: B 122 PHE cc_start: 0.8173 (m-80) cc_final: 0.7971 (m-80) REVERT: B 246 ASN cc_start: 0.8295 (p0) cc_final: 0.8046 (p0) REVERT: B 259 GLU cc_start: 0.8132 (tt0) cc_final: 0.7861 (mt-10) REVERT: B 268 ASN cc_start: 0.8393 (t0) cc_final: 0.7961 (t0) REVERT: B 303 GLU cc_start: 0.7341 (mp0) cc_final: 0.7043 (mp0) REVERT: B 305 ILE cc_start: 0.8410 (tp) cc_final: 0.8155 (pt) REVERT: B 318 ASN cc_start: 0.8004 (t0) cc_final: 0.7547 (t0) REVERT: B 361 TYR cc_start: 0.8463 (t80) cc_final: 0.7624 (t80) REVERT: B 369 LYS cc_start: 0.8310 (mmtt) cc_final: 0.8016 (mmtt) REVERT: B 384 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7191 (mm-30) REVERT: B 385 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7751 (m-80) REVERT: B 394 PHE cc_start: 0.8246 (t80) cc_final: 0.7750 (t80) REVERT: B 414 GLU cc_start: 0.6887 (tm-30) cc_final: 0.6521 (tm-30) REVERT: B 573 ASP cc_start: 0.7354 (t0) cc_final: 0.7141 (t0) REVERT: B 580 LYS cc_start: 0.7734 (mmtt) cc_final: 0.7322 (mmmm) REVERT: B 687 ASP cc_start: 0.7664 (t0) cc_final: 0.7340 (t0) REVERT: B 717 ARG cc_start: 0.8487 (ttm-80) cc_final: 0.7990 (ttm170) outliers start: 44 outliers final: 33 residues processed: 318 average time/residue: 0.2879 time to fit residues: 120.2496 Evaluate side-chains 328 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 291 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 103 MET Chi-restraints excluded: chain A residue 138 VAL 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 473 LYS Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 114 GLN 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 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 385 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 473 LYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 727 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.0770 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 75 optimal weight: 0.2980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS B 160 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.125117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.106673 restraints weight = 16471.370| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.41 r_work: 0.3307 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4068 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= 0.234 Angle : 0.668 10.917 14136 Z= 0.340 Chirality : 0.044 0.176 1718 Planarity : 0.005 0.050 1758 Dihedral : 5.125 56.400 1430 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.81 % Favored : 93.12 % Rotamer: Outliers : 3.74 % Allowed : 21.39 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1322 helix: 0.84 (0.18), residues: 874 sheet: -1.74 (0.88), residues: 36 loop : -2.16 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 482 HIS 0.006 0.001 HIS A 656 PHE 0.045 0.001 PHE A 385 TYR 0.035 0.002 TYR A 361 ARG 0.009 0.001 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3045.26 seconds wall clock time: 55 minutes 55.18 seconds (3355.18 seconds total)