Starting phenix.real_space_refine on Thu Jul 31 07:45:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cxi_45992/07_2025/9cxi_45992.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cxi_45992/07_2025/9cxi_45992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cxi_45992/07_2025/9cxi_45992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cxi_45992/07_2025/9cxi_45992.map" model { file = "/net/cci-nas-00/data/ceres_data/9cxi_45992/07_2025/9cxi_45992.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cxi_45992/07_2025/9cxi_45992.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 Mg 2 5.21 5 S 78 5.16 5 C 8516 2.51 5 N 2229 2.21 5 O 2474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13303 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6307 Classifications: {'peptide': 773} Link IDs: {'PTRANS': 31, 'TRANS': 741} Chain: "B" Number of atoms: 6306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6306 Classifications: {'peptide': 773} Link IDs: {'PTRANS': 31, 'TRANS': 741} Chain: "C" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 318 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 35} Chain breaks: 2 Chain: "D" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 322 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 36} Chain breaks: 2 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' MG': 1, ' ZN': 1, 'PCG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' MG': 1, ' ZN': 1, 'PCG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.46, per 1000 atoms: 0.64 Number of scatterers: 13303 At special positions: 0 Unit cell: (86.835, 125.704, 148.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 78 16.00 P 2 15.00 Mg 2 11.99 O 2474 8.00 N 2229 7.00 C 8516 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: 3.15 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 602 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 566 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 566 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 602 " 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3102 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 4 sheets defined 63.4% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 54 through 70 Processing helix chain 'A' and resid 75 through 92 removed outlier: 3.866A pdb=" N GLY A 79 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.796A pdb=" N ASN A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 150 removed outlier: 3.874A pdb=" N GLY A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 206 through 251 removed outlier: 4.237A pdb=" N PHE A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 removed outlier: 3.545A pdb=" N VAL A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 289 through 298 Proline residue: A 295 - end of helix Processing helix chain 'A' and resid 341 through 346 removed outlier: 4.637A pdb=" N SER A 346 " --> pdb=" O TRP A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 364 through 367 Processing helix chain 'A' and resid 415 through 432 Processing helix chain 'A' and resid 432 through 461 removed outlier: 3.885A pdb=" N THR A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 removed outlier: 3.710A pdb=" N ILE A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 478 removed outlier: 3.633A pdb=" N LYS A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 498 Processing helix chain 'A' and resid 517 through 532 removed outlier: 3.610A pdb=" N ILE A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.750A pdb=" N LYS A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 556 Processing helix chain 'A' and resid 563 through 580 Processing helix chain 'A' and resid 582 through 587 removed outlier: 4.033A pdb=" N LYS A 585 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR A 586 " --> pdb=" O LEU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 601 Processing helix chain 'A' and resid 610 through 618 Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 628 through 644 removed outlier: 4.017A pdb=" N ASP A 644 " --> pdb=" O THR A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 671 Processing helix chain 'A' and resid 673 through 693 removed outlier: 3.687A pdb=" N TYR A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N THR A 682 " --> pdb=" O PHE A 678 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N MET A 683 " --> pdb=" O LYS A 679 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 684 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN A 693 " --> pdb=" O ASP A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 707 removed outlier: 3.624A pdb=" N ALA A 700 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP A 707 " --> pdb=" O TYR A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 724 Processing helix chain 'A' and resid 725 through 729 Processing helix chain 'A' and resid 730 through 755 removed outlier: 4.220A pdb=" N GLN A 736 " --> pdb=" O GLU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 770 removed outlier: 3.683A pdb=" N ASP A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG A 766 " --> pdb=" O MET A 763 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN A 767 " --> pdb=" O MET A 764 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASP A 770 " --> pdb=" O ASN A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 783 Processing helix chain 'A' and resid 783 through 795 removed outlier: 4.159A pdb=" N VAL A 787 " --> pdb=" O VAL A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 823 removed outlier: 3.552A pdb=" N LEU A 802 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 819 " --> pdb=" O LEU A 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 68 Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 75 through 92 removed outlier: 3.985A pdb=" N GLY B 79 " --> pdb=" O THR B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 127 Processing helix chain 'B' and resid 140 through 150 removed outlier: 3.683A pdb=" N GLY B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 206 through 251 removed outlier: 3.910A pdb=" N PHE B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 273 removed outlier: 5.156A pdb=" N SER B 270 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N TYR B 271 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 298 Proline residue: B 295 - end of helix Processing helix chain 'B' and resid 341 through 346 removed outlier: 4.591A pdb=" N SER B 346 " --> pdb=" O TRP B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 356 Processing helix chain 'B' and resid 364 through 367 Processing helix chain 'B' and resid 415 through 461 removed outlier: 3.525A pdb=" N GLU B 419 " --> pdb=" O ASP B 415 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASN B 435 " --> pdb=" O TRP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 Processing helix chain 'B' and resid 472 through 478 removed outlier: 3.627A pdb=" N LYS B 476 " --> pdb=" O LYS B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 495 Processing helix chain 'B' and resid 502 through 506 removed outlier: 4.069A pdb=" N GLU B 505 " --> pdb=" O ARG B 502 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 506 " --> pdb=" O SER B 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 502 through 506' Processing helix chain 'B' and resid 517 through 532 Processing helix chain 'B' and resid 541 through 556 Processing helix chain 'B' and resid 563 through 580 Processing helix chain 'B' and resid 582 through 587 removed outlier: 3.798A pdb=" N LYS B 585 " --> pdb=" O ARG B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 601 Processing helix chain 'B' and resid 610 through 617 Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 628 through 644 removed outlier: 3.884A pdb=" N ASP B 644 " --> pdb=" O THR B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 671 Processing helix chain 'B' and resid 673 through 694 removed outlier: 5.390A pdb=" N THR B 682 " --> pdb=" O PHE B 678 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N MET B 683 " --> pdb=" O LYS B 679 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN B 693 " --> pdb=" O ASP B 689 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N MET B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 706 Processing helix chain 'B' and resid 707 through 724 Processing helix chain 'B' and resid 725 through 729 Processing helix chain 'B' and resid 730 through 757 Processing helix chain 'B' and resid 765 through 770 removed outlier: 4.993A pdb=" N ASP B 770 " --> pdb=" O ASN B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 783 Processing helix chain 'B' and resid 783 through 795 removed outlier: 4.077A pdb=" N VAL B 787 " --> pdb=" O VAL B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 823 removed outlier: 3.872A pdb=" N LEU B 802 " --> pdb=" O ILE B 798 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 39 removed outlier: 3.563A pdb=" N GLN C 37 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE C 38 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS C 39 " --> pdb=" O ARG C 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 34 through 39' Processing helix chain 'C' and resid 76 through 84 removed outlier: 4.490A pdb=" N GLU C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 85 removed outlier: 3.664A pdb=" N GLU D 80 " --> pdb=" O LEU D 76 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 137 removed outlier: 6.388A pdb=" N MET A 98 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU A 115 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS A 96 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL A 117 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ASP A 94 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ARG A 95 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL A 197 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU A 191 " --> pdb=" O CYS A 101 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N SER A 103 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 13.355A pdb=" N GLU A 189 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N VAL A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A 186 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 192 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 330 through 335 removed outlier: 3.731A pdb=" N LYS A 319 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL A 400 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 401 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 135 through 137 removed outlier: 6.426A pdb=" N MET B 98 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LEU B 115 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N CYS B 96 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL B 117 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ASP B 94 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ARG B 95 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL B 197 " --> pdb=" O ARG B 95 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU B 191 " --> pdb=" O CYS B 101 " (cutoff:3.500A) removed outlier: 11.640A pdb=" N SER B 103 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 14.054A pdb=" N GLU B 189 " --> pdb=" O SER B 103 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL B 190 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B 186 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA B 192 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 331 through 335 removed outlier: 3.683A pdb=" N LYS B 319 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL B 400 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY B 401 " --> pdb=" O ILE B 392 " (cutoff:3.500A) 766 hydrogen bonds defined for protein. 2223 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: 4.42 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2654 1.33 - 1.45: 3180 1.45 - 1.57: 7627 1.57 - 1.69: 8 1.69 - 1.81: 134 Bond restraints: 13603 Sorted by residual: bond pdb=" C6 PCG A 903 " pdb=" O6 PCG A 903 " ideal model delta sigma weight residual 1.219 1.337 -0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" C6 PCG B 903 " pdb=" O6 PCG B 903 " ideal model delta sigma weight residual 1.219 1.335 -0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" CA ALA A 594 " pdb=" CB ALA A 594 " ideal model delta sigma weight residual 1.529 1.471 0.058 1.58e-02 4.01e+03 1.35e+01 bond pdb=" CA SER A 121 " pdb=" CB SER A 121 " ideal model delta sigma weight residual 1.531 1.483 0.048 1.52e-02 4.33e+03 9.81e+00 bond pdb=" C2 PCG B 903 " pdb=" N3 PCG B 903 " ideal model delta sigma weight residual 1.311 1.371 -0.060 2.00e-02 2.50e+03 8.97e+00 ... (remaining 13598 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 18051 2.58 - 5.17: 293 5.17 - 7.75: 39 7.75 - 10.34: 10 10.34 - 12.92: 5 Bond angle restraints: 18398 Sorted by residual: angle pdb=" N TYR D 84 " pdb=" CA TYR D 84 " pdb=" CB TYR D 84 " ideal model delta sigma weight residual 110.46 101.32 9.14 1.57e+00 4.06e-01 3.39e+01 angle pdb=" C ASN A 458 " pdb=" N GLN A 459 " pdb=" CA GLN A 459 " ideal model delta sigma weight residual 120.58 111.03 9.55 1.71e+00 3.42e-01 3.12e+01 angle pdb=" N ASN A 458 " pdb=" CA ASN A 458 " pdb=" C ASN A 458 " ideal model delta sigma weight residual 111.71 105.57 6.14 1.15e+00 7.56e-01 2.85e+01 angle pdb=" N LEU D 81 " pdb=" CA LEU D 81 " pdb=" C LEU D 81 " ideal model delta sigma weight residual 111.71 105.58 6.13 1.15e+00 7.56e-01 2.85e+01 angle pdb=" CA PHE B 473 " pdb=" CB PHE B 473 " pdb=" CG PHE B 473 " ideal model delta sigma weight residual 113.80 118.57 -4.77 1.00e+00 1.00e+00 2.28e+01 ... (remaining 18393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7161 17.97 - 35.94: 774 35.94 - 53.91: 239 53.91 - 71.89: 58 71.89 - 89.86: 28 Dihedral angle restraints: 8260 sinusoidal: 3483 harmonic: 4777 Sorted by residual: dihedral pdb=" CA TYR A 406 " pdb=" C TYR A 406 " pdb=" N ASN A 407 " pdb=" CA ASN A 407 " ideal model delta harmonic sigma weight residual -180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" C GLU A 397 " pdb=" N GLU A 397 " pdb=" CA GLU A 397 " pdb=" CB GLU A 397 " ideal model delta harmonic sigma weight residual -122.60 -133.52 10.92 0 2.50e+00 1.60e-01 1.91e+01 dihedral pdb=" CA LEU B 217 " pdb=" C LEU B 217 " pdb=" N ASN B 218 " pdb=" CA ASN B 218 " ideal model delta harmonic sigma weight residual 180.00 159.05 20.95 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 8257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1694 0.062 - 0.123: 293 0.123 - 0.185: 27 0.185 - 0.247: 9 0.247 - 0.308: 5 Chirality restraints: 2028 Sorted by residual: chirality pdb=" C4' PCG B 903 " pdb=" C3' PCG B 903 " pdb=" C5' PCG B 903 " pdb=" O4' PCG B 903 " both_signs ideal model delta sigma weight residual False -2.50 -2.19 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA GLU A 397 " pdb=" N GLU A 397 " pdb=" C GLU A 397 " pdb=" CB GLU A 397 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CG LEU B 272 " pdb=" CB LEU B 272 " pdb=" CD1 LEU B 272 " pdb=" CD2 LEU B 272 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 2025 not shown) Planarity restraints: 2345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 455 " -0.023 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C MET A 455 " 0.078 2.00e-02 2.50e+03 pdb=" O MET A 455 " -0.029 2.00e-02 2.50e+03 pdb=" N LEU A 456 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 593 " 0.023 2.00e-02 2.50e+03 4.42e-02 1.95e+01 pdb=" C PHE A 593 " -0.076 2.00e-02 2.50e+03 pdb=" O PHE A 593 " 0.028 2.00e-02 2.50e+03 pdb=" N ALA A 594 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 85 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C GLN B 85 " 0.060 2.00e-02 2.50e+03 pdb=" O GLN B 85 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG B 86 " -0.020 2.00e-02 2.50e+03 ... (remaining 2342 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 79 2.56 - 3.14: 10353 3.14 - 3.73: 20642 3.73 - 4.31: 28566 4.31 - 4.90: 49095 Nonbonded interactions: 108735 Sorted by model distance: nonbonded pdb=" OD2 ASP B 603 " pdb="ZN ZN B 901 " model vdw 1.973 2.230 nonbonded pdb=" OD1 ASP B 723 " pdb="ZN ZN B 901 " model vdw 1.986 2.230 nonbonded pdb=" OD2 ASP A 723 " pdb="ZN ZN A 901 " model vdw 2.012 2.230 nonbonded pdb=" OD1 ASP A 723 " pdb="ZN ZN A 901 " model vdw 2.045 2.230 nonbonded pdb=" OD1 ASP A 603 " pdb="ZN ZN A 901 " model vdw 2.069 2.230 ... (remaining 108730 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' and (resid 53 through 823 or resid 901 through 903)) selection = (chain 'B' and (resid 53 through 823 or resid 901 through 903)) } ncs_group { reference = (chain 'C' and resid 26 through 87) selection = (chain 'D' and (resid 26 through 40 or resid 54 through 61 or resid 73 through 8 \ 7)) } 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: 2.720 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: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 34.730 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:13.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 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 : 0.007 0.283 13607 Z= 0.326 Angle : 0.796 12.919 18398 Z= 0.457 Chirality : 0.050 0.308 2028 Planarity : 0.005 0.053 2345 Dihedral : 17.498 89.858 5158 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.43 % Allowed : 18.14 % Favored : 80.42 % Cbeta Deviations : 0.13 % 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: 0.85 (0.21), residues: 1609 helix: 0.95 (0.17), residues: 901 sheet: -0.25 (0.43), residues: 137 loop : 0.38 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 564 HIS 0.009 0.001 HIS A 81 PHE 0.016 0.002 PHE B 213 TYR 0.018 0.002 TYR A 788 ARG 0.011 0.001 ARG B 82 Details of bonding type rmsd hydrogen bonds : bond 0.14563 ( 766) hydrogen bonds : angle 6.15908 ( 2223) metal coordination : bond 0.26571 ( 4) covalent geometry : bond 0.00556 (13603) covalent geometry : angle 0.79649 (18398) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 2.240 Fit side-chains REVERT: A 132 LYS cc_start: 0.8247 (mmmt) cc_final: 0.7834 (tptt) REVERT: A 207 LYS cc_start: 0.6358 (tptt) cc_final: 0.5812 (ttpp) REVERT: A 807 ASN cc_start: 0.7976 (t0) cc_final: 0.7646 (t0) REVERT: B 99 PHE cc_start: 0.7965 (m-80) cc_final: 0.7642 (m-80) REVERT: B 340 ASP cc_start: 0.7975 (t0) cc_final: 0.7649 (p0) REVERT: B 823 MET cc_start: 0.5370 (tmm) cc_final: 0.4267 (mmp) REVERT: C 29 LYS cc_start: 0.6850 (mttt) cc_final: 0.6564 (mptt) outliers start: 21 outliers final: 11 residues processed: 172 average time/residue: 1.3244 time to fit residues: 249.4319 Evaluate side-chains 158 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 665 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 135 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 81 HIS A 153 HIS A 241 GLN A 326 HIS A 355 ASN A 651 GLN A 795 HIS ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN B 533 ASN B 569 ASN B 693 GLN B 758 GLN B 795 HIS D 83 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.148995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.109173 restraints weight = 16498.949| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.02 r_work: 0.3157 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13607 Z= 0.126 Angle : 0.497 8.407 18398 Z= 0.263 Chirality : 0.041 0.217 2028 Planarity : 0.004 0.047 2345 Dihedral : 6.757 70.534 1827 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.80 % Allowed : 18.21 % Favored : 78.99 % 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: 1.61 (0.21), residues: 1609 helix: 1.68 (0.17), residues: 918 sheet: -0.33 (0.44), residues: 139 loop : 0.58 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 145 HIS 0.007 0.001 HIS A 81 PHE 0.017 0.001 PHE A 473 TYR 0.020 0.001 TYR B 369 ARG 0.007 0.000 ARG B 82 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 766) hydrogen bonds : angle 4.55345 ( 2223) metal coordination : bond 0.00284 ( 4) covalent geometry : bond 0.00277 (13603) covalent geometry : angle 0.49662 (18398) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 1.362 Fit side-chains REVERT: A 75 THR cc_start: 0.8070 (p) cc_final: 0.7782 (t) REVERT: A 235 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7551 (mt) REVERT: A 287 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7601 (pm20) REVERT: A 330 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7735 (tp30) REVERT: A 394 ASN cc_start: 0.7845 (t0) cc_final: 0.7513 (t0) REVERT: A 805 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8409 (tp) REVERT: B 99 PHE cc_start: 0.8181 (m-80) cc_final: 0.7924 (m-80) REVERT: C 29 LYS cc_start: 0.7086 (mttt) cc_final: 0.6738 (mptt) outliers start: 41 outliers final: 16 residues processed: 185 average time/residue: 1.2676 time to fit residues: 256.7789 Evaluate side-chains 161 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 815 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 37 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN B 435 ASN B 759 GLN D 83 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.145648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.105558 restraints weight = 16741.852| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.03 r_work: 0.3107 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13607 Z= 0.186 Angle : 0.526 7.411 18398 Z= 0.277 Chirality : 0.043 0.201 2028 Planarity : 0.004 0.046 2345 Dihedral : 6.440 67.216 1818 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.96 % Allowed : 16.98 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.63 (0.21), residues: 1609 helix: 1.73 (0.17), residues: 916 sheet: -0.31 (0.44), residues: 136 loop : 0.52 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 145 HIS 0.004 0.001 HIS B 562 PHE 0.013 0.001 PHE B 213 TYR 0.016 0.002 TYR B 369 ARG 0.004 0.000 ARG B 82 Details of bonding type rmsd hydrogen bonds : bond 0.04895 ( 766) hydrogen bonds : angle 4.47321 ( 2223) metal coordination : bond 0.00272 ( 4) covalent geometry : bond 0.00452 (13603) covalent geometry : angle 0.52580 (18398) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 149 time to evaluate : 1.392 Fit side-chains REVERT: A 75 THR cc_start: 0.8146 (p) cc_final: 0.7846 (t) REVERT: A 235 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7623 (mt) REVERT: A 287 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7572 (pm20) REVERT: B 124 GLU cc_start: 0.6735 (mp0) cc_final: 0.6464 (mp0) REVERT: B 340 ASP cc_start: 0.7962 (t0) cc_final: 0.7554 (p0) REVERT: C 29 LYS cc_start: 0.7165 (mttt) cc_final: 0.6782 (mptt) outliers start: 58 outliers final: 20 residues processed: 182 average time/residue: 1.2431 time to fit residues: 248.1813 Evaluate side-chains 163 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 815 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 125 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.145941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.106106 restraints weight = 16534.619| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.02 r_work: 0.3114 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13607 Z= 0.154 Angle : 0.497 7.046 18398 Z= 0.262 Chirality : 0.042 0.201 2028 Planarity : 0.004 0.043 2345 Dihedral : 6.103 66.160 1814 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.48 % Allowed : 18.01 % Favored : 78.51 % 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: 1.68 (0.21), residues: 1609 helix: 1.82 (0.17), residues: 917 sheet: -0.41 (0.44), residues: 137 loop : 0.48 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 145 HIS 0.004 0.001 HIS B 81 PHE 0.011 0.001 PHE A 219 TYR 0.015 0.002 TYR A 788 ARG 0.005 0.000 ARG B 82 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 766) hydrogen bonds : angle 4.33329 ( 2223) metal coordination : bond 0.00210 ( 4) covalent geometry : bond 0.00369 (13603) covalent geometry : angle 0.49738 (18398) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 145 time to evaluate : 1.406 Fit side-chains REVERT: A 75 THR cc_start: 0.8217 (p) cc_final: 0.7887 (t) REVERT: A 78 GLN cc_start: 0.6718 (mt0) cc_final: 0.5745 (mm-40) REVERT: A 90 LEU cc_start: 0.7690 (mm) cc_final: 0.7409 (tt) REVERT: A 132 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7872 (tptt) REVERT: A 235 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7693 (mt) REVERT: A 287 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7549 (pm20) REVERT: A 557 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.8846 (mtt90) REVERT: B 124 GLU cc_start: 0.6736 (mp0) cc_final: 0.6495 (mp0) REVERT: B 132 LYS cc_start: 0.8275 (tptt) cc_final: 0.8071 (tptt) REVERT: B 340 ASP cc_start: 0.7963 (t0) cc_final: 0.7559 (p0) REVERT: B 764 MET cc_start: 0.8656 (mtm) cc_final: 0.8427 (mtt) REVERT: C 29 LYS cc_start: 0.7211 (mttt) cc_final: 0.6830 (mptt) outliers start: 51 outliers final: 23 residues processed: 174 average time/residue: 1.2711 time to fit residues: 241.6984 Evaluate side-chains 166 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 815 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 90 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.146805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.106879 restraints weight = 16538.487| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.04 r_work: 0.3128 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13607 Z= 0.130 Angle : 0.481 8.207 18398 Z= 0.253 Chirality : 0.041 0.197 2028 Planarity : 0.004 0.045 2345 Dihedral : 5.964 65.605 1814 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.21 % Allowed : 18.55 % Favored : 78.24 % 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: 1.78 (0.21), residues: 1609 helix: 1.95 (0.17), residues: 917 sheet: -0.45 (0.44), residues: 137 loop : 0.45 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 145 HIS 0.003 0.001 HIS B 81 PHE 0.011 0.001 PHE B 213 TYR 0.014 0.001 TYR B 369 ARG 0.004 0.000 ARG B 82 Details of bonding type rmsd hydrogen bonds : bond 0.04303 ( 766) hydrogen bonds : angle 4.22125 ( 2223) metal coordination : bond 0.00158 ( 4) covalent geometry : bond 0.00305 (13603) covalent geometry : angle 0.48068 (18398) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 2.336 Fit side-chains REVERT: A 75 THR cc_start: 0.8140 (p) cc_final: 0.7801 (t) REVERT: A 78 GLN cc_start: 0.6811 (mt0) cc_final: 0.5828 (mm-40) REVERT: A 90 LEU cc_start: 0.7664 (mm) cc_final: 0.7398 (tt) REVERT: A 132 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7882 (tptt) REVERT: A 235 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7671 (mt) REVERT: A 287 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7509 (pm20) REVERT: A 686 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7043 (mtpm) REVERT: B 124 GLU cc_start: 0.6710 (mp0) cc_final: 0.6473 (mp0) REVERT: B 132 LYS cc_start: 0.8262 (tptt) cc_final: 0.8061 (tptt) REVERT: B 340 ASP cc_start: 0.7953 (t0) cc_final: 0.7574 (p0) REVERT: B 764 MET cc_start: 0.8667 (mtm) cc_final: 0.8445 (mtt) REVERT: C 29 LYS cc_start: 0.7187 (mttt) cc_final: 0.6786 (mptt) outliers start: 47 outliers final: 25 residues processed: 177 average time/residue: 1.3202 time to fit residues: 256.9712 Evaluate side-chains 171 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain D residue 60 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 122 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 118 optimal weight: 0.1980 chunk 44 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.147170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.107133 restraints weight = 16667.171| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.04 r_work: 0.3134 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13607 Z= 0.125 Angle : 0.477 7.682 18398 Z= 0.251 Chirality : 0.041 0.198 2028 Planarity : 0.004 0.045 2345 Dihedral : 5.875 65.117 1814 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.41 % Allowed : 18.28 % Favored : 78.31 % 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: 1.83 (0.21), residues: 1609 helix: 1.99 (0.17), residues: 918 sheet: -0.44 (0.44), residues: 136 loop : 0.46 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 145 HIS 0.003 0.001 HIS B 81 PHE 0.011 0.001 PHE A 219 TYR 0.013 0.001 TYR B 369 ARG 0.006 0.000 ARG B 82 Details of bonding type rmsd hydrogen bonds : bond 0.04193 ( 766) hydrogen bonds : angle 4.16846 ( 2223) metal coordination : bond 0.00149 ( 4) covalent geometry : bond 0.00292 (13603) covalent geometry : angle 0.47658 (18398) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 150 time to evaluate : 2.231 Fit side-chains REVERT: A 78 GLN cc_start: 0.6835 (mt0) cc_final: 0.5856 (mm-40) REVERT: A 90 LEU cc_start: 0.7683 (mm) cc_final: 0.7396 (tt) REVERT: A 132 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7892 (tptt) REVERT: A 235 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7649 (mt) REVERT: A 287 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7514 (pm20) REVERT: B 92 GLN cc_start: 0.8537 (tt0) cc_final: 0.8311 (tt0) REVERT: B 124 GLU cc_start: 0.6646 (mp0) cc_final: 0.6404 (mp0) REVERT: B 340 ASP cc_start: 0.7948 (t0) cc_final: 0.7564 (p0) REVERT: B 764 MET cc_start: 0.8658 (mtm) cc_final: 0.8436 (mtt) REVERT: C 29 LYS cc_start: 0.7186 (mttt) cc_final: 0.6775 (mptt) outliers start: 50 outliers final: 29 residues processed: 184 average time/residue: 1.4769 time to fit residues: 300.0946 Evaluate side-chains 178 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 775 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 61 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 135 optimal weight: 0.2980 chunk 95 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.148188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.108547 restraints weight = 16662.747| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.04 r_work: 0.3151 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13607 Z= 0.109 Angle : 0.471 8.105 18398 Z= 0.245 Chirality : 0.040 0.200 2028 Planarity : 0.004 0.046 2345 Dihedral : 5.772 64.979 1814 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.86 % Allowed : 19.17 % Favored : 77.97 % 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: 1.93 (0.21), residues: 1609 helix: 2.10 (0.17), residues: 918 sheet: -0.44 (0.44), residues: 137 loop : 0.46 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 145 HIS 0.003 0.000 HIS B 81 PHE 0.024 0.001 PHE A 473 TYR 0.013 0.001 TYR B 369 ARG 0.005 0.000 ARG B 82 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 766) hydrogen bonds : angle 4.06188 ( 2223) metal coordination : bond 0.00124 ( 4) covalent geometry : bond 0.00244 (13603) covalent geometry : angle 0.47099 (18398) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 1.413 Fit side-chains REVERT: A 78 GLN cc_start: 0.6789 (mt0) cc_final: 0.5798 (mm-40) REVERT: A 90 LEU cc_start: 0.7677 (mm) cc_final: 0.7379 (tt) REVERT: A 132 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7884 (tptt) REVERT: A 171 GLN cc_start: 0.6745 (tt0) cc_final: 0.6295 (mt0) REVERT: A 287 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7499 (pm20) REVERT: A 686 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7045 (mtpm) REVERT: B 92 GLN cc_start: 0.8544 (tt0) cc_final: 0.8299 (tt0) REVERT: B 124 GLU cc_start: 0.6625 (mp0) cc_final: 0.6374 (mp0) REVERT: B 132 LYS cc_start: 0.8102 (tptt) cc_final: 0.7365 (mmtt) REVERT: B 340 ASP cc_start: 0.7922 (t0) cc_final: 0.7541 (p0) REVERT: C 29 LYS cc_start: 0.7158 (mttt) cc_final: 0.6747 (mptt) outliers start: 42 outliers final: 25 residues processed: 183 average time/residue: 1.2359 time to fit residues: 247.7060 Evaluate side-chains 173 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 815 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 9 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 734 GLN ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.148137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.108394 restraints weight = 16723.612| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.05 r_work: 0.3153 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13607 Z= 0.115 Angle : 0.480 8.155 18398 Z= 0.248 Chirality : 0.041 0.206 2028 Planarity : 0.004 0.045 2345 Dihedral : 5.729 64.601 1814 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.80 % Allowed : 19.30 % Favored : 77.90 % 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: 1.96 (0.21), residues: 1609 helix: 2.12 (0.17), residues: 918 sheet: -0.41 (0.44), residues: 137 loop : 0.47 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 145 HIS 0.003 0.001 HIS B 81 PHE 0.011 0.001 PHE A 219 TYR 0.012 0.001 TYR B 231 ARG 0.004 0.000 ARG B 82 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 766) hydrogen bonds : angle 4.05363 ( 2223) metal coordination : bond 0.00128 ( 4) covalent geometry : bond 0.00262 (13603) covalent geometry : angle 0.48043 (18398) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 1.640 Fit side-chains REVERT: A 78 GLN cc_start: 0.6855 (mt0) cc_final: 0.5858 (mm-40) REVERT: A 90 LEU cc_start: 0.7692 (mm) cc_final: 0.7401 (tt) REVERT: A 126 ASN cc_start: 0.8121 (m110) cc_final: 0.7884 (m110) REVERT: A 132 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7887 (tptt) REVERT: A 171 GLN cc_start: 0.6731 (tt0) cc_final: 0.6325 (mt0) REVERT: A 287 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7519 (pm20) REVERT: A 686 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7044 (mtpm) REVERT: B 92 GLN cc_start: 0.8495 (tt0) cc_final: 0.8255 (tt0) REVERT: B 124 GLU cc_start: 0.6620 (mp0) cc_final: 0.6396 (mp0) REVERT: B 340 ASP cc_start: 0.7952 (t0) cc_final: 0.7560 (p0) REVERT: B 415 ASP cc_start: 0.7905 (m-30) cc_final: 0.7500 (p0) REVERT: B 764 MET cc_start: 0.8674 (mtm) cc_final: 0.8461 (mtt) REVERT: C 29 LYS cc_start: 0.7160 (mttt) cc_final: 0.6741 (mptt) outliers start: 41 outliers final: 26 residues processed: 175 average time/residue: 1.1789 time to fit residues: 227.3279 Evaluate side-chains 177 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 754 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 59 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 111 optimal weight: 0.0370 chunk 42 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 158 optimal weight: 7.9990 chunk 72 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.149756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.110548 restraints weight = 16608.505| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.04 r_work: 0.3180 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 13607 Z= 0.100 Angle : 0.477 8.372 18398 Z= 0.244 Chirality : 0.040 0.207 2028 Planarity : 0.004 0.046 2345 Dihedral : 5.626 64.592 1814 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.25 % Allowed : 19.99 % Favored : 77.76 % 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: 2.04 (0.21), residues: 1609 helix: 2.20 (0.17), residues: 917 sheet: -0.35 (0.44), residues: 137 loop : 0.48 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 145 HIS 0.003 0.000 HIS B 81 PHE 0.024 0.001 PHE A 473 TYR 0.012 0.001 TYR B 369 ARG 0.004 0.000 ARG B 82 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 766) hydrogen bonds : angle 3.97105 ( 2223) metal coordination : bond 0.00083 ( 4) covalent geometry : bond 0.00218 (13603) covalent geometry : angle 0.47674 (18398) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 1.763 Fit side-chains REVERT: A 78 GLN cc_start: 0.6775 (mt0) cc_final: 0.5808 (mm-40) REVERT: A 90 LEU cc_start: 0.7686 (mm) cc_final: 0.7395 (tt) REVERT: A 126 ASN cc_start: 0.8072 (m110) cc_final: 0.7842 (m110) REVERT: A 132 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7875 (tptt) REVERT: A 171 GLN cc_start: 0.6760 (tt0) cc_final: 0.6369 (mt0) REVERT: A 287 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7511 (pm20) REVERT: A 686 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7024 (mtpm) REVERT: B 92 GLN cc_start: 0.8512 (tt0) cc_final: 0.8281 (tt0) REVERT: B 124 GLU cc_start: 0.6620 (mp0) cc_final: 0.6385 (mp0) REVERT: B 340 ASP cc_start: 0.7886 (t0) cc_final: 0.7525 (p0) REVERT: B 415 ASP cc_start: 0.7776 (m-30) cc_final: 0.7500 (p0) REVERT: B 764 MET cc_start: 0.8655 (mtm) cc_final: 0.8232 (mtt) REVERT: C 29 LYS cc_start: 0.7180 (mttt) cc_final: 0.6765 (mptt) outliers start: 33 outliers final: 25 residues processed: 177 average time/residue: 1.3433 time to fit residues: 264.0121 Evaluate side-chains 178 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 775 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 157 optimal weight: 0.0030 chunk 79 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 GLN D 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.146761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.107273 restraints weight = 16578.990| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.01 r_work: 0.3132 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13607 Z= 0.155 Angle : 0.521 9.294 18398 Z= 0.266 Chirality : 0.042 0.216 2028 Planarity : 0.004 0.046 2345 Dihedral : 5.700 64.003 1814 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.32 % Allowed : 20.05 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.92 (0.21), residues: 1609 helix: 2.10 (0.17), residues: 917 sheet: -0.38 (0.44), residues: 137 loop : 0.43 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 145 HIS 0.004 0.001 HIS B 562 PHE 0.011 0.001 PHE A 568 TYR 0.016 0.002 TYR A 420 ARG 0.008 0.000 ARG B 82 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 766) hydrogen bonds : angle 4.10508 ( 2223) metal coordination : bond 0.00220 ( 4) covalent geometry : bond 0.00372 (13603) covalent geometry : angle 0.52077 (18398) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 1.237 Fit side-chains REVERT: A 78 GLN cc_start: 0.6889 (mt0) cc_final: 0.5909 (mm-40) REVERT: A 90 LEU cc_start: 0.7690 (mm) cc_final: 0.7397 (tt) REVERT: A 126 ASN cc_start: 0.8153 (m110) cc_final: 0.7930 (m110) REVERT: A 132 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7873 (tptt) REVERT: A 171 GLN cc_start: 0.6768 (tt0) cc_final: 0.6383 (mt0) REVERT: A 287 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7505 (pm20) REVERT: A 686 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7066 (mtpm) REVERT: B 92 GLN cc_start: 0.8515 (tt0) cc_final: 0.8287 (tt0) REVERT: B 124 GLU cc_start: 0.6680 (mp0) cc_final: 0.6450 (mp0) REVERT: B 340 ASP cc_start: 0.7929 (t0) cc_final: 0.7546 (p0) REVERT: B 748 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8690 (tm-30) REVERT: B 764 MET cc_start: 0.8604 (mtm) cc_final: 0.8356 (mtt) REVERT: C 29 LYS cc_start: 0.7200 (mttt) cc_final: 0.6802 (mptt) outliers start: 34 outliers final: 22 residues processed: 167 average time/residue: 1.5295 time to fit residues: 281.0432 Evaluate side-chains 172 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 748 GLN Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 775 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 123 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 119 optimal weight: 0.0270 chunk 75 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 GLN D 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.146985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.107409 restraints weight = 16677.332| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.03 r_work: 0.3135 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 13607 Z= 0.156 Angle : 0.767 59.125 18398 Z= 0.446 Chirality : 0.044 0.642 2028 Planarity : 0.004 0.046 2345 Dihedral : 5.713 63.996 1814 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.11 % Allowed : 20.19 % Favored : 77.69 % Cbeta Deviations : 0.06 % 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: 1.91 (0.21), residues: 1609 helix: 2.09 (0.17), residues: 917 sheet: -0.39 (0.44), residues: 137 loop : 0.43 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 431 HIS 0.003 0.001 HIS B 81 PHE 0.012 0.001 PHE A 473 TYR 0.015 0.001 TYR A 420 ARG 0.008 0.000 ARG B 82 Details of bonding type rmsd hydrogen bonds : bond 0.04224 ( 766) hydrogen bonds : angle 4.11474 ( 2223) metal coordination : bond 0.00162 ( 4) covalent geometry : bond 0.00350 (13603) covalent geometry : angle 0.76697 (18398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10257.49 seconds wall clock time: 181 minutes 19.89 seconds (10879.89 seconds total)