Starting phenix.real_space_refine on Tue Nov 18 10:13:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cxi_45992/11_2025/9cxi_45992.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cxi_45992/11_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_45992/11_2025/9cxi_45992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cxi_45992/11_2025/9cxi_45992.map" model { file = "/net/cci-nas-00/data/ceres_data/9cxi_45992/11_2025/9cxi_45992.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cxi_45992/11_2025/9cxi_45992.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: 2.94, per 1000 atoms: 0.22 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: 1.10 Conformation dependent library (CDL) restraints added in 599.7 milliseconds 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: 0.57 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: 2.22 Time building geometry restraints manager: 1.53 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 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: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.610 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.680 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (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 ARG 0.011 0.001 ARG B 82 TYR 0.018 0.002 TYR A 788 PHE 0.016 0.002 PHE B 213 TRP 0.006 0.001 TRP B 564 HIS 0.009 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00556 (13603) covalent geometry : angle 0.79649 (18398) hydrogen bonds : bond 0.14563 ( 766) hydrogen bonds : angle 6.15908 ( 2223) metal coordination : bond 0.26571 ( 4) *********************** 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 : 0.502 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: 0.6358 time to fit residues: 119.0518 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 : 0.544 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.148116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.108346 restraints weight = 16641.143| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.03 r_work: 0.3148 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13607 Z= 0.140 Angle : 0.507 8.360 18398 Z= 0.269 Chirality : 0.042 0.214 2028 Planarity : 0.004 0.046 2345 Dihedral : 6.779 70.466 1827 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.86 % Allowed : 18.21 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.21), residues: 1609 helix: 1.63 (0.17), residues: 918 sheet: -0.35 (0.43), residues: 139 loop : 0.56 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 82 TYR 0.019 0.002 TYR B 369 PHE 0.014 0.001 PHE A 473 TRP 0.007 0.001 TRP A 342 HIS 0.008 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00322 (13603) covalent geometry : angle 0.50746 (18398) hydrogen bonds : bond 0.04848 ( 766) hydrogen bonds : angle 4.60349 ( 2223) metal coordination : bond 0.01134 ( 4) *********************** 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 194 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.493 Fit side-chains REVERT: A 75 THR cc_start: 0.8043 (p) cc_final: 0.7749 (t) REVERT: A 235 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7546 (mt) REVERT: A 287 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7597 (pm20) REVERT: A 805 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8440 (tp) REVERT: B 99 PHE cc_start: 0.8183 (m-80) cc_final: 0.7928 (m-80) REVERT: B 340 ASP cc_start: 0.8034 (t0) cc_final: 0.7642 (p0) REVERT: C 29 LYS cc_start: 0.7108 (mttt) cc_final: 0.6770 (mptt) outliers start: 42 outliers final: 18 residues processed: 179 average time/residue: 0.6154 time to fit residues: 120.3316 Evaluate side-chains 164 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 440 ASP Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 542 VAL 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 77 optimal weight: 8.9990 chunk 158 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 D 83 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.147267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.107188 restraints weight = 16737.182| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.05 r_work: 0.3135 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13607 Z= 0.141 Angle : 0.490 7.532 18398 Z= 0.259 Chirality : 0.042 0.205 2028 Planarity : 0.004 0.046 2345 Dihedral : 6.449 67.999 1820 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.89 % Allowed : 17.19 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.21), residues: 1609 helix: 1.82 (0.17), residues: 917 sheet: -0.23 (0.45), residues: 136 loop : 0.59 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 82 TYR 0.016 0.002 TYR B 369 PHE 0.012 0.001 PHE B 213 TRP 0.006 0.001 TRP B 145 HIS 0.003 0.001 HIS B 602 Details of bonding type rmsd covalent geometry : bond 0.00330 (13603) covalent geometry : angle 0.49006 (18398) hydrogen bonds : bond 0.04543 ( 766) hydrogen bonds : angle 4.36959 ( 2223) metal coordination : bond 0.00290 ( 4) *********************** 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 208 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 151 time to evaluate : 0.401 Fit side-chains REVERT: A 75 THR cc_start: 0.8121 (p) cc_final: 0.7824 (t) REVERT: A 235 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7611 (mt) REVERT: A 287 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: B 124 GLU cc_start: 0.6708 (mp0) cc_final: 0.6435 (mp0) REVERT: C 29 LYS cc_start: 0.7095 (mttt) cc_final: 0.6720 (mptt) outliers start: 57 outliers final: 18 residues processed: 184 average time/residue: 0.5939 time to fit residues: 119.7770 Evaluate side-chains 164 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 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 78 GLN 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 542 VAL 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 104 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3758 r_free = 0.3758 target = 0.148611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.108906 restraints weight = 16597.469| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.03 r_work: 0.3152 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1266 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= 0.113 Angle : 0.465 5.743 18398 Z= 0.245 Chirality : 0.041 0.203 2028 Planarity : 0.003 0.043 2345 Dihedral : 6.136 67.489 1816 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.27 % Allowed : 17.94 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.21), residues: 1609 helix: 1.97 (0.17), residues: 918 sheet: -0.26 (0.45), residues: 136 loop : 0.56 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 82 TYR 0.014 0.001 TYR B 369 PHE 0.019 0.001 PHE A 473 TRP 0.006 0.001 TRP B 145 HIS 0.003 0.001 HIS B 602 Details of bonding type rmsd covalent geometry : bond 0.00254 (13603) covalent geometry : angle 0.46519 (18398) hydrogen bonds : bond 0.04144 ( 766) hydrogen bonds : angle 4.20424 ( 2223) metal coordination : bond 0.00144 ( 4) *********************** 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 200 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 0.576 Fit side-chains REVERT: A 75 THR cc_start: 0.8139 (p) cc_final: 0.7828 (t) REVERT: A 287 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7519 (pm20) REVERT: B 124 GLU cc_start: 0.6691 (mp0) cc_final: 0.6410 (mp0) REVERT: C 29 LYS cc_start: 0.7169 (mttt) cc_final: 0.6780 (mptt) outliers start: 48 outliers final: 25 residues processed: 178 average time/residue: 0.6289 time to fit residues: 122.2737 Evaluate side-chains 171 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU 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 185 VAL 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 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 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 345 ILE Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 665 PHE 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 54 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 113 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** B 435 ASN D 83 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.148171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.108204 restraints weight = 16610.236| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.04 r_work: 0.3145 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1361 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= 0.123 Angle : 0.478 6.805 18398 Z= 0.250 Chirality : 0.041 0.204 2028 Planarity : 0.004 0.045 2345 Dihedral : 5.958 66.670 1814 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.41 % Allowed : 18.42 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.21), residues: 1609 helix: 2.02 (0.17), residues: 918 sheet: -0.31 (0.44), residues: 136 loop : 0.54 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 82 TYR 0.014 0.001 TYR B 369 PHE 0.011 0.001 PHE A 219 TRP 0.006 0.001 TRP B 145 HIS 0.003 0.001 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00285 (13603) covalent geometry : angle 0.47790 (18398) hydrogen bonds : bond 0.04137 ( 766) hydrogen bonds : angle 4.15525 ( 2223) metal coordination : bond 0.00157 ( 4) *********************** 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 200 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 150 time to evaluate : 0.494 Fit side-chains REVERT: A 75 THR cc_start: 0.8140 (p) cc_final: 0.7802 (t) REVERT: A 78 GLN cc_start: 0.6693 (mt0) cc_final: 0.5743 (mm-40) REVERT: A 235 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7624 (mt) REVERT: A 287 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7524 (pm20) REVERT: A 418 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7317 (m-30) REVERT: B 124 GLU cc_start: 0.6622 (mp0) cc_final: 0.6367 (mp0) REVERT: B 340 ASP cc_start: 0.7923 (t0) cc_final: 0.7521 (p0) REVERT: B 764 MET cc_start: 0.8656 (mtm) cc_final: 0.8440 (mtt) REVERT: C 29 LYS cc_start: 0.7141 (mttt) cc_final: 0.6760 (mptt) outliers start: 50 outliers final: 26 residues processed: 180 average time/residue: 0.6118 time to fit residues: 120.0854 Evaluate side-chains 173 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 418 ASP 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 751 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain B residue 63 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 90 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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** 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 = 0.3712 r_free = 0.3712 target = 0.144627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.104492 restraints weight = 16708.003| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.04 r_work: 0.3095 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1497 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= 0.200 Angle : 0.535 7.929 18398 Z= 0.280 Chirality : 0.043 0.204 2028 Planarity : 0.004 0.045 2345 Dihedral : 6.025 65.039 1814 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.48 % Allowed : 18.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.21), residues: 1609 helix: 1.85 (0.17), residues: 917 sheet: -0.46 (0.44), residues: 137 loop : 0.40 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.016 0.002 TYR A 788 PHE 0.023 0.001 PHE A 473 TRP 0.007 0.001 TRP A 431 HIS 0.005 0.001 HIS B 562 Details of bonding type rmsd covalent geometry : bond 0.00490 (13603) covalent geometry : angle 0.53478 (18398) hydrogen bonds : bond 0.04848 ( 766) hydrogen bonds : angle 4.34008 ( 2223) metal coordination : bond 0.00263 ( 4) *********************** 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 204 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 153 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 78 GLN cc_start: 0.6822 (mt0) cc_final: 0.5864 (mm-40) REVERT: A 126 ASN cc_start: 0.8089 (m110) cc_final: 0.7863 (m110) REVERT: A 132 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7896 (tptt) REVERT: A 235 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7657 (mt) REVERT: A 287 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7557 (pm20) REVERT: B 92 GLN cc_start: 0.8557 (tt0) cc_final: 0.8317 (tt0) REVERT: B 124 GLU cc_start: 0.6772 (mp0) cc_final: 0.6524 (mp0) REVERT: B 340 ASP cc_start: 0.7984 (t0) cc_final: 0.7570 (p0) REVERT: B 385 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8224 (ttmm) REVERT: B 764 MET cc_start: 0.8704 (mtm) cc_final: 0.8474 (mtt) REVERT: C 29 LYS cc_start: 0.7257 (mttt) cc_final: 0.6855 (mptt) outliers start: 51 outliers final: 28 residues processed: 185 average time/residue: 0.6241 time to fit residues: 126.0277 Evaluate side-chains 177 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 672 THR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 96 CYS 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 272 LEU Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 815 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 145 optimal weight: 2.9990 chunk 101 optimal weight: 0.0770 chunk 25 optimal weight: 0.0670 chunk 111 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 7 optimal weight: 0.0570 chunk 107 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.148805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.109274 restraints weight = 16590.934| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.03 r_work: 0.3161 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13607 Z= 0.102 Angle : 0.471 8.142 18398 Z= 0.247 Chirality : 0.040 0.198 2028 Planarity : 0.004 0.047 2345 Dihedral : 5.798 65.728 1814 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.86 % Allowed : 19.58 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.21), residues: 1609 helix: 2.08 (0.17), residues: 917 sheet: -0.36 (0.44), residues: 136 loop : 0.46 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 82 TYR 0.013 0.001 TYR B 369 PHE 0.018 0.001 PHE A 167 TRP 0.006 0.001 TRP B 145 HIS 0.003 0.000 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00216 (13603) covalent geometry : angle 0.47083 (18398) hydrogen bonds : bond 0.03895 ( 766) hydrogen bonds : angle 4.06607 ( 2223) metal coordination : bond 0.00103 ( 4) *********************** 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 202 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 0.526 Fit side-chains REVERT: A 78 GLN cc_start: 0.6715 (mt0) cc_final: 0.5746 (mm-40) REVERT: A 90 LEU cc_start: 0.7656 (mm) cc_final: 0.7391 (tt) REVERT: A 126 ASN cc_start: 0.8056 (m110) cc_final: 0.7833 (m110) REVERT: A 132 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7894 (tptt) REVERT: A 287 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7522 (pm20) REVERT: A 686 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7062 (mtpm) REVERT: B 92 GLN cc_start: 0.8551 (tt0) cc_final: 0.8338 (tt0) REVERT: B 124 GLU cc_start: 0.6629 (mp0) cc_final: 0.6384 (mp0) REVERT: B 340 ASP cc_start: 0.7956 (t0) cc_final: 0.7538 (p0) REVERT: B 415 ASP cc_start: 0.8008 (m-30) cc_final: 0.7701 (p0) REVERT: B 764 MET cc_start: 0.8673 (mtm) cc_final: 0.8421 (mtt) REVERT: C 29 LYS cc_start: 0.7154 (mttt) cc_final: 0.6747 (mptt) outliers start: 42 outliers final: 17 residues processed: 187 average time/residue: 0.6106 time to fit residues: 124.8300 Evaluate side-chains 173 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 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 672 THR Chi-restraints excluded: chain A residue 686 LYS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 130 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 158 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 435 ASN D 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.148001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.108274 restraints weight = 16549.659| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.03 r_work: 0.3156 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13607 Z= 0.116 Angle : 0.479 8.179 18398 Z= 0.248 Chirality : 0.041 0.204 2028 Planarity : 0.004 0.046 2345 Dihedral : 5.751 65.358 1814 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.46 % Allowed : 19.99 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.21), residues: 1609 helix: 2.11 (0.17), residues: 917 sheet: -0.40 (0.44), residues: 137 loop : 0.44 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 82 TYR 0.012 0.001 TYR B 369 PHE 0.024 0.001 PHE A 473 TRP 0.006 0.001 TRP B 145 HIS 0.003 0.001 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00264 (13603) covalent geometry : angle 0.47916 (18398) hydrogen bonds : bond 0.03987 ( 766) hydrogen bonds : angle 4.05376 ( 2223) metal coordination : bond 0.00127 ( 4) *********************** 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 188 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.541 Fit side-chains REVERT: A 78 GLN cc_start: 0.6753 (mt0) cc_final: 0.5776 (mm-40) REVERT: A 90 LEU cc_start: 0.7616 (mm) cc_final: 0.7358 (tt) REVERT: A 126 ASN cc_start: 0.8061 (m110) cc_final: 0.7856 (m110) REVERT: A 132 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7861 (tptt) REVERT: A 287 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7509 (pm20) REVERT: A 686 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.6994 (mtpm) REVERT: B 92 GLN cc_start: 0.8561 (tt0) cc_final: 0.8336 (tt0) REVERT: B 124 GLU cc_start: 0.6625 (mp0) cc_final: 0.6380 (mp0) REVERT: B 340 ASP cc_start: 0.7965 (t0) cc_final: 0.7551 (p0) REVERT: B 415 ASP cc_start: 0.7961 (m-30) cc_final: 0.7565 (p0) REVERT: B 764 MET cc_start: 0.8672 (mtm) cc_final: 0.8403 (mtt) REVERT: C 29 LYS cc_start: 0.7185 (mttt) cc_final: 0.6767 (mptt) outliers start: 36 outliers final: 18 residues processed: 174 average time/residue: 0.6098 time to fit residues: 116.1739 Evaluate side-chains 172 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 686 LYS 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 775 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 70 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 118 optimal weight: 0.1980 chunk 157 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 28 optimal weight: 0.0970 chunk 58 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN D 83 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.148729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.109265 restraints weight = 16655.730| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.04 r_work: 0.3165 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13607 Z= 0.110 Angle : 0.484 8.310 18398 Z= 0.249 Chirality : 0.041 0.207 2028 Planarity : 0.004 0.047 2345 Dihedral : 5.694 65.407 1814 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.18 % Allowed : 20.33 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.21), residues: 1609 helix: 2.15 (0.17), residues: 917 sheet: -0.36 (0.44), residues: 137 loop : 0.45 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 82 TYR 0.013 0.001 TYR B 231 PHE 0.012 0.001 PHE A 167 TRP 0.008 0.001 TRP B 67 HIS 0.003 0.001 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00249 (13603) covalent geometry : angle 0.48400 (18398) hydrogen bonds : bond 0.03866 ( 766) hydrogen bonds : angle 4.01633 ( 2223) metal coordination : bond 0.00123 ( 4) *********************** 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 189 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.523 Fit side-chains REVERT: A 78 GLN cc_start: 0.6833 (mt0) cc_final: 0.5845 (mm-40) REVERT: A 126 ASN cc_start: 0.8055 (m110) cc_final: 0.7849 (m110) REVERT: A 132 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7883 (tptt) REVERT: A 287 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7534 (pm20) REVERT: A 686 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7051 (mtpm) REVERT: B 92 GLN cc_start: 0.8554 (tt0) cc_final: 0.8341 (tt0) REVERT: B 124 GLU cc_start: 0.6631 (mp0) cc_final: 0.6387 (mp0) REVERT: B 340 ASP cc_start: 0.7938 (t0) cc_final: 0.7554 (p0) REVERT: B 415 ASP cc_start: 0.8000 (m-30) cc_final: 0.7641 (p0) REVERT: C 29 LYS cc_start: 0.7164 (mttt) cc_final: 0.6762 (mptt) outliers start: 32 outliers final: 19 residues processed: 176 average time/residue: 0.6258 time to fit residues: 120.3349 Evaluate side-chains 175 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 686 LYS 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 497 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 28 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 435 ASN D 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.148842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.109289 restraints weight = 16593.867| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.04 r_work: 0.3168 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13607 Z= 0.112 Angle : 0.491 9.805 18398 Z= 0.251 Chirality : 0.041 0.212 2028 Planarity : 0.004 0.047 2345 Dihedral : 5.657 65.285 1814 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.91 % Allowed : 20.46 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.21), residues: 1609 helix: 2.14 (0.17), residues: 917 sheet: -0.36 (0.44), residues: 137 loop : 0.45 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 82 TYR 0.012 0.001 TYR B 369 PHE 0.024 0.001 PHE A 473 TRP 0.008 0.001 TRP B 67 HIS 0.003 0.001 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00256 (13603) covalent geometry : angle 0.49125 (18398) hydrogen bonds : bond 0.03852 ( 766) hydrogen bonds : angle 4.01343 ( 2223) metal coordination : bond 0.00115 ( 4) ********************** 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 181 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.620 Fit side-chains REVERT: A 78 GLN cc_start: 0.6771 (mt0) cc_final: 0.5749 (mm-40) REVERT: A 126 ASN cc_start: 0.8046 (m110) cc_final: 0.7748 (m110) REVERT: A 132 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7866 (tptt) REVERT: A 287 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7524 (pm20) REVERT: A 395 LYS cc_start: 0.8810 (tttm) cc_final: 0.8179 (ttmt) REVERT: A 686 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7041 (mtpm) REVERT: B 92 GLN cc_start: 0.8561 (tt0) cc_final: 0.8347 (tt0) REVERT: B 124 GLU cc_start: 0.6654 (mp0) cc_final: 0.6403 (mp0) REVERT: B 340 ASP cc_start: 0.7940 (t0) cc_final: 0.7557 (p0) REVERT: B 415 ASP cc_start: 0.7993 (m-30) cc_final: 0.7616 (p0) REVERT: B 508 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8505 (mm-30) REVERT: B 764 MET cc_start: 0.8688 (mtm) cc_final: 0.8429 (mtt) REVERT: C 29 LYS cc_start: 0.7164 (mttt) cc_final: 0.6760 (mptt) outliers start: 28 outliers final: 19 residues processed: 167 average time/residue: 0.6268 time to fit residues: 114.5469 Evaluate side-chains 173 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 686 LYS 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 497 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 104 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 109 optimal weight: 0.0970 chunk 79 optimal weight: 8.9990 chunk 65 optimal weight: 0.1980 chunk 69 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 146 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 435 ASN D 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.150058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.110775 restraints weight = 16656.782| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.05 r_work: 0.3188 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 13607 Z= 0.103 Angle : 0.489 10.267 18398 Z= 0.248 Chirality : 0.040 0.214 2028 Planarity : 0.004 0.048 2345 Dihedral : 5.568 65.382 1814 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.91 % Allowed : 20.53 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.21), residues: 1609 helix: 2.19 (0.17), residues: 917 sheet: -0.30 (0.44), residues: 137 loop : 0.46 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 82 TYR 0.013 0.001 TYR A 420 PHE 0.018 0.001 PHE A 167 TRP 0.009 0.001 TRP B 67 HIS 0.003 0.000 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00229 (13603) covalent geometry : angle 0.48912 (18398) hydrogen bonds : bond 0.03665 ( 766) hydrogen bonds : angle 3.96365 ( 2223) metal coordination : bond 0.00088 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4700.33 seconds wall clock time: 80 minutes 53.88 seconds (4853.88 seconds total)