Starting phenix.real_space_refine on Thu Aug 6 06:12:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cxh_45991/08_2026/9cxh_45991.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cxh_45991/08_2026/9cxh_45991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cxh_45991/08_2026/9cxh_45991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cxh_45991/08_2026/9cxh_45991.map" model { file = "/net/cci-nas-00/data/ceres_data/9cxh_45991/08_2026/9cxh_45991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cxh_45991/08_2026/9cxh_45991.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.035 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 4 5.49 5 Mg 2 5.21 5 S 80 5.16 5 C 8867 2.51 5 N 2323 2.21 5 O 2599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13877 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 6597 Classifications: {'peptide': 808} Link IDs: {'PTRANS': 32, 'TRANS': 775} Chain: "B" Number of atoms: 6445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6445 Classifications: {'peptide': 791} Link IDs: {'PTRANS': 32, 'TRANS': 758} Chain: "D" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 364 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 42} Chain breaks: 2 Chain: "C" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 373 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 43} Chain breaks: 2 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {' MG': 1, ' ZN': 1, '5GP%rna3p': 1, 'PCG': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {' MG': 1, ' ZN': 1, '5GP%rna3p': 1, 'PCG': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 3.43, per 1000 atoms: 0.25 Number of scatterers: 13877 At special positions: 0 Unit cell: (113.85, 120.45, 162.525, 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 80 16.00 P 4 15.00 Mg 2 11.99 O 2599 8.00 N 2323 7.00 C 8867 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 527.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 602 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 566 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" NE2 HIS B 602 " pdb="ZN ZN B 902 " - pdb=" NE2 HIS B 566 " 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3226 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 4 sheets defined 61.3% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 22 through 42 removed outlier: 4.886A pdb=" N VAL A 30 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N GLU A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL A 42 " --> pdb=" O LYS A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 70 Processing helix chain 'A' and resid 75 through 92 removed outlier: 4.014A pdb=" N GLY A 79 " --> pdb=" O THR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.808A pdb=" N ASN A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 150 removed outlier: 3.861A pdb=" N GLY A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 161 Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 206 through 251 removed outlier: 4.291A pdb=" N PHE A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 removed outlier: 3.559A pdb=" N VAL A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 298 Proline residue: A 295 - end of helix 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 433 through 461 Processing helix chain 'A' and resid 463 through 471 removed outlier: 3.595A pdb=" N ILE A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 removed outlier: 3.540A pdb=" N LYS A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 498 removed outlier: 3.559A pdb=" N GLU A 496 " --> pdb=" O ALA A 492 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 532 removed outlier: 3.583A pdb=" N ILE A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 541 through 556 Processing helix chain 'A' and resid 563 through 580 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: 3.774A pdb=" N ASP A 644 " --> pdb=" O THR A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 672 Processing helix chain 'A' and resid 673 through 693 removed outlier: 3.866A pdb=" N TYR A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N THR A 682 " --> pdb=" O PHE A 678 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N MET A 683 " --> pdb=" O LYS A 679 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 684 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A 693 " --> pdb=" O ASP A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 707 removed outlier: 4.245A pdb=" N ASP A 707 " --> pdb=" O TYR A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 724 removed outlier: 3.508A pdb=" N LYS A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 729 Processing helix chain 'A' and resid 730 through 755 removed outlier: 3.695A pdb=" N GLN A 736 " --> pdb=" O GLU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 770 removed outlier: 3.532A pdb=" N ASP A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ARG A 766 " --> pdb=" O MET A 763 " (cutoff:3.500A) removed outlier: 6.522A 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 781 Processing helix chain 'A' and resid 783 through 795 removed outlier: 4.148A pdb=" N VAL A 787 " --> pdb=" O VAL A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 823 removed outlier: 3.822A pdb=" N LEU A 802 " --> pdb=" O ILE A 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 71 removed outlier: 4.077A pdb=" N VAL B 69 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 92 removed outlier: 3.805A 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 141 through 150 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 Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 268 through 273 removed outlier: 3.765A pdb=" N ASN B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 292 Processing helix chain 'B' and resid 293 through 298 Processing helix chain 'B' and resid 341 through 346 removed outlier: 4.683A 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: 4.461A pdb=" N LEU B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 4.341A 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 473 through 478 removed outlier: 3.543A pdb=" N ASN B 478 " --> pdb=" O GLN B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 496 removed outlier: 3.647A pdb=" N GLU B 496 " --> pdb=" O ALA B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.881A pdb=" N GLU B 505 " --> pdb=" O ARG B 502 " (cutoff:3.500A) removed outlier: 3.704A 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 removed outlier: 3.698A pdb=" N ILE B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) 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: 3.739A 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: 3.721A pdb=" N ASP B 644 " --> pdb=" O THR B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 672 removed outlier: 3.587A pdb=" N THR B 672 " --> pdb=" O ALA B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 693 removed outlier: 5.105A pdb=" N THR B 682 " --> pdb=" O PHE B 678 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N MET B 683 " --> pdb=" O LYS B 679 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 693 " --> pdb=" O ASP B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 706 Processing helix chain 'B' and resid 707 through 725 Processing helix chain 'B' and resid 726 through 729 removed outlier: 3.572A pdb=" N LYS B 729 " --> pdb=" O ALA B 726 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 726 through 729' Processing helix chain 'B' and resid 730 through 757 Processing helix chain 'B' and resid 765 through 770 removed outlier: 5.011A 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: 4.318A pdb=" N VAL B 787 " --> pdb=" O VAL B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 823 removed outlier: 3.924A pdb=" N LEU B 802 " --> pdb=" O ILE B 798 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU B 818 " --> pdb=" O SER B 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 removed outlier: 3.854A pdb=" N GLY D 59 " --> pdb=" O GLY D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 84 removed outlier: 4.143A pdb=" N ALA D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 removed outlier: 3.850A pdb=" N GLY C 59 " --> pdb=" O GLY C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 84 removed outlier: 4.045A pdb=" N ALA C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 137 removed outlier: 6.739A pdb=" N GLU A 109 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ARG A 104 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ALA A 111 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ARG A 102 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ARG A 113 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU A 100 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU A 115 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N MET A 98 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG A 95 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL A 197 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU A 191 " --> pdb=" O CYS A 101 " (cutoff:3.500A) removed outlier: 11.541A pdb=" N SER A 103 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 14.108A pdb=" N GLU A 189 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N VAL A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 186 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 3.644A 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: 3.938A pdb=" N LYS A 319 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL A 400 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.738A 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: 6.643A pdb=" N GLU B 109 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ARG B 104 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ALA B 111 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ARG B 102 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARG B 113 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU B 100 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU B 115 " --> pdb=" O MET B 98 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N MET B 98 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ARG B 95 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL B 197 " --> pdb=" O ARG B 95 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU B 191 " --> pdb=" O CYS B 101 " (cutoff:3.500A) removed outlier: 11.539A pdb=" N SER B 103 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 14.119A pdb=" N GLU B 189 " --> pdb=" O SER B 103 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL B 190 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL B 186 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA B 192 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 194 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 331 through 335 removed outlier: 3.735A pdb=" N LYS B 319 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL B 400 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY B 401 " --> pdb=" O ILE B 392 " (cutoff:3.500A) 772 hydrogen bonds defined for protein. 2247 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: 2.33 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4327 1.34 - 1.46: 2079 1.46 - 1.58: 7641 1.58 - 1.70: 6 1.70 - 1.82: 138 Bond restraints: 14191 Sorted by residual: bond pdb=" C1' PCG B 901 " pdb=" O4' PCG B 901 " ideal model delta sigma weight residual 1.409 1.601 -0.192 2.00e-02 2.50e+03 9.21e+01 bond pdb=" C1' PCG A 901 " pdb=" O4' PCG A 901 " ideal model delta sigma weight residual 1.409 1.599 -0.190 2.00e-02 2.50e+03 9.03e+01 bond pdb=" C6 PCG A 901 " pdb=" O6 PCG A 901 " ideal model delta sigma weight residual 1.219 1.398 -0.179 2.00e-02 2.50e+03 7.97e+01 bond pdb=" C6 PCG B 901 " pdb=" O6 PCG B 901 " ideal model delta sigma weight residual 1.219 1.396 -0.177 2.00e-02 2.50e+03 7.86e+01 bond pdb=" C5 PCG A 901 " pdb=" N7 PCG A 901 " ideal model delta sigma weight residual 1.370 1.525 -0.155 2.00e-02 2.50e+03 6.00e+01 ... (remaining 14186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 19033 2.79 - 5.57: 112 5.57 - 8.36: 34 8.36 - 11.15: 18 11.15 - 13.93: 2 Bond angle restraints: 19199 Sorted by residual: angle pdb=" C4 PCG A 901 " pdb=" N9 PCG A 901 " pdb=" C8 PCG A 901 " ideal model delta sigma weight residual 106.51 120.44 -13.93 3.00e+00 1.11e-01 2.16e+01 angle pdb=" C4 PCG B 901 " pdb=" N9 PCG B 901 " pdb=" C8 PCG B 901 " ideal model delta sigma weight residual 106.51 120.33 -13.82 3.00e+00 1.11e-01 2.12e+01 angle pdb=" N GLN A 776 " pdb=" CA GLN A 776 " pdb=" CB GLN A 776 " ideal model delta sigma weight residual 110.16 116.64 -6.48 1.48e+00 4.57e-01 1.92e+01 angle pdb=" N SER A 49 " pdb=" CA SER A 49 " pdb=" CB SER A 49 " ideal model delta sigma weight residual 114.17 109.63 4.54 1.14e+00 7.69e-01 1.58e+01 angle pdb=" O3' PCG A 901 " pdb=" PA PCG A 901 " pdb=" O5' PCG A 901 " ideal model delta sigma weight residual 103.94 114.81 -10.87 3.00e+00 1.11e-01 1.31e+01 ... (remaining 19194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 7493 17.88 - 35.77: 833 35.77 - 53.65: 206 53.65 - 71.54: 87 71.54 - 89.42: 15 Dihedral angle restraints: 8634 sinusoidal: 3665 harmonic: 4969 Sorted by residual: dihedral pdb=" CA MET A 48 " pdb=" C MET A 48 " pdb=" N SER A 49 " pdb=" CA SER A 49 " ideal model delta harmonic sigma weight residual 180.00 159.93 20.07 0 5.00e+00 4.00e-02 1.61e+01 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 -160.38 -19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA TYR B 406 " pdb=" C TYR B 406 " pdb=" N ASN B 407 " pdb=" CA ASN B 407 " ideal model delta harmonic sigma weight residual -180.00 -161.94 -18.06 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 8631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1745 0.053 - 0.105: 319 0.105 - 0.158: 47 0.158 - 0.210: 0 0.210 - 0.263: 2 Chirality restraints: 2113 Sorted by residual: chirality pdb=" C2' PCG B 901 " pdb=" C1' PCG B 901 " pdb=" C3' PCG B 901 " pdb=" O2' PCG B 901 " both_signs ideal model delta sigma weight residual False -2.74 -2.48 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C2' PCG A 901 " pdb=" C1' PCG A 901 " pdb=" C3' PCG A 901 " pdb=" O2' PCG A 901 " both_signs ideal model delta sigma weight residual False -2.74 -2.50 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ILE B 324 " pdb=" N ILE B 324 " pdb=" C ILE B 324 " pdb=" CB ILE B 324 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 2110 not shown) Planarity restraints: 2444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 219 " -0.013 2.00e-02 2.50e+03 1.53e-02 4.12e+00 pdb=" CG PHE A 219 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 219 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 219 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 219 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 219 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 219 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 118 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO A 119 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 772 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A 773 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 773 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 773 " -0.021 5.00e-02 4.00e+02 ... (remaining 2441 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 50 2.51 - 3.11: 10169 3.11 - 3.71: 21123 3.71 - 4.30: 29804 4.30 - 4.90: 51124 Nonbonded interactions: 112270 Sorted by model distance: nonbonded pdb="ZN ZN A 902 " pdb=" O3P 5GP A 904 " model vdw 1.914 2.230 nonbonded pdb="MG MG A 903 " pdb=" O2P 5GP A 904 " model vdw 1.928 2.170 nonbonded pdb=" OD2 ASP A 603 " pdb="ZN ZN A 902 " model vdw 1.946 2.230 nonbonded pdb="ZN ZN B 902 " pdb=" O3P 5GP B 904 " model vdw 1.969 2.230 nonbonded pdb=" OD2 ASP B 603 " pdb="ZN ZN B 902 " model vdw 1.983 2.230 ... (remaining 112265 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 33 through 823 or resid 901 through 904)) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 26 through 49 or resid 52 through 87)) selection = (chain 'D' and (resid 26 through 63 or resid 72 through 87)) } 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: 2.880 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: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.720 Find NCS groups from input model: 0.410 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 : 0.006 0.192 14195 Z= 0.319 Angle : 0.662 13.934 19199 Z= 0.304 Chirality : 0.041 0.263 2113 Planarity : 0.004 0.040 2444 Dihedral : 16.885 89.423 5408 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 17.43 % Favored : 82.57 % 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: 1.60 (0.21), residues: 1676 helix: 1.73 (0.17), residues: 919 sheet: 0.06 (0.43), residues: 143 loop : 0.42 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 86 TYR 0.015 0.001 TYR B 406 PHE 0.035 0.001 PHE A 219 TRP 0.015 0.001 TRP A 67 HIS 0.007 0.001 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.32 (14191) covalent geometry : angle 0.66158 / 0.30 (19199) hydrogen bonds : bond 0.14298 / 9.88 ( 772) hydrogen bonds : angle 5.82101 / 4.14 ( 2247) metal coordination : bond 0.00325 / 0.16 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.546 Fit side-chains REVERT: A 48 MET cc_start: 0.6281 (mmp) cc_final: 0.5114 (ptt) REVERT: A 82 ARG cc_start: 0.7268 (ttm110) cc_final: 0.6607 (mtm180) REVERT: A 136 PHE cc_start: 0.8414 (m-80) cc_final: 0.8111 (m-80) REVERT: A 145 TRP cc_start: 0.7081 (t-100) cc_final: 0.6143 (t60) REVERT: A 151 LYS cc_start: 0.7422 (mmtt) cc_final: 0.6555 (mttm) REVERT: A 182 THR cc_start: 0.8455 (m) cc_final: 0.7923 (p) REVERT: A 232 MET cc_start: 0.8416 (mmm) cc_final: 0.8090 (mmm) REVERT: A 293 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7202 (mt-10) REVERT: A 367 ASP cc_start: 0.7981 (t0) cc_final: 0.7501 (t0) REVERT: A 440 ASP cc_start: 0.7582 (m-30) cc_final: 0.7105 (t70) REVERT: A 465 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6800 (tp30) REVERT: B 48 MET cc_start: 0.3617 (mmp) cc_final: 0.3389 (mmp) REVERT: B 133 GLU cc_start: 0.8241 (pt0) cc_final: 0.8007 (pt0) REVERT: B 151 LYS cc_start: 0.7363 (pttt) cc_final: 0.6777 (mttp) REVERT: B 170 LYS cc_start: 0.7805 (mmtp) cc_final: 0.7324 (mmmt) REVERT: B 232 MET cc_start: 0.8599 (mmt) cc_final: 0.8319 (mmm) REVERT: B 273 ASN cc_start: 0.8133 (t0) cc_final: 0.7740 (t0) REVERT: B 369 TYR cc_start: 0.7914 (t80) cc_final: 0.7648 (t80) REVERT: B 394 ASN cc_start: 0.7082 (t0) cc_final: 0.6762 (t0) REVERT: B 415 ASP cc_start: 0.8354 (m-30) cc_final: 0.8042 (m-30) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1250 time to fit residues: 35.6572 Evaluate side-chains 164 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 GLN A 126 ASN A 148 HIS A 153 HIS A 316 ASN A 651 GLN A 652 ASN A 734 GLN B 126 ASN B 153 HIS B 569 ASN B 572 GLN B 734 GLN D 34 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.147434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.112238 restraints weight = 17287.758| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.07 r_work: 0.3179 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14195 Z= 0.127 Angle : 0.485 7.519 19199 Z= 0.257 Chirality : 0.041 0.180 2113 Planarity : 0.004 0.042 2444 Dihedral : 6.008 55.664 1931 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.56 % Allowed : 16.51 % Favored : 80.93 % 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: 1676 helix: 1.97 (0.17), residues: 933 sheet: -0.12 (0.41), residues: 143 loop : 0.59 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 809 TYR 0.016 0.001 TYR B 406 PHE 0.011 0.001 PHE A 219 TRP 0.006 0.001 TRP A 67 HIS 0.008 0.001 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (14191) covalent geometry : angle 0.48462 / 0.26 (19199) hydrogen bonds : bond 0.04790 / 3.21 ( 772) hydrogen bonds : angle 4.52154 / 3.23 ( 2247) metal coordination : bond 0.00271 / 0.13 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6496 (OUTLIER) cc_final: 0.5101 (ptm) REVERT: A 82 ARG cc_start: 0.7627 (ttm110) cc_final: 0.6951 (mtm180) REVERT: A 136 PHE cc_start: 0.8645 (m-80) cc_final: 0.8360 (m-80) REVERT: A 151 LYS cc_start: 0.7772 (mmtt) cc_final: 0.6901 (mttm) REVERT: A 293 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7692 (mt-10) REVERT: A 326 HIS cc_start: 0.8160 (p90) cc_final: 0.7891 (p90) REVERT: A 367 ASP cc_start: 0.8244 (t0) cc_final: 0.7811 (t0) REVERT: A 379 GLU cc_start: 0.7880 (mp0) cc_final: 0.7529 (mp0) REVERT: A 440 ASP cc_start: 0.7937 (m-30) cc_final: 0.7608 (t70) REVERT: A 465 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7352 (tp30) REVERT: B 48 MET cc_start: 0.4015 (mmp) cc_final: 0.3510 (mmp) REVERT: B 151 LYS cc_start: 0.7585 (pttt) cc_final: 0.6947 (pptt) REVERT: B 170 LYS cc_start: 0.7910 (mmtp) cc_final: 0.7429 (mmmt) REVERT: B 232 MET cc_start: 0.8938 (mmt) cc_final: 0.8721 (mmm) REVERT: B 273 ASN cc_start: 0.8385 (t0) cc_final: 0.8115 (t0) REVERT: B 340 ASP cc_start: 0.7553 (t0) cc_final: 0.6979 (m-30) REVERT: B 369 TYR cc_start: 0.8133 (t80) cc_final: 0.7840 (t80) REVERT: B 397 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7626 (mt-10) REVERT: B 418 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7585 (m-30) REVERT: B 653 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7923 (pp) outliers start: 39 outliers final: 20 residues processed: 209 average time/residue: 0.1101 time to fit residues: 34.9546 Evaluate side-chains 194 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain D residue 34 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 120 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 HIS A 316 ASN A 734 GLN B 435 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.145836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110454 restraints weight = 17406.369| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.05 r_work: 0.3155 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14195 Z= 0.146 Angle : 0.479 7.039 19199 Z= 0.255 Chirality : 0.041 0.180 2113 Planarity : 0.004 0.042 2444 Dihedral : 5.951 55.766 1931 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.95 % Allowed : 16.51 % Favored : 80.54 % 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: 1.86 (0.21), residues: 1676 helix: 1.99 (0.17), residues: 933 sheet: -0.25 (0.42), residues: 145 loop : 0.56 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 553 TYR 0.015 0.001 TYR B 406 PHE 0.011 0.001 PHE B 568 TRP 0.005 0.001 TRP A 145 HIS 0.008 0.001 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (14191) covalent geometry : angle 0.47896 / 0.25 (19199) hydrogen bonds : bond 0.04736 / 3.17 ( 772) hydrogen bonds : angle 4.38656 / 3.12 ( 2247) metal coordination : bond 0.00458 / 0.22 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6470 (OUTLIER) cc_final: 0.5145 (ptp) REVERT: A 82 ARG cc_start: 0.7705 (ttm110) cc_final: 0.7028 (mtm180) REVERT: A 136 PHE cc_start: 0.8700 (m-80) cc_final: 0.8378 (m-80) REVERT: A 151 LYS cc_start: 0.7817 (mmtt) cc_final: 0.6972 (mtmm) REVERT: A 293 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7648 (mt-10) REVERT: A 367 ASP cc_start: 0.8285 (t0) cc_final: 0.7840 (t0) REVERT: A 440 ASP cc_start: 0.8012 (m-30) cc_final: 0.7661 (t70) REVERT: A 465 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7356 (tp30) REVERT: B 133 GLU cc_start: 0.8249 (pt0) cc_final: 0.8043 (pt0) REVERT: B 151 LYS cc_start: 0.7588 (pttt) cc_final: 0.7020 (mttp) REVERT: B 170 LYS cc_start: 0.7915 (mmtp) cc_final: 0.7436 (mmmt) REVERT: B 273 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.8118 (t0) REVERT: B 340 ASP cc_start: 0.7569 (t0) cc_final: 0.6986 (m-30) REVERT: B 369 TYR cc_start: 0.8220 (t80) cc_final: 0.7913 (t80) REVERT: B 418 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7617 (m-30) REVERT: B 595 MET cc_start: 0.8645 (mmm) cc_final: 0.8393 (mtt) REVERT: B 653 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7886 (pp) outliers start: 45 outliers final: 25 residues processed: 207 average time/residue: 0.1105 time to fit residues: 34.5149 Evaluate side-chains 196 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 785 THR Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain D residue 87 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 87 optimal weight: 0.2980 chunk 63 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 HIS B 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.147320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.111908 restraints weight = 17347.254| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.05 r_work: 0.3178 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14195 Z= 0.113 Angle : 0.454 6.870 19199 Z= 0.240 Chirality : 0.040 0.173 2113 Planarity : 0.003 0.043 2444 Dihedral : 5.842 55.412 1931 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.62 % Allowed : 17.37 % Favored : 80.01 % 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: 1.96 (0.21), residues: 1676 helix: 2.10 (0.17), residues: 933 sheet: -0.26 (0.42), residues: 145 loop : 0.55 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 553 TYR 0.015 0.001 TYR B 406 PHE 0.010 0.001 PHE B 568 TRP 0.004 0.001 TRP B 67 HIS 0.007 0.001 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (14191) covalent geometry : angle 0.45403 / 0.24 (19199) hydrogen bonds : bond 0.04346 / 2.90 ( 772) hydrogen bonds : angle 4.23355 / 3.02 ( 2247) metal coordination : bond 0.00281 / 0.14 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6422 (OUTLIER) cc_final: 0.5101 (ptp) REVERT: A 82 ARG cc_start: 0.7740 (ttm110) cc_final: 0.7056 (mtm180) REVERT: A 136 PHE cc_start: 0.8662 (m-80) cc_final: 0.8371 (m-80) REVERT: A 151 LYS cc_start: 0.7795 (mmtt) cc_final: 0.6895 (mttm) REVERT: A 293 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7672 (mt-10) REVERT: A 367 ASP cc_start: 0.8292 (t0) cc_final: 0.7878 (t0) REVERT: A 442 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7583 (mtp) REVERT: A 465 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7419 (tp30) REVERT: B 57 GLU cc_start: 0.6904 (pp20) cc_final: 0.6212 (pp20) REVERT: B 86 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7654 (tpt-90) REVERT: B 133 GLU cc_start: 0.8225 (pt0) cc_final: 0.8008 (pt0) REVERT: B 151 LYS cc_start: 0.7570 (pttt) cc_final: 0.7019 (mttp) REVERT: B 170 LYS cc_start: 0.7902 (mmtp) cc_final: 0.7429 (mmmt) REVERT: B 273 ASN cc_start: 0.8341 (t0) cc_final: 0.8136 (t0) REVERT: B 340 ASP cc_start: 0.7527 (t0) cc_final: 0.6916 (m-30) REVERT: B 369 TYR cc_start: 0.8235 (t80) cc_final: 0.7972 (t80) REVERT: B 418 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7556 (m-30) REVERT: B 442 MET cc_start: 0.8220 (tpp) cc_final: 0.7941 (mmm) REVERT: B 595 MET cc_start: 0.8620 (mmm) cc_final: 0.8328 (mtt) REVERT: B 653 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7833 (pp) outliers start: 40 outliers final: 26 residues processed: 210 average time/residue: 0.1133 time to fit residues: 35.9595 Evaluate side-chains 202 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 785 THR Chi-restraints excluded: chain B residue 805 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 85 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 80 optimal weight: 0.0030 chunk 150 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 HIS A 734 GLN B 435 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.146667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.111214 restraints weight = 17424.217| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.05 r_work: 0.3148 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14195 Z= 0.124 Angle : 0.461 7.235 19199 Z= 0.243 Chirality : 0.040 0.184 2113 Planarity : 0.003 0.043 2444 Dihedral : 5.812 55.480 1931 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.21 % Allowed : 16.58 % Favored : 80.21 % 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: 1.99 (0.21), residues: 1676 helix: 2.13 (0.17), residues: 933 sheet: -0.17 (0.42), residues: 143 loop : 0.54 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 553 TYR 0.015 0.001 TYR B 406 PHE 0.010 0.001 PHE B 568 TRP 0.005 0.001 TRP A 145 HIS 0.006 0.001 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (14191) covalent geometry : angle 0.46070 / 0.24 (19199) hydrogen bonds : bond 0.04354 / 2.90 ( 772) hydrogen bonds : angle 4.19655 / 2.99 ( 2247) metal coordination : bond 0.00354 / 0.17 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 175 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6442 (OUTLIER) cc_final: 0.4983 (ptm) REVERT: A 82 ARG cc_start: 0.7711 (ttm110) cc_final: 0.7024 (mtm180) REVERT: A 136 PHE cc_start: 0.8643 (m-80) cc_final: 0.8312 (m-80) REVERT: A 151 LYS cc_start: 0.7803 (mmtt) cc_final: 0.6943 (mtmm) REVERT: A 293 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7721 (mt-10) REVERT: A 367 ASP cc_start: 0.8344 (t0) cc_final: 0.7950 (t0) REVERT: A 442 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7638 (mtp) REVERT: A 465 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7390 (tp30) REVERT: A 557 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8559 (mtt180) REVERT: B 57 GLU cc_start: 0.6802 (pp20) cc_final: 0.6115 (pp20) REVERT: B 86 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7678 (tpt-90) REVERT: B 133 GLU cc_start: 0.8263 (pt0) cc_final: 0.8018 (pt0) REVERT: B 151 LYS cc_start: 0.7566 (pttt) cc_final: 0.7017 (mttp) REVERT: B 170 LYS cc_start: 0.7939 (mmtp) cc_final: 0.7471 (mmmt) REVERT: B 177 LYS cc_start: 0.6240 (OUTLIER) cc_final: 0.5587 (mttp) REVERT: B 340 ASP cc_start: 0.7478 (t0) cc_final: 0.6896 (m-30) REVERT: B 369 TYR cc_start: 0.8284 (t80) cc_final: 0.8032 (t80) REVERT: B 397 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7603 (mt-10) REVERT: B 418 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7579 (m-30) REVERT: B 595 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8355 (mtt) REVERT: B 653 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7877 (pp) outliers start: 49 outliers final: 30 residues processed: 211 average time/residue: 0.1151 time to fit residues: 36.4355 Evaluate side-chains 207 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 785 THR Chi-restraints excluded: chain B residue 805 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 76 optimal weight: 0.1980 chunk 72 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 51 optimal weight: 0.1980 chunk 109 optimal weight: 1.9990 chunk 107 optimal weight: 0.0770 chunk 99 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 164 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 HIS A 316 ASN A 734 GLN B 435 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.147799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.112475 restraints weight = 17263.841| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.04 r_work: 0.3166 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14195 Z= 0.108 Angle : 0.452 8.102 19199 Z= 0.238 Chirality : 0.040 0.174 2113 Planarity : 0.003 0.044 2444 Dihedral : 5.755 54.666 1931 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.56 % Allowed : 17.76 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.21), residues: 1676 helix: 2.20 (0.17), residues: 934 sheet: -0.14 (0.43), residues: 143 loop : 0.55 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 553 TYR 0.015 0.001 TYR B 406 PHE 0.009 0.001 PHE B 568 TRP 0.005 0.001 TRP B 245 HIS 0.006 0.001 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (14191) covalent geometry : angle 0.45155 / 0.24 (19199) hydrogen bonds : bond 0.04177 / 2.78 ( 772) hydrogen bonds : angle 4.12905 / 2.94 ( 2247) metal coordination : bond 0.00268 / 0.13 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 173 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6403 (mmp) cc_final: 0.4931 (ptm) REVERT: A 82 ARG cc_start: 0.7710 (ttm110) cc_final: 0.7014 (mtm180) REVERT: A 136 PHE cc_start: 0.8608 (m-80) cc_final: 0.8292 (m-80) REVERT: A 151 LYS cc_start: 0.7831 (mmtt) cc_final: 0.6931 (mttm) REVERT: A 293 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7688 (mt-10) REVERT: A 367 ASP cc_start: 0.8334 (t0) cc_final: 0.7942 (t0) REVERT: A 465 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7408 (tp30) REVERT: A 557 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8570 (mtt180) REVERT: B 57 GLU cc_start: 0.6694 (pp20) cc_final: 0.6121 (pp20) REVERT: B 86 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7642 (tpt-90) REVERT: B 133 GLU cc_start: 0.8272 (pt0) cc_final: 0.8055 (pt0) REVERT: B 151 LYS cc_start: 0.7555 (pttt) cc_final: 0.7015 (mttp) REVERT: B 170 LYS cc_start: 0.7915 (mmtp) cc_final: 0.7458 (mmmt) REVERT: B 177 LYS cc_start: 0.6345 (OUTLIER) cc_final: 0.5720 (mttp) REVERT: B 397 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7602 (mt-10) REVERT: B 595 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8337 (mtt) REVERT: B 653 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7830 (pp) outliers start: 39 outliers final: 24 residues processed: 203 average time/residue: 0.1198 time to fit residues: 36.1546 Evaluate side-chains 199 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 785 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 162 optimal weight: 0.1980 chunk 3 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 93 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 HIS B 234 ASN B 435 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.147554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112310 restraints weight = 17279.191| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.04 r_work: 0.3166 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14195 Z= 0.115 Angle : 0.460 9.034 19199 Z= 0.241 Chirality : 0.040 0.174 2113 Planarity : 0.003 0.044 2444 Dihedral : 5.739 54.379 1931 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.21 % Allowed : 17.23 % Favored : 79.55 % 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: 2.08 (0.21), residues: 1676 helix: 2.21 (0.17), residues: 934 sheet: -0.13 (0.43), residues: 143 loop : 0.56 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 553 TYR 0.015 0.001 TYR B 406 PHE 0.010 0.001 PHE B 568 TRP 0.005 0.001 TRP A 67 HIS 0.006 0.001 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (14191) covalent geometry : angle 0.45997 / 0.24 (19199) hydrogen bonds : bond 0.04170 / 2.77 ( 772) hydrogen bonds : angle 4.11800 / 2.94 ( 2247) metal coordination : bond 0.00312 / 0.15 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 173 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6425 (OUTLIER) cc_final: 0.4946 (ptm) REVERT: A 82 ARG cc_start: 0.7726 (ttm110) cc_final: 0.7027 (mtm180) REVERT: A 136 PHE cc_start: 0.8606 (m-80) cc_final: 0.8310 (m-80) REVERT: A 151 LYS cc_start: 0.7853 (mmtt) cc_final: 0.6961 (mttm) REVERT: A 293 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7706 (mt-10) REVERT: A 367 ASP cc_start: 0.8335 (t0) cc_final: 0.7920 (t0) REVERT: A 465 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7383 (tp30) REVERT: A 557 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8574 (mtt180) REVERT: B 57 GLU cc_start: 0.6703 (pp20) cc_final: 0.6133 (pp20) REVERT: B 86 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7688 (tpt-90) REVERT: B 133 GLU cc_start: 0.8261 (pt0) cc_final: 0.8042 (pt0) REVERT: B 151 LYS cc_start: 0.7571 (pttt) cc_final: 0.7001 (mttp) REVERT: B 170 LYS cc_start: 0.7926 (mmtp) cc_final: 0.7478 (mmmt) REVERT: B 177 LYS cc_start: 0.6372 (OUTLIER) cc_final: 0.5821 (mttp) REVERT: B 340 ASP cc_start: 0.7536 (t0) cc_final: 0.7063 (m-30) REVERT: B 397 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7581 (mt-10) REVERT: B 408 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7985 (mtp180) REVERT: B 418 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7567 (m-30) REVERT: B 595 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8351 (mtt) REVERT: B 653 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7850 (pp) outliers start: 49 outliers final: 34 residues processed: 211 average time/residue: 0.1229 time to fit residues: 38.6301 Evaluate side-chains 211 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 785 THR Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain D residue 87 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 110 optimal weight: 4.9990 chunk 74 optimal weight: 0.0270 chunk 127 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.3980 chunk 52 optimal weight: 0.1980 chunk 33 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 5 optimal weight: 0.0870 overall best weight: 0.2616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 HIS A 734 GLN B 326 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.150363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.115357 restraints weight = 17239.675| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.04 r_work: 0.3219 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14195 Z= 0.097 Angle : 0.447 7.111 19199 Z= 0.235 Chirality : 0.039 0.170 2113 Planarity : 0.003 0.044 2444 Dihedral : 5.630 53.269 1931 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.82 % Allowed : 18.22 % Favored : 78.96 % 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: 2.17 (0.21), residues: 1676 helix: 2.29 (0.17), residues: 937 sheet: -0.11 (0.43), residues: 143 loop : 0.59 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 553 TYR 0.015 0.001 TYR B 406 PHE 0.009 0.001 PHE C 30 TRP 0.010 0.001 TRP B 245 HIS 0.005 0.000 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.10 (14191) covalent geometry : angle 0.44727 / 0.23 (19199) hydrogen bonds : bond 0.03855 / 2.56 ( 772) hydrogen bonds : angle 4.02019 / 2.86 ( 2247) metal coordination : bond 0.00138 / 0.07 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6356 (OUTLIER) cc_final: 0.4882 (ptm) REVERT: A 82 ARG cc_start: 0.7667 (ttm110) cc_final: 0.6973 (mtm180) REVERT: A 136 PHE cc_start: 0.8552 (m-80) cc_final: 0.8216 (m-80) REVERT: A 151 LYS cc_start: 0.7818 (mmtt) cc_final: 0.6935 (mttm) REVERT: A 188 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7944 (ptmm) REVERT: A 284 MET cc_start: 0.8667 (mmm) cc_final: 0.8318 (mmm) REVERT: A 293 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7553 (mt-10) REVERT: A 367 ASP cc_start: 0.8319 (t0) cc_final: 0.7917 (t0) REVERT: A 465 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7398 (tp30) REVERT: A 539 LYS cc_start: 0.8157 (mttm) cc_final: 0.7890 (mmtp) REVERT: A 557 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8540 (mtt180) REVERT: B 57 GLU cc_start: 0.6577 (pp20) cc_final: 0.6020 (pp20) REVERT: B 86 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7607 (tpt-90) REVERT: B 133 GLU cc_start: 0.8205 (pt0) cc_final: 0.7980 (pt0) REVERT: B 151 LYS cc_start: 0.7537 (pttt) cc_final: 0.6992 (mttp) REVERT: B 170 LYS cc_start: 0.7900 (mmtp) cc_final: 0.7468 (mmmt) REVERT: B 340 ASP cc_start: 0.7395 (t0) cc_final: 0.6916 (m-30) REVERT: B 397 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7548 (mt-10) REVERT: B 418 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7463 (m-30) REVERT: B 595 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8324 (mtt) REVERT: B 653 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7728 (pp) outliers start: 43 outliers final: 26 residues processed: 215 average time/residue: 0.1328 time to fit residues: 41.6824 Evaluate side-chains 208 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 751 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 0.0470 chunk 83 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 49 optimal weight: 0.4980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.149721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114676 restraints weight = 17330.965| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.05 r_work: 0.3193 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14195 Z= 0.103 Angle : 0.453 7.229 19199 Z= 0.237 Chirality : 0.040 0.173 2113 Planarity : 0.003 0.044 2444 Dihedral : 5.600 53.214 1931 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.36 % Allowed : 18.68 % Favored : 78.96 % 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: 2.20 (0.21), residues: 1676 helix: 2.32 (0.17), residues: 936 sheet: -0.08 (0.43), residues: 143 loop : 0.58 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 553 TYR 0.015 0.001 TYR B 406 PHE 0.009 0.001 PHE B 568 TRP 0.007 0.001 TRP B 245 HIS 0.005 0.000 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (14191) covalent geometry : angle 0.45340 / 0.24 (19199) hydrogen bonds : bond 0.03886 / 2.59 ( 772) hydrogen bonds : angle 4.01538 / 2.86 ( 2247) metal coordination : bond 0.00207 / 0.10 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6354 (OUTLIER) cc_final: 0.4866 (ptm) REVERT: A 82 ARG cc_start: 0.7713 (ttm110) cc_final: 0.7023 (mtm180) REVERT: A 136 PHE cc_start: 0.8550 (m-80) cc_final: 0.8220 (m-80) REVERT: A 151 LYS cc_start: 0.7833 (mmtt) cc_final: 0.6960 (mttm) REVERT: A 188 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7962 (ptmm) REVERT: A 293 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7553 (mt-10) REVERT: A 367 ASP cc_start: 0.8316 (t0) cc_final: 0.7914 (t0) REVERT: A 465 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7422 (tp30) REVERT: A 539 LYS cc_start: 0.8151 (mttm) cc_final: 0.7885 (mmtp) REVERT: A 557 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8549 (mtt180) REVERT: B 57 GLU cc_start: 0.6534 (pp20) cc_final: 0.5972 (pp20) REVERT: B 86 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7640 (tpt-90) REVERT: B 151 LYS cc_start: 0.7558 (pttt) cc_final: 0.6994 (mttp) REVERT: B 170 LYS cc_start: 0.7911 (mmtp) cc_final: 0.7498 (mmmt) REVERT: B 340 ASP cc_start: 0.7381 (t0) cc_final: 0.6907 (m-30) REVERT: B 397 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7520 (mt-10) REVERT: B 418 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7482 (m-30) REVERT: B 595 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8347 (mtt) REVERT: B 653 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7751 (pp) outliers start: 36 outliers final: 24 residues processed: 204 average time/residue: 0.1279 time to fit residues: 37.9122 Evaluate side-chains 200 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 665 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 15 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 130 optimal weight: 0.0980 chunk 149 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.149389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.114300 restraints weight = 17323.042| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.04 r_work: 0.3189 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14195 Z= 0.108 Angle : 0.465 8.272 19199 Z= 0.243 Chirality : 0.040 0.173 2113 Planarity : 0.003 0.044 2444 Dihedral : 5.618 53.273 1931 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.29 % Allowed : 18.68 % Favored : 79.03 % 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: 2.20 (0.21), residues: 1676 helix: 2.32 (0.17), residues: 936 sheet: -0.12 (0.43), residues: 143 loop : 0.59 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 553 TYR 0.014 0.001 TYR B 406 PHE 0.009 0.001 PHE B 568 TRP 0.009 0.001 TRP B 245 HIS 0.005 0.000 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (14191) covalent geometry : angle 0.46463 / 0.24 (19199) hydrogen bonds : bond 0.03919 / 2.61 ( 772) hydrogen bonds : angle 4.02409 / 2.86 ( 2247) metal coordination : bond 0.00246 / 0.12 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6320 (OUTLIER) cc_final: 0.4826 (ptm) REVERT: A 82 ARG cc_start: 0.7700 (ttm110) cc_final: 0.7010 (mtm180) REVERT: A 136 PHE cc_start: 0.8542 (m-80) cc_final: 0.8206 (m-80) REVERT: A 151 LYS cc_start: 0.7891 (mmtt) cc_final: 0.7017 (mttm) REVERT: A 188 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7945 (ptmm) REVERT: A 293 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7563 (mt-10) REVERT: A 367 ASP cc_start: 0.8318 (t0) cc_final: 0.7918 (t0) REVERT: A 465 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7422 (tp30) REVERT: A 539 LYS cc_start: 0.8128 (mttm) cc_final: 0.7861 (mmtp) REVERT: A 557 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8567 (mtt180) REVERT: B 57 GLU cc_start: 0.6524 (pp20) cc_final: 0.6132 (pp20) REVERT: B 86 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7754 (tpt170) REVERT: B 132 LYS cc_start: 0.8146 (mmtp) cc_final: 0.7834 (mmmt) REVERT: B 151 LYS cc_start: 0.7553 (pttt) cc_final: 0.6977 (mttp) REVERT: B 170 LYS cc_start: 0.7885 (mmtp) cc_final: 0.7465 (mmmt) REVERT: B 340 ASP cc_start: 0.7416 (t0) cc_final: 0.6921 (m-30) REVERT: B 397 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7512 (mt-10) REVERT: B 418 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7499 (m-30) REVERT: B 510 ARG cc_start: 0.7985 (mtm-85) cc_final: 0.7291 (ptt-90) REVERT: B 595 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8351 (mtt) REVERT: B 653 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7769 (pp) outliers start: 35 outliers final: 23 residues processed: 197 average time/residue: 0.1288 time to fit residues: 36.7930 Evaluate side-chains 198 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 665 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 93 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 160 optimal weight: 0.0040 chunk 153 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.152831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.118607 restraints weight = 17286.298| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.90 r_work: 0.3239 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14195 Z= 0.104 Angle : 0.467 8.130 19199 Z= 0.243 Chirality : 0.040 0.171 2113 Planarity : 0.003 0.044 2444 Dihedral : 5.646 55.368 1931 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.03 % Allowed : 19.00 % Favored : 78.96 % 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: 2.25 (0.21), residues: 1676 helix: 2.35 (0.17), residues: 937 sheet: -0.03 (0.44), residues: 141 loop : 0.61 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 553 TYR 0.014 0.001 TYR B 406 PHE 0.009 0.001 PHE B 568 TRP 0.009 0.001 TRP B 245 HIS 0.005 0.000 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (14191) covalent geometry : angle 0.46719 / 0.24 (19199) hydrogen bonds : bond 0.03860 / 2.58 ( 772) hydrogen bonds : angle 4.00361 / 2.85 ( 2247) metal coordination : bond 0.00205 / 0.10 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4023.37 seconds wall clock time: 69 minutes 32.33 seconds (4172.33 seconds total)