Starting phenix.real_space_refine on Tue Nov 18 11:58:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cxh_45991/11_2025/9cxh_45991.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cxh_45991/11_2025/9cxh_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 { model { file = "/net/cci-nas-00/data/ceres_data/9cxh_45991/11_2025/9cxh_45991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cxh_45991/11_2025/9cxh_45991.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cxh_45991/11_2025/9cxh_45991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cxh_45991/11_2025/9cxh_45991.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.38, per 1000 atoms: 0.24 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: 1.38 Conformation dependent library (CDL) restraints added in 699.6 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: 0.41 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: 2.29 Time building geometry restraints manager: 1.80 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: 19030 2.79 - 5.57: 115 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: 1739 0.053 - 0.105: 323 0.105 - 0.158: 47 0.158 - 0.210: 2 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=" C1' 5GP A 904 " pdb=" C2' 5GP A 904 " pdb=" N9 5GP A 904 " pdb=" O4' 5GP A 904 " both_signs ideal model delta sigma weight residual False 2.29 2.46 -0.16 2.00e-01 2.50e+01 6.71e-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: 3.120 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.730 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.192 14195 Z= 0.324 Angle : 0.666 13.934 19199 Z= 0.305 Chirality : 0.041 0.263 2113 Planarity : 0.004 0.040 2444 Dihedral : 16.887 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 covalent geometry : bond 0.00658 (14191) covalent geometry : angle 0.66630 (19199) hydrogen bonds : bond 0.14298 ( 772) hydrogen bonds : angle 5.82101 ( 2247) metal coordination : bond 0.00325 ( 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 : 0.536 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: 0.8318 (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: 0.7083 (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: 0.1241 time to fit residues: 35.0188 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 : 0.529 ------------------------------------------------------------------------------- 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: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3731 r_free = 0.3731 target = 0.147178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.112042 restraints weight = 17287.122| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.05 r_work: 0.3178 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14195 Z= 0.131 Angle : 0.485 7.529 19199 Z= 0.257 Chirality : 0.041 0.181 2113 Planarity : 0.004 0.041 2444 Dihedral : 5.877 55.949 1931 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.56 % Allowed : 16.38 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.11 (0.41), residues: 143 loop : 0.60 (0.27), 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 0.012 0.001 PHE A 219 TRP 0.006 0.001 TRP A 145 HIS 0.009 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00285 (14191) covalent geometry : angle 0.48479 (19199) hydrogen bonds : bond 0.04902 ( 772) hydrogen bonds : angle 4.55351 ( 2247) metal coordination : bond 0.00346 ( 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 218 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6506 (OUTLIER) cc_final: 0.5109 (ptm) REVERT: A 82 ARG cc_start: 0.7623 (ttm110) cc_final: 0.6947 (mtm180) REVERT: A 136 PHE cc_start: 0.8643 (m-80) cc_final: 0.8355 (m-80) REVERT: A 151 LYS cc_start: 0.7768 (mmtt) cc_final: 0.6895 (mttm) REVERT: A 293 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7691 (mt-10) REVERT: A 326 HIS cc_start: 0.8163 (p90) cc_final: 0.7896 (p90) REVERT: A 367 ASP cc_start: 0.8238 (t0) cc_final: 0.7797 (t0) REVERT: A 379 GLU cc_start: 0.7872 (mp0) cc_final: 0.7529 (mp0) REVERT: A 440 ASP cc_start: 0.7937 (m-30) cc_final: 0.7606 (t70) REVERT: A 465 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7347 (tp30) REVERT: B 48 MET cc_start: 0.3993 (mmp) cc_final: 0.3487 (mmp) REVERT: B 151 LYS cc_start: 0.7577 (pttt) cc_final: 0.6935 (pptt) REVERT: B 170 LYS cc_start: 0.7914 (mmtp) cc_final: 0.7426 (mmmt) REVERT: B 232 MET cc_start: 0.8936 (mmt) cc_final: 0.8715 (mmm) REVERT: B 273 ASN cc_start: 0.8397 (t0) cc_final: 0.8118 (t0) REVERT: B 340 ASP cc_start: 0.7585 (t0) cc_final: 0.6999 (m-30) REVERT: B 369 TYR cc_start: 0.8145 (t80) cc_final: 0.7847 (t80) REVERT: B 397 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7631 (mt-10) REVERT: B 418 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7601 (m-30) REVERT: B 653 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7911 (pp) outliers start: 39 outliers final: 19 residues processed: 207 average time/residue: 0.1113 time to fit residues: 34.4968 Evaluate side-chains 190 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 165 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 HIS A 316 ASN A 734 GLN B 435 ASN ** B 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.141910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.106356 restraints weight = 17546.025| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.05 r_work: 0.3095 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14195 Z= 0.227 Angle : 0.550 7.110 19199 Z= 0.291 Chirality : 0.044 0.194 2113 Planarity : 0.004 0.045 2444 Dihedral : 6.077 57.079 1931 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.08 % Allowed : 17.04 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.63 (0.21), residues: 1676 helix: 1.80 (0.17), residues: 930 sheet: -0.29 (0.42), residues: 146 loop : 0.45 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 553 TYR 0.017 0.002 TYR B 406 PHE 0.016 0.001 PHE B 794 TRP 0.006 0.001 TRP A 145 HIS 0.010 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00550 (14191) covalent geometry : angle 0.55002 (19199) hydrogen bonds : bond 0.05391 ( 772) hydrogen bonds : angle 4.56812 ( 2247) metal coordination : bond 0.00808 ( 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 226 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.6472 (OUTLIER) cc_final: 0.5213 (ptp) REVERT: A 82 ARG cc_start: 0.7755 (ttm110) cc_final: 0.7033 (mtm180) REVERT: A 136 PHE cc_start: 0.8757 (m-80) cc_final: 0.8443 (m-80) REVERT: A 145 TRP cc_start: 0.7512 (t-100) cc_final: 0.6381 (t60) REVERT: A 151 LYS cc_start: 0.7878 (mmtt) cc_final: 0.7025 (mtmm) REVERT: A 293 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7780 (mt-10) REVERT: A 367 ASP cc_start: 0.8316 (t0) cc_final: 0.7894 (t0) REVERT: A 440 ASP cc_start: 0.8032 (m-30) cc_final: 0.7671 (t70) REVERT: A 442 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7546 (mtp) REVERT: A 465 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7388 (tp30) REVERT: B 133 GLU cc_start: 0.8328 (pt0) cc_final: 0.8093 (pt0) REVERT: B 151 LYS cc_start: 0.7570 (pttt) cc_final: 0.6986 (mttp) REVERT: B 170 LYS cc_start: 0.8025 (mmtp) cc_final: 0.7529 (mmmt) REVERT: B 225 ARG cc_start: 0.7677 (ttp80) cc_final: 0.7440 (ttp80) REVERT: B 232 MET cc_start: 0.9010 (mmt) cc_final: 0.8806 (mmm) REVERT: B 273 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.8095 (t0) REVERT: B 324 ILE cc_start: 0.8137 (mm) cc_final: 0.7875 (mm) REVERT: B 340 ASP cc_start: 0.7675 (t0) cc_final: 0.7071 (m-30) REVERT: B 369 TYR cc_start: 0.8318 (t80) cc_final: 0.8076 (t80) REVERT: B 415 ASP cc_start: 0.8341 (m-30) cc_final: 0.7966 (m-30) REVERT: B 418 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7732 (m-30) REVERT: B 442 MET cc_start: 0.8322 (tpp) cc_final: 0.7973 (mmm) REVERT: B 595 MET cc_start: 0.8697 (mmm) cc_final: 0.8449 (mtt) REVERT: B 653 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8075 (pp) outliers start: 47 outliers final: 27 residues processed: 214 average time/residue: 0.1102 time to fit residues: 35.3022 Evaluate side-chains 204 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 138 LEU Chi-restraints excluded: chain A residue 235 ILE 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 442 MET 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 69 VAL 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 255 THR Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 309 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 627 SER Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 755 VAL 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: 0.6980 chunk 43 optimal weight: 0.9990 chunk 130 optimal weight: 0.0060 chunk 101 optimal weight: 0.9980 chunk 87 optimal weight: 0.1980 chunk 63 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 160 optimal weight: 0.0060 chunk 132 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 overall best weight: 0.3212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 HIS A 316 ASN A 734 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.147218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.112007 restraints weight = 17317.703| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.06 r_work: 0.3159 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14195 Z= 0.104 Angle : 0.452 7.072 19199 Z= 0.241 Chirality : 0.039 0.171 2113 Planarity : 0.003 0.042 2444 Dihedral : 5.795 55.975 1931 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.29 % Allowed : 18.02 % 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: 1.92 (0.21), residues: 1676 helix: 2.07 (0.17), residues: 933 sheet: -0.24 (0.42), residues: 143 loop : 0.53 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 553 TYR 0.017 0.001 TYR B 406 PHE 0.010 0.001 PHE A 219 TRP 0.006 0.001 TRP A 431 HIS 0.006 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00208 (14191) covalent geometry : angle 0.45164 (19199) hydrogen bonds : bond 0.04305 ( 772) hydrogen bonds : angle 4.24031 ( 2247) metal coordination : bond 0.00204 ( 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 213 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6426 (OUTLIER) cc_final: 0.5106 (ptp) REVERT: A 82 ARG cc_start: 0.7706 (ttm110) cc_final: 0.6995 (mtm180) REVERT: A 136 PHE cc_start: 0.8659 (m-80) cc_final: 0.8369 (m-80) REVERT: A 151 LYS cc_start: 0.7825 (mmtt) cc_final: 0.6968 (mtmm) REVERT: A 293 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7745 (mt-10) REVERT: A 367 ASP cc_start: 0.8312 (t0) cc_final: 0.7902 (t0) REVERT: A 442 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7518 (mtp) REVERT: A 465 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7357 (tp30) REVERT: A 557 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8522 (mtt180) REVERT: B 151 LYS cc_start: 0.7557 (pttt) cc_final: 0.7003 (mttp) REVERT: B 170 LYS cc_start: 0.7940 (mmtp) cc_final: 0.7447 (mmmt) REVERT: B 177 LYS cc_start: 0.6227 (OUTLIER) cc_final: 0.5545 (mttp) REVERT: B 324 ILE cc_start: 0.8106 (mm) cc_final: 0.7844 (mm) REVERT: B 369 TYR cc_start: 0.8253 (t80) cc_final: 0.7981 (t80) REVERT: B 418 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7562 (m-30) REVERT: B 442 MET cc_start: 0.8212 (tpp) cc_final: 0.7990 (mmm) REVERT: B 595 MET cc_start: 0.8616 (mmm) cc_final: 0.8337 (mtt) REVERT: B 653 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7837 (pp) outliers start: 35 outliers final: 16 residues processed: 203 average time/residue: 0.1130 time to fit residues: 34.2434 Evaluate side-chains 188 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 255 THR 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 665 PHE 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 418 ASP Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 653 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 85 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 150 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 15 optimal weight: 0.0980 chunk 49 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 HIS A 316 ASN A 734 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.147128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.111847 restraints weight = 17425.441| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.06 r_work: 0.3139 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14195 Z= 0.111 Angle : 0.452 6.863 19199 Z= 0.240 Chirality : 0.039 0.163 2113 Planarity : 0.003 0.043 2444 Dihedral : 5.663 55.682 1931 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.49 % Allowed : 18.02 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.21), residues: 1676 helix: 2.13 (0.17), residues: 934 sheet: -0.33 (0.42), residues: 145 loop : 0.53 (0.26), residues: 597 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 0.009 0.001 PHE B 568 TRP 0.005 0.001 TRP B 548 HIS 0.006 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00242 (14191) covalent geometry : angle 0.45245 (19199) hydrogen bonds : bond 0.04220 ( 772) hydrogen bonds : angle 4.16756 ( 2247) metal coordination : bond 0.00293 ( 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 211 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6428 (OUTLIER) cc_final: 0.4995 (ptm) REVERT: A 82 ARG cc_start: 0.7752 (ttm110) cc_final: 0.7044 (mtm180) REVERT: A 136 PHE cc_start: 0.8642 (m-80) cc_final: 0.8326 (m-80) REVERT: A 151 LYS cc_start: 0.7884 (mmtt) cc_final: 0.6991 (mttm) REVERT: A 293 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7754 (mt-10) REVERT: A 367 ASP cc_start: 0.8344 (t0) cc_final: 0.7947 (t0) REVERT: A 442 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7640 (mtp) REVERT: A 465 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7389 (tp30) REVERT: A 528 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8145 (mt) REVERT: A 557 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8540 (mtt180) REVERT: B 132 LYS cc_start: 0.8171 (mmtp) cc_final: 0.7867 (mmmt) REVERT: B 151 LYS cc_start: 0.7568 (pttt) cc_final: 0.6992 (mttp) REVERT: B 170 LYS cc_start: 0.7939 (mmtp) cc_final: 0.7457 (mmmt) REVERT: B 177 LYS cc_start: 0.6263 (OUTLIER) cc_final: 0.5585 (mttp) REVERT: B 340 ASP cc_start: 0.7526 (t0) cc_final: 0.7035 (m-30) REVERT: B 369 TYR cc_start: 0.8293 (t80) cc_final: 0.8067 (t80) REVERT: B 397 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7805 (mm-30) REVERT: B 595 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8367 (mtt) REVERT: B 653 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7913 (pp) outliers start: 38 outliers final: 23 residues processed: 200 average time/residue: 0.1161 time to fit residues: 34.6968 Evaluate side-chains 197 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 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 442 MET Chi-restraints excluded: chain A residue 528 LEU 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 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 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 805 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 76 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 107 optimal weight: 0.1980 chunk 99 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 HIS A 316 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.146946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111736 restraints weight = 17284.934| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.03 r_work: 0.3177 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14195 Z= 0.114 Angle : 0.452 6.597 19199 Z= 0.239 Chirality : 0.040 0.166 2113 Planarity : 0.003 0.044 2444 Dihedral : 5.609 54.792 1931 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.88 % Allowed : 17.76 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.04 (0.21), residues: 1676 helix: 2.18 (0.17), residues: 934 sheet: -0.21 (0.43), residues: 143 loop : 0.55 (0.26), residues: 599 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 0.010 0.001 PHE B 568 TRP 0.006 0.001 TRP A 67 HIS 0.006 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00253 (14191) covalent geometry : angle 0.45245 (19199) hydrogen bonds : bond 0.04195 ( 772) hydrogen bonds : angle 4.12733 ( 2247) metal coordination : bond 0.00305 ( 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 218 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6436 (mmp) cc_final: 0.4963 (ptm) REVERT: A 136 PHE cc_start: 0.8611 (m-80) cc_final: 0.8309 (m-80) REVERT: A 151 LYS cc_start: 0.7848 (mmtt) cc_final: 0.7017 (mtmm) REVERT: A 293 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7710 (mt-10) REVERT: A 367 ASP cc_start: 0.8346 (t0) cc_final: 0.7934 (t0) REVERT: A 442 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7547 (mtp) REVERT: A 465 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7364 (tp30) REVERT: A 528 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8096 (mt) REVERT: A 557 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8541 (mtt180) REVERT: B 86 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7631 (tpt-90) REVERT: B 132 LYS cc_start: 0.8127 (mmtp) cc_final: 0.7820 (mmmt) REVERT: B 151 LYS cc_start: 0.7552 (pttt) cc_final: 0.6983 (mttp) REVERT: B 170 LYS cc_start: 0.7941 (mmtp) cc_final: 0.7485 (mmmt) REVERT: B 177 LYS cc_start: 0.6284 (OUTLIER) cc_final: 0.5721 (mttp) REVERT: B 340 ASP cc_start: 0.7469 (t0) cc_final: 0.6952 (m-30) REVERT: B 397 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7614 (mt-10) REVERT: B 418 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7563 (m-30) REVERT: B 595 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8370 (mtt) REVERT: B 653 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7833 (pp) outliers start: 44 outliers final: 26 residues processed: 208 average time/residue: 0.1180 time to fit residues: 36.2322 Evaluate side-chains 202 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 226 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 309 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 442 MET Chi-restraints excluded: chain A residue 528 LEU 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 674 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ARG 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 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 653 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 805 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 162 optimal weight: 0.0770 chunk 3 optimal weight: 20.0000 chunk 96 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 111 optimal weight: 0.1980 chunk 61 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 HIS A 316 ASN A 734 GLN B 234 ASN B 435 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.110147 restraints weight = 17341.609| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.04 r_work: 0.3137 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1500 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= 0.134 Angle : 0.474 9.613 19199 Z= 0.249 Chirality : 0.040 0.161 2113 Planarity : 0.004 0.044 2444 Dihedral : 5.664 55.010 1931 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.01 % Allowed : 18.15 % Favored : 78.83 % 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: 2.00 (0.21), residues: 1676 helix: 2.14 (0.17), residues: 934 sheet: -0.18 (0.43), residues: 143 loop : 0.53 (0.26), residues: 599 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 0.012 0.001 PHE C 30 TRP 0.007 0.001 TRP A 67 HIS 0.006 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00312 (14191) covalent geometry : angle 0.47378 (19199) hydrogen bonds : bond 0.04364 ( 772) hydrogen bonds : angle 4.16417 ( 2247) metal coordination : bond 0.00466 ( 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 215 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6372 (OUTLIER) cc_final: 0.4899 (ptm) REVERT: A 136 PHE cc_start: 0.8617 (m-80) cc_final: 0.8315 (m-80) REVERT: A 151 LYS cc_start: 0.7884 (mmtt) cc_final: 0.7038 (mtmm) REVERT: A 188 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7936 (ptmm) REVERT: A 293 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7727 (mt-10) REVERT: A 314 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8338 (mt-10) REVERT: A 367 ASP cc_start: 0.8337 (t0) cc_final: 0.7927 (t0) REVERT: A 442 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7592 (mtp) REVERT: A 465 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7387 (tp30) REVERT: A 557 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8570 (mtt180) REVERT: B 132 LYS cc_start: 0.8120 (mmtp) cc_final: 0.7844 (mmmt) REVERT: B 151 LYS cc_start: 0.7544 (pttt) cc_final: 0.6973 (mttp) REVERT: B 170 LYS cc_start: 0.7978 (mmtp) cc_final: 0.7518 (mmmt) REVERT: B 177 LYS cc_start: 0.6356 (OUTLIER) cc_final: 0.5894 (mttp) REVERT: B 340 ASP cc_start: 0.7482 (t0) cc_final: 0.6952 (m-30) REVERT: B 397 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7565 (mt-10) REVERT: B 408 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7990 (ttp-170) REVERT: B 418 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7628 (m-30) REVERT: B 502 ARG cc_start: 0.7493 (mmm160) cc_final: 0.7251 (mmm160) REVERT: B 595 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8392 (mtt) REVERT: B 653 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7893 (pp) outliers start: 46 outliers final: 29 residues processed: 204 average time/residue: 0.1126 time to fit residues: 33.6823 Evaluate side-chains 206 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 309 THR Chi-restraints excluded: chain A residue 314 GLU 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 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 619 SER Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 66 LEU 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 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 653 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 805 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 110 optimal weight: 0.0270 chunk 74 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 HIS A 316 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 = 0.147413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.112288 restraints weight = 17287.083| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.03 r_work: 0.3179 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14195 Z= 0.107 Angle : 0.460 8.137 19199 Z= 0.241 Chirality : 0.039 0.158 2113 Planarity : 0.003 0.045 2444 Dihedral : 5.769 60.119 1931 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.82 % Allowed : 18.55 % Favored : 78.64 % 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: 2.21 (0.17), residues: 935 sheet: -0.20 (0.43), residues: 143 loop : 0.53 (0.26), residues: 598 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 0.024 0.001 PHE C 30 TRP 0.008 0.001 TRP B 245 HIS 0.006 0.000 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00233 (14191) covalent geometry : angle 0.46031 (19199) hydrogen bonds : bond 0.04102 ( 772) hydrogen bonds : angle 4.10233 ( 2247) metal coordination : bond 0.00239 ( 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 217 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6349 (OUTLIER) cc_final: 0.4853 (ptm) REVERT: A 136 PHE cc_start: 0.8593 (m-80) cc_final: 0.8303 (m-80) REVERT: A 151 LYS cc_start: 0.7876 (mmtt) cc_final: 0.7016 (mtmm) REVERT: A 293 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7706 (mt-10) REVERT: A 314 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8336 (mt-10) REVERT: A 367 ASP cc_start: 0.8322 (t0) cc_final: 0.7915 (t0) REVERT: A 442 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7592 (mtp) REVERT: A 465 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7362 (tp30) REVERT: A 539 LYS cc_start: 0.8165 (mttm) cc_final: 0.7884 (mmtp) REVERT: A 557 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8527 (mtt180) REVERT: B 57 GLU cc_start: 0.6893 (pp20) cc_final: 0.6192 (pp20) REVERT: B 86 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7613 (tpt-90) REVERT: B 132 LYS cc_start: 0.8060 (mmtp) cc_final: 0.7776 (mmmt) REVERT: B 151 LYS cc_start: 0.7526 (pttt) cc_final: 0.6959 (mttp) REVERT: B 170 LYS cc_start: 0.7934 (mmtp) cc_final: 0.7483 (mmmt) REVERT: B 177 LYS cc_start: 0.6339 (OUTLIER) cc_final: 0.5907 (mttp) REVERT: B 340 ASP cc_start: 0.7484 (t0) cc_final: 0.6908 (m-30) REVERT: B 397 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7575 (mt-10) REVERT: B 408 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7967 (mtp180) REVERT: B 418 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7550 (m-30) REVERT: B 502 ARG cc_start: 0.7469 (mmm160) cc_final: 0.7188 (mmm160) REVERT: B 595 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8360 (mtt) REVERT: B 653 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7805 (pp) outliers start: 43 outliers final: 27 residues processed: 206 average time/residue: 0.1207 time to fit residues: 36.1162 Evaluate side-chains 207 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 314 GLU 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 442 MET 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 619 SER Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 66 LEU 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 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 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: 0.7980 chunk 46 optimal weight: 0.0010 chunk 83 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 316 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.112618 restraints weight = 17346.680| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.04 r_work: 0.3184 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1579 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 : 0.460 8.279 19199 Z= 0.241 Chirality : 0.040 0.157 2113 Planarity : 0.003 0.045 2444 Dihedral : 5.734 61.436 1931 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.88 % Allowed : 18.68 % Favored : 78.44 % 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: 2.24 (0.17), residues: 936 sheet: -0.21 (0.43), residues: 143 loop : 0.52 (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 0.016 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 covalent geometry : bond 0.00237 (14191) covalent geometry : angle 0.45956 (19199) hydrogen bonds : bond 0.04029 ( 772) hydrogen bonds : angle 4.08590 ( 2247) metal coordination : bond 0.00266 ( 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 219 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 175 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6368 (OUTLIER) cc_final: 0.4834 (ptm) REVERT: A 136 PHE cc_start: 0.8587 (m-80) cc_final: 0.8309 (m-80) REVERT: A 151 LYS cc_start: 0.7858 (mmtt) cc_final: 0.7003 (mtmm) REVERT: A 188 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7945 (ptmm) REVERT: A 293 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7709 (mt-10) REVERT: A 314 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8317 (mt-10) REVERT: A 367 ASP cc_start: 0.8324 (t0) cc_final: 0.7914 (t0) REVERT: A 465 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7382 (tp30) REVERT: A 528 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8119 (mt) REVERT: A 539 LYS cc_start: 0.8155 (mttm) cc_final: 0.7889 (mmtp) REVERT: A 557 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8556 (mtt180) REVERT: B 57 GLU cc_start: 0.6796 (pp20) cc_final: 0.6204 (pp20) REVERT: B 86 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7647 (tpt-90) REVERT: B 132 LYS cc_start: 0.8214 (mmtp) cc_final: 0.7906 (mmmt) REVERT: B 151 LYS cc_start: 0.7547 (pttt) cc_final: 0.6972 (mttp) REVERT: B 170 LYS cc_start: 0.7922 (mmtp) cc_final: 0.7483 (mmmt) REVERT: B 177 LYS cc_start: 0.6338 (OUTLIER) cc_final: 0.5983 (mttp) REVERT: B 340 ASP cc_start: 0.7441 (t0) cc_final: 0.6889 (m-30) REVERT: B 397 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7546 (mt-10) REVERT: B 408 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7967 (mtp180) REVERT: B 418 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7543 (m-30) REVERT: B 502 ARG cc_start: 0.7516 (mmm160) cc_final: 0.7245 (mmm160) REVERT: B 595 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8362 (mtt) REVERT: B 653 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7814 (pp) outliers start: 44 outliers final: 28 residues processed: 206 average time/residue: 0.1228 time to fit residues: 36.6187 Evaluate side-chains 209 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 314 GLU 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 528 LEU 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 619 SER Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 66 LEU 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 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 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 805 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 15 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.149088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.115500 restraints weight = 17437.754| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.08 r_work: 0.3067 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14195 Z= 0.131 Angle : 0.481 8.493 19199 Z= 0.251 Chirality : 0.041 0.159 2113 Planarity : 0.003 0.045 2444 Dihedral : 5.840 62.769 1931 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.62 % Allowed : 18.87 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.07 (0.21), residues: 1676 helix: 2.21 (0.17), residues: 935 sheet: -0.10 (0.44), residues: 141 loop : 0.52 (0.26), residues: 600 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 0.012 0.001 PHE C 30 TRP 0.010 0.001 TRP A 67 HIS 0.006 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00304 (14191) covalent geometry : angle 0.48081 (19199) hydrogen bonds : bond 0.04253 ( 772) hydrogen bonds : angle 4.14100 ( 2247) metal coordination : bond 0.00427 ( 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 208 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.6323 (OUTLIER) cc_final: 0.4810 (ptm) REVERT: A 136 PHE cc_start: 0.8560 (m-80) cc_final: 0.8267 (m-80) REVERT: A 151 LYS cc_start: 0.7865 (mmtt) cc_final: 0.7038 (mtmm) REVERT: A 188 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7815 (ptmm) REVERT: A 293 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7731 (mt-10) REVERT: A 314 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8327 (mt-10) REVERT: A 367 ASP cc_start: 0.8357 (t0) cc_final: 0.7963 (t0) REVERT: A 465 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7402 (tp30) REVERT: A 539 LYS cc_start: 0.8143 (mttm) cc_final: 0.7872 (mmtp) REVERT: A 557 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8533 (mtt180) REVERT: B 57 GLU cc_start: 0.6704 (pp20) cc_final: 0.6148 (pp20) REVERT: B 86 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7633 (tpt-90) REVERT: B 132 LYS cc_start: 0.8190 (mmtp) cc_final: 0.7924 (mmmt) REVERT: B 151 LYS cc_start: 0.7479 (pttt) cc_final: 0.6918 (mttp) REVERT: B 170 LYS cc_start: 0.7874 (mmtp) cc_final: 0.7423 (mmmt) REVERT: B 177 LYS cc_start: 0.6328 (OUTLIER) cc_final: 0.6003 (mttp) REVERT: B 340 ASP cc_start: 0.7465 (t0) cc_final: 0.6901 (m-30) REVERT: B 397 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7555 (mt-10) REVERT: B 408 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7918 (mtp180) REVERT: B 418 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7564 (m-30) REVERT: B 502 ARG cc_start: 0.7535 (mmm160) cc_final: 0.7248 (mmm160) REVERT: B 595 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8354 (mtt) REVERT: B 653 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7862 (pp) outliers start: 40 outliers final: 27 residues processed: 198 average time/residue: 0.1316 time to fit residues: 37.4492 Evaluate side-chains 205 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 314 GLU 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 582 ARG Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 66 LEU 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 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 559 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 805 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 93 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 160 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.149415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.114874 restraints weight = 17316.339| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.91 r_work: 0.3104 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14195 Z= 0.123 Angle : 0.481 8.059 19199 Z= 0.250 Chirality : 0.040 0.158 2113 Planarity : 0.003 0.045 2444 Dihedral : 5.871 63.528 1931 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.69 % Allowed : 18.87 % Favored : 78.44 % 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: 2.09 (0.21), residues: 1676 helix: 2.22 (0.17), residues: 937 sheet: -0.12 (0.44), residues: 141 loop : 0.54 (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 0.012 0.001 PHE C 30 TRP 0.006 0.001 TRP B 245 HIS 0.006 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00284 (14191) covalent geometry : angle 0.48111 (19199) hydrogen bonds : bond 0.04204 ( 772) hydrogen bonds : angle 4.13590 ( 2247) metal coordination : bond 0.00377 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4043.50 seconds wall clock time: 69 minutes 57.31 seconds (4197.31 seconds total)