Starting phenix.real_space_refine on Fri May 16 02:49:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cxh_45991/05_2025/9cxh_45991.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cxh_45991/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cxh_45991/05_2025/9cxh_45991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cxh_45991/05_2025/9cxh_45991.map" model { file = "/net/cci-nas-00/data/ceres_data/9cxh_45991/05_2025/9cxh_45991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cxh_45991/05_2025/9cxh_45991.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.035 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'PCG': 1} Classifications: {'RNA': 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, 'PCG': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 8.71, per 1000 atoms: 0.63 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: 3.25 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.52 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: 4.10 Time building geometry restraints manager: 3.80 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: 19033 2.79 - 5.57: 112 5.57 - 8.36: 34 8.36 - 11.15: 18 11.15 - 13.93: 2 Bond angle restraints: 19199 Sorted by residual: angle pdb=" C4 PCG A 901 " pdb=" N9 PCG A 901 " pdb=" C8 PCG A 901 " ideal model delta sigma weight residual 106.51 120.44 -13.93 3.00e+00 1.11e-01 2.16e+01 angle pdb=" C4 PCG B 901 " pdb=" N9 PCG B 901 " pdb=" C8 PCG B 901 " ideal model delta sigma weight residual 106.51 120.33 -13.82 3.00e+00 1.11e-01 2.12e+01 angle pdb=" N GLN A 776 " pdb=" CA GLN A 776 " pdb=" CB GLN A 776 " ideal model delta sigma weight residual 110.16 116.64 -6.48 1.48e+00 4.57e-01 1.92e+01 angle pdb=" N SER A 49 " pdb=" CA SER A 49 " pdb=" CB SER A 49 " ideal model delta sigma weight residual 114.17 109.63 4.54 1.14e+00 7.69e-01 1.58e+01 angle pdb=" O3' PCG A 901 " pdb=" PA PCG A 901 " pdb=" O5' PCG A 901 " ideal model delta sigma weight residual 103.94 114.81 -10.87 3.00e+00 1.11e-01 1.31e+01 ... (remaining 19194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 7493 17.88 - 35.77: 833 35.77 - 53.65: 206 53.65 - 71.54: 87 71.54 - 89.42: 15 Dihedral angle restraints: 8634 sinusoidal: 3665 harmonic: 4969 Sorted by residual: dihedral pdb=" CA MET A 48 " pdb=" C MET A 48 " pdb=" N SER A 49 " pdb=" CA SER A 49 " ideal model delta harmonic sigma weight residual 180.00 159.93 20.07 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA TYR A 406 " pdb=" C TYR A 406 " pdb=" N ASN A 407 " pdb=" CA ASN A 407 " ideal model delta harmonic sigma weight residual -180.00 -160.38 -19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA TYR B 406 " pdb=" C TYR B 406 " pdb=" N ASN B 407 " pdb=" CA ASN B 407 " ideal model delta harmonic sigma weight residual -180.00 -161.94 -18.06 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 8631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1745 0.053 - 0.105: 319 0.105 - 0.158: 47 0.158 - 0.210: 0 0.210 - 0.263: 2 Chirality restraints: 2113 Sorted by residual: chirality pdb=" C2' PCG B 901 " pdb=" C1' PCG B 901 " pdb=" C3' PCG B 901 " pdb=" O2' PCG B 901 " both_signs ideal model delta sigma weight residual False -2.74 -2.48 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C2' PCG A 901 " pdb=" C1' PCG A 901 " pdb=" C3' PCG A 901 " pdb=" O2' PCG A 901 " both_signs ideal model delta sigma weight residual False -2.74 -2.50 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ILE B 324 " pdb=" N ILE B 324 " pdb=" C ILE B 324 " pdb=" CB ILE B 324 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 2110 not shown) Planarity restraints: 2444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 219 " -0.013 2.00e-02 2.50e+03 1.53e-02 4.12e+00 pdb=" CG PHE A 219 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 219 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 219 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 219 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 219 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 219 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 118 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO A 119 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 772 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A 773 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 773 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 773 " -0.021 5.00e-02 4.00e+02 ... (remaining 2441 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 50 2.51 - 3.11: 10169 3.11 - 3.71: 21123 3.71 - 4.30: 29804 4.30 - 4.90: 51124 Nonbonded interactions: 112270 Sorted by model distance: nonbonded pdb="ZN ZN A 902 " pdb=" O3P 5GP A 904 " model vdw 1.914 2.230 nonbonded pdb="MG MG A 903 " pdb=" O2P 5GP A 904 " model vdw 1.928 2.170 nonbonded pdb=" OD2 ASP A 603 " pdb="ZN ZN A 902 " model vdw 1.946 2.230 nonbonded pdb="ZN ZN B 902 " pdb=" O3P 5GP B 904 " model vdw 1.969 2.230 nonbonded pdb=" OD2 ASP B 603 " pdb="ZN ZN B 902 " model vdw 1.983 2.230 ... (remaining 112265 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 823 or resid 901 through 904)) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 26 through 49 or resid 52 through 87)) selection = (chain 'D' and (resid 26 through 63 or resid 72 through 87)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 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: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 35.270 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.570 ------------------------------------------------------------------------------- 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 : 0.006 0.192 14195 Z= 0.319 Angle : 0.662 13.934 19199 Z= 0.304 Chirality : 0.041 0.263 2113 Planarity : 0.004 0.040 2444 Dihedral : 16.885 89.423 5408 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 17.43 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (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 TRP 0.015 0.001 TRP A 67 HIS 0.007 0.001 HIS A 89 PHE 0.035 0.001 PHE A 219 TYR 0.015 0.001 TYR B 406 ARG 0.005 0.000 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.14298 ( 772) hydrogen bonds : angle 5.82101 ( 2247) metal coordination : bond 0.00325 ( 4) covalent geometry : bond 0.00649 (14191) covalent geometry : angle 0.66158 (19199) *********************** 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 : 1.589 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: 0.2830 time to fit residues: 79.5623 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 : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 130 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 151 optimal weight: 0.6980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 70 GLN A 126 ASN A 148 HIS A 153 HIS A 316 ASN A 651 GLN A 652 ASN B 126 ASN B 153 HIS B 572 GLN B 734 GLN D 34 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.144936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.109509 restraints weight = 17266.159| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.07 r_work: 0.3141 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14195 Z= 0.169 Angle : 0.511 7.562 19199 Z= 0.271 Chirality : 0.042 0.186 2113 Planarity : 0.004 0.043 2444 Dihedral : 6.141 56.567 1931 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.82 % Allowed : 16.58 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.21), residues: 1676 helix: 1.87 (0.17), residues: 931 sheet: -0.20 (0.41), residues: 145 loop : 0.54 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 145 HIS 0.009 0.001 HIS A 89 PHE 0.013 0.001 PHE B 568 TYR 0.016 0.001 TYR B 406 ARG 0.003 0.000 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.05250 ( 772) hydrogen bonds : angle 4.62569 ( 2247) metal coordination : bond 0.00483 ( 4) covalent geometry : bond 0.00396 (14191) covalent geometry : angle 0.51136 (19199) *********************** 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 215 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 1.514 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6524 (OUTLIER) cc_final: 0.5133 (ptm) REVERT: A 82 ARG cc_start: 0.7666 (ttm110) cc_final: 0.6969 (mtm180) REVERT: A 136 PHE cc_start: 0.8682 (m-80) cc_final: 0.8397 (m-80) REVERT: A 151 LYS cc_start: 0.7806 (mmtt) cc_final: 0.6974 (mtmm) REVERT: A 293 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7714 (mt-10) REVERT: A 367 ASP cc_start: 0.8282 (t0) cc_final: 0.7835 (t0) REVERT: A 440 ASP cc_start: 0.8003 (m-30) cc_final: 0.7645 (t70) REVERT: A 465 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7339 (tp30) REVERT: B 133 GLU cc_start: 0.8256 (pt0) cc_final: 0.8045 (pt0) REVERT: B 151 LYS cc_start: 0.7543 (pttt) cc_final: 0.6967 (pptt) REVERT: B 170 LYS cc_start: 0.7950 (mmtp) cc_final: 0.7447 (mmmt) REVERT: B 232 MET cc_start: 0.8986 (mmt) cc_final: 0.8758 (mmm) REVERT: B 273 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.8127 (t0) REVERT: B 340 ASP cc_start: 0.7617 (t0) cc_final: 0.7054 (m-30) REVERT: B 415 ASP cc_start: 0.8238 (m-30) cc_final: 0.7905 (m-30) REVERT: B 418 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7583 (m-30) REVERT: B 653 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7974 (pp) REVERT: B 694 MET cc_start: 0.7197 (mtt) cc_final: 0.6522 (mtt) outliers start: 43 outliers final: 22 residues processed: 204 average time/residue: 0.2376 time to fit residues: 72.7972 Evaluate side-chains 187 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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 185 VAL Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain D residue 34 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 115 optimal weight: 5.9990 chunk 58 optimal weight: 0.3980 chunk 14 optimal weight: 0.0270 chunk 23 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN A 148 HIS A 316 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.147392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112118 restraints weight = 17240.429| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.05 r_work: 0.3181 rms_B_bonded: 2.72 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: 0.8197 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14195 Z= 0.112 Angle : 0.458 7.190 19199 Z= 0.245 Chirality : 0.039 0.175 2113 Planarity : 0.003 0.042 2444 Dihedral : 5.937 55.536 1931 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.62 % Allowed : 16.78 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.21), residues: 1676 helix: 2.02 (0.17), residues: 932 sheet: -0.26 (0.41), residues: 145 loop : 0.56 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 145 HIS 0.007 0.001 HIS A 89 PHE 0.009 0.001 PHE B 568 TYR 0.016 0.001 TYR B 406 ARG 0.004 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.04546 ( 772) hydrogen bonds : angle 4.37082 ( 2247) metal coordination : bond 0.00265 ( 4) covalent geometry : bond 0.00241 (14191) covalent geometry : angle 0.45846 (19199) *********************** 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 217 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 1.789 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.5016 (ptm) REVERT: A 82 ARG cc_start: 0.7599 (ttm110) cc_final: 0.6922 (mtm180) REVERT: A 136 PHE cc_start: 0.8694 (m-80) cc_final: 0.8356 (m-80) REVERT: A 151 LYS cc_start: 0.7797 (mmtt) cc_final: 0.6907 (mttm) REVERT: A 293 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7647 (mt-10) REVERT: A 326 HIS cc_start: 0.8098 (p90) cc_final: 0.7861 (p90) REVERT: A 367 ASP cc_start: 0.8297 (t0) cc_final: 0.7873 (t0) REVERT: A 465 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7391 (tp30) REVERT: B 133 GLU cc_start: 0.8207 (pt0) cc_final: 0.7997 (pt0) REVERT: B 151 LYS cc_start: 0.7610 (pttt) cc_final: 0.7019 (mttp) REVERT: B 170 LYS cc_start: 0.7891 (mmtp) cc_final: 0.7418 (mmmt) REVERT: B 273 ASN cc_start: 0.8372 (t0) cc_final: 0.8107 (t0) REVERT: B 340 ASP cc_start: 0.7567 (t0) cc_final: 0.6999 (m-30) REVERT: B 397 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7621 (mt-10) REVERT: B 418 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7561 (m-30) REVERT: B 595 MET cc_start: 0.8624 (mmm) cc_final: 0.8282 (mtt) REVERT: B 653 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7822 (pp) outliers start: 40 outliers final: 22 residues processed: 206 average time/residue: 0.2554 time to fit residues: 79.6595 Evaluate side-chains 194 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 785 THR Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain D residue 87 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 HIS A 734 GLN B 435 ASN B 569 ASN ** B 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.104071 restraints weight = 17500.702| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.05 r_work: 0.3045 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14195 Z= 0.259 Angle : 0.586 7.372 19199 Z= 0.309 Chirality : 0.045 0.191 2113 Planarity : 0.004 0.045 2444 Dihedral : 6.349 58.071 1931 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.60 % Allowed : 16.45 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.20), residues: 1676 helix: 1.69 (0.17), residues: 929 sheet: -0.29 (0.42), residues: 146 loop : 0.27 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 731 HIS 0.009 0.001 HIS A 89 PHE 0.018 0.002 PHE B 794 TYR 0.017 0.002 TYR B 406 ARG 0.005 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.05688 ( 772) hydrogen bonds : angle 4.61567 ( 2247) metal coordination : bond 0.00882 ( 4) covalent geometry : bond 0.00633 (14191) covalent geometry : angle 0.58633 (19199) *********************** 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 225 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 170 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.6538 (OUTLIER) cc_final: 0.5118 (ptm) REVERT: A 151 LYS cc_start: 0.7898 (mmtt) cc_final: 0.7029 (mtmm) REVERT: A 442 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7598 (mtp) REVERT: A 465 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7431 (tp30) REVERT: A 483 ASP cc_start: 0.6178 (m-30) cc_final: 0.5074 (t0) REVERT: A 557 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8511 (mtt180) REVERT: B 86 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7823 (tpt-90) REVERT: B 133 GLU cc_start: 0.8379 (pt0) cc_final: 0.8138 (pt0) REVERT: B 170 LYS cc_start: 0.8066 (mmtp) cc_final: 0.7583 (mmmt) REVERT: B 177 LYS cc_start: 0.6138 (OUTLIER) cc_final: 0.5400 (mttp) REVERT: B 225 ARG cc_start: 0.7740 (ttp80) cc_final: 0.7490 (ttp80) REVERT: B 273 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.8070 (t0) REVERT: B 340 ASP cc_start: 0.7739 (t0) cc_final: 0.7191 (m-30) REVERT: B 415 ASP cc_start: 0.8386 (m-30) cc_final: 0.7975 (m-30) REVERT: B 442 MET cc_start: 0.8411 (tpp) cc_final: 0.7998 (mmm) REVERT: B 595 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8441 (mtt) REVERT: B 653 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8120 (pp) outliers start: 55 outliers final: 31 residues processed: 210 average time/residue: 0.2639 time to fit residues: 82.7133 Evaluate side-chains 197 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 1.574 ------------------------------------------------------------------------------- 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 235 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 410 ASP 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 615 MET Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 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 435 ASN Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain D residue 87 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 116 optimal weight: 0.8980 chunk 166 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 11 optimal weight: 0.0470 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 B 234 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.145353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.110071 restraints weight = 17396.438| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.06 r_work: 0.3153 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1519 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= 0.111 Angle : 0.461 6.916 19199 Z= 0.246 Chirality : 0.040 0.164 2113 Planarity : 0.003 0.042 2444 Dihedral : 6.004 56.891 1931 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.56 % Allowed : 17.76 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.21), residues: 1676 helix: 2.01 (0.17), residues: 931 sheet: -0.24 (0.43), residues: 143 loop : 0.39 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 431 HIS 0.007 0.001 HIS A 89 PHE 0.011 0.001 PHE A 219 TYR 0.017 0.001 TYR B 406 ARG 0.004 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.04432 ( 772) hydrogen bonds : angle 4.25752 ( 2247) metal coordination : bond 0.00321 ( 4) covalent geometry : bond 0.00236 (14191) covalent geometry : angle 0.46103 (19199) *********************** 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 206 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 1.609 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6468 (mmp) cc_final: 0.4991 (ptm) REVERT: A 86 ARG cc_start: 0.6469 (tpp-160) cc_final: 0.6247 (tpp-160) REVERT: A 136 PHE cc_start: 0.8705 (m-80) cc_final: 0.8386 (m-80) REVERT: A 145 TRP cc_start: 0.7446 (t-100) cc_final: 0.6219 (t60) REVERT: A 151 LYS cc_start: 0.7803 (mmtt) cc_final: 0.6969 (mtmm) REVERT: A 314 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8339 (mt-10) REVERT: A 367 ASP cc_start: 0.8346 (t0) cc_final: 0.7938 (t0) REVERT: A 398 ASP cc_start: 0.7319 (t70) cc_final: 0.7059 (t70) REVERT: A 465 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7344 (tp30) REVERT: B 57 GLU cc_start: 0.6726 (pp20) cc_final: 0.6142 (pp20) REVERT: B 58 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6893 (tt0) REVERT: B 86 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7679 (tpt-90) REVERT: B 133 GLU cc_start: 0.8218 (pt0) cc_final: 0.7976 (pt0) REVERT: B 151 LYS cc_start: 0.7636 (pttt) cc_final: 0.6960 (mttp) REVERT: B 170 LYS cc_start: 0.7994 (mmtp) cc_final: 0.7513 (mmmt) REVERT: B 273 ASN cc_start: 0.8349 (t0) cc_final: 0.8099 (t0) REVERT: B 397 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7580 (mt-10) REVERT: B 418 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7638 (m-30) REVERT: B 442 MET cc_start: 0.8308 (tpp) cc_final: 0.7977 (mmm) REVERT: B 595 MET cc_start: 0.8613 (mmm) cc_final: 0.8291 (mtt) REVERT: B 653 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7848 (pp) outliers start: 39 outliers final: 22 residues processed: 195 average time/residue: 0.2520 time to fit residues: 73.2613 Evaluate side-chains 189 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 1.639 ------------------------------------------------------------------------------- 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 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 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 A residue 672 THR Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 559 VAL 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 751 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 101 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 chunk 58 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 23 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.146072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.110938 restraints weight = 17498.829| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.04 r_work: 0.3163 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14195 Z= 0.111 Angle : 0.455 6.845 19199 Z= 0.241 Chirality : 0.040 0.161 2113 Planarity : 0.003 0.042 2444 Dihedral : 6.028 63.711 1931 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.95 % Allowed : 17.96 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.21), residues: 1676 helix: 2.12 (0.17), residues: 932 sheet: -0.26 (0.43), residues: 145 loop : 0.44 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 245 HIS 0.005 0.001 HIS A 89 PHE 0.009 0.001 PHE B 568 TYR 0.016 0.001 TYR B 406 ARG 0.003 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.04256 ( 772) hydrogen bonds : angle 4.16972 ( 2247) metal coordination : bond 0.00311 ( 4) covalent geometry : bond 0.00242 (14191) covalent geometry : angle 0.45461 (19199) *********************** 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 215 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 170 time to evaluate : 1.644 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6412 (OUTLIER) cc_final: 0.4921 (ptm) REVERT: A 136 PHE cc_start: 0.8652 (m-80) cc_final: 0.8367 (m-80) REVERT: A 151 LYS cc_start: 0.7833 (mmtt) cc_final: 0.6992 (mtmm) REVERT: A 314 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8329 (mt-10) REVERT: A 367 ASP cc_start: 0.8331 (t0) cc_final: 0.7934 (t0) REVERT: A 398 ASP cc_start: 0.7294 (t70) cc_final: 0.7052 (t70) REVERT: A 442 MET cc_start: 0.7884 (mmm) cc_final: 0.7548 (mtp) REVERT: A 465 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7342 (tp30) REVERT: B 57 GLU cc_start: 0.6689 (pp20) cc_final: 0.6116 (pp20) REVERT: B 86 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7649 (tpt-90) REVERT: B 133 GLU cc_start: 0.8220 (pt0) cc_final: 0.7966 (pt0) REVERT: B 151 LYS cc_start: 0.7691 (pttt) cc_final: 0.7036 (mttp) REVERT: B 170 LYS cc_start: 0.7997 (mmtp) cc_final: 0.7527 (mmmt) REVERT: B 177 LYS cc_start: 0.6201 (OUTLIER) cc_final: 0.5546 (mttp) REVERT: B 340 ASP cc_start: 0.7598 (t0) cc_final: 0.7071 (m-30) REVERT: B 397 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7562 (mt-10) REVERT: B 408 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.8012 (ttp-170) REVERT: B 418 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7636 (m-30) REVERT: B 442 MET cc_start: 0.8259 (tpp) cc_final: 0.8050 (mmm) REVERT: B 595 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8307 (mtt) REVERT: B 653 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7872 (pp) outliers start: 45 outliers final: 24 residues processed: 201 average time/residue: 0.2585 time to fit residues: 77.1936 Evaluate side-chains 198 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 1.674 ------------------------------------------------------------------------------- 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 383 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 140 ILE 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 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 627 SER 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 81 optimal weight: 0.0770 chunk 130 optimal weight: 0.0070 chunk 128 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 134 optimal weight: 0.6980 chunk 160 optimal weight: 0.1980 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 HIS A 734 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.146427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.111229 restraints weight = 17434.903| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.05 r_work: 0.3147 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14195 Z= 0.113 Angle : 0.458 6.871 19199 Z= 0.241 Chirality : 0.040 0.157 2113 Planarity : 0.003 0.042 2444 Dihedral : 5.999 64.605 1931 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.88 % Allowed : 18.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.21), residues: 1676 helix: 2.17 (0.17), residues: 933 sheet: -0.24 (0.43), residues: 145 loop : 0.44 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 67 HIS 0.006 0.001 HIS A 89 PHE 0.012 0.001 PHE C 30 TYR 0.016 0.001 TYR B 406 ARG 0.003 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 772) hydrogen bonds : angle 4.13746 ( 2247) metal coordination : bond 0.00301 ( 4) covalent geometry : bond 0.00251 (14191) covalent geometry : angle 0.45756 (19199) *********************** 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 218 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 1.573 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6410 (OUTLIER) cc_final: 0.4974 (ptp) REVERT: A 136 PHE cc_start: 0.8637 (m-80) cc_final: 0.8306 (m-80) REVERT: A 151 LYS cc_start: 0.7849 (mmtt) cc_final: 0.7010 (mtmm) REVERT: A 188 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7951 (ptmm) REVERT: A 314 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8328 (mt-10) REVERT: A 367 ASP cc_start: 0.8337 (t0) cc_final: 0.7947 (t0) REVERT: A 398 ASP cc_start: 0.7293 (t70) cc_final: 0.7057 (t70) REVERT: A 442 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7635 (mtp) REVERT: A 465 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7381 (tp30) REVERT: A 539 LYS cc_start: 0.8196 (mttm) cc_final: 0.7924 (mmtp) REVERT: A 557 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8547 (mtt180) REVERT: B 86 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7788 (tpt-90) REVERT: B 133 GLU cc_start: 0.8209 (pt0) cc_final: 0.7962 (pt0) REVERT: B 151 LYS cc_start: 0.7724 (pttt) cc_final: 0.7001 (mttp) REVERT: B 170 LYS cc_start: 0.7983 (mmtp) cc_final: 0.7523 (mmmt) REVERT: B 340 ASP cc_start: 0.7504 (t0) cc_final: 0.6997 (m-30) REVERT: B 397 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7594 (mt-10) REVERT: B 408 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.8021 (ttp-170) REVERT: B 418 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7660 (m-30) REVERT: B 442 MET cc_start: 0.8277 (tpp) cc_final: 0.8055 (ttm) REVERT: B 502 ARG cc_start: 0.7479 (mmm160) cc_final: 0.7232 (mmm160) REVERT: B 505 GLU cc_start: 0.7837 (pm20) cc_final: 0.6528 (mm-30) REVERT: B 595 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8320 (mtt) REVERT: B 653 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7851 (pp) outliers start: 44 outliers final: 27 residues processed: 208 average time/residue: 0.2646 time to fit residues: 80.4674 Evaluate side-chains 209 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 1.575 ------------------------------------------------------------------------------- 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 438 THR 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 672 THR Chi-restraints excluded: chain A residue 751 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 182 THR Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 255 THR 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 627 SER Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 751 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 2 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 B 148 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.143098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.107850 restraints weight = 17366.366| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.04 r_work: 0.3081 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14195 Z= 0.165 Angle : 0.503 10.557 19199 Z= 0.264 Chirality : 0.041 0.161 2113 Planarity : 0.004 0.042 2444 Dihedral : 6.202 65.972 1931 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.15 % Allowed : 18.28 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.21), residues: 1676 helix: 2.08 (0.17), residues: 932 sheet: -0.20 (0.44), residues: 144 loop : 0.33 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 67 HIS 0.007 0.001 HIS A 89 PHE 0.014 0.001 PHE C 30 TYR 0.016 0.002 TYR B 406 ARG 0.005 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.04696 ( 772) hydrogen bonds : angle 4.27572 ( 2247) metal coordination : bond 0.00628 ( 4) covalent geometry : bond 0.00395 (14191) covalent geometry : angle 0.50347 (19199) *********************** 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 216 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.6406 (OUTLIER) cc_final: 0.5041 (ptp) REVERT: A 136 PHE cc_start: 0.8653 (m-80) cc_final: 0.8365 (m-80) REVERT: A 145 TRP cc_start: 0.7406 (t-100) cc_final: 0.6089 (t60) REVERT: A 151 LYS cc_start: 0.7912 (mmtt) cc_final: 0.7051 (mtmm) REVERT: A 188 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7837 (ptmm) REVERT: A 314 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8362 (mt-10) REVERT: A 367 ASP cc_start: 0.8306 (t0) cc_final: 0.7932 (t0) REVERT: A 442 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7615 (mtp) REVERT: A 465 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7414 (tp30) REVERT: A 557 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8607 (mtt180) REVERT: B 133 GLU cc_start: 0.8313 (pt0) cc_final: 0.8084 (pt0) REVERT: B 151 LYS cc_start: 0.7715 (pttt) cc_final: 0.7002 (mttp) REVERT: B 170 LYS cc_start: 0.7971 (mmtp) cc_final: 0.7525 (mmmt) REVERT: B 177 LYS cc_start: 0.6294 (OUTLIER) cc_final: 0.5821 (mttp) REVERT: B 340 ASP cc_start: 0.7596 (t0) cc_final: 0.7009 (m-30) REVERT: B 397 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7601 (mt-10) REVERT: B 502 ARG cc_start: 0.7559 (mmm160) cc_final: 0.7338 (mmm160) REVERT: B 595 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8390 (mtt) REVERT: B 653 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.7904 (pp) outliers start: 48 outliers final: 32 residues processed: 204 average time/residue: 0.2579 time to fit residues: 78.0552 Evaluate side-chains 204 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 1.669 ------------------------------------------------------------------------------- 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 438 THR 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 582 ARG Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 140 ILE 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 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 595 MET Chi-restraints excluded: chain B residue 627 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 0.0570 chunk 79 optimal weight: 5.9990 chunk 154 optimal weight: 0.6980 chunk 28 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 734 GLN B 126 ASN B 148 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.149586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.116400 restraints weight = 17356.515| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.94 r_work: 0.3206 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14195 Z= 0.109 Angle : 0.464 9.030 19199 Z= 0.244 Chirality : 0.039 0.153 2113 Planarity : 0.003 0.042 2444 Dihedral : 6.089 66.871 1931 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.95 % Allowed : 18.48 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.21), residues: 1676 helix: 2.19 (0.17), residues: 936 sheet: -0.21 (0.44), residues: 145 loop : 0.41 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 67 HIS 0.005 0.000 HIS A 89 PHE 0.022 0.001 PHE C 30 TYR 0.016 0.001 TYR B 406 ARG 0.002 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 772) hydrogen bonds : angle 4.14566 ( 2247) metal coordination : bond 0.00246 ( 4) covalent geometry : bond 0.00240 (14191) covalent geometry : angle 0.46437 (19199) *********************** 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: 45 poor density : 174 time to evaluate : 1.617 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6411 (OUTLIER) cc_final: 0.5000 (ptp) REVERT: A 136 PHE cc_start: 0.8670 (m-80) cc_final: 0.8412 (m-80) REVERT: A 151 LYS cc_start: 0.7931 (mmtt) cc_final: 0.7100 (mtmm) REVERT: A 188 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7982 (ptmm) REVERT: A 314 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8342 (mt-10) REVERT: A 367 ASP cc_start: 0.8316 (t0) cc_final: 0.7963 (t0) REVERT: A 398 ASP cc_start: 0.7294 (t70) cc_final: 0.7030 (t70) REVERT: A 465 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7543 (tp30) REVERT: A 539 LYS cc_start: 0.8250 (mttm) cc_final: 0.7997 (mmtp) REVERT: A 557 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8523 (mtt180) REVERT: B 57 GLU cc_start: 0.6739 (pp20) cc_final: 0.6206 (pp20) REVERT: B 133 GLU cc_start: 0.8183 (pt0) cc_final: 0.7944 (pt0) REVERT: B 151 LYS cc_start: 0.7774 (pttt) cc_final: 0.7059 (mttp) REVERT: B 170 LYS cc_start: 0.8026 (mmtp) cc_final: 0.7565 (mmmt) REVERT: B 177 LYS cc_start: 0.6425 (OUTLIER) cc_final: 0.6051 (mttp) REVERT: B 340 ASP cc_start: 0.7588 (t0) cc_final: 0.7081 (m-30) REVERT: B 397 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7579 (mt-10) REVERT: B 408 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8144 (ttp-170) REVERT: B 418 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7660 (m-30) REVERT: B 502 ARG cc_start: 0.7645 (mmm160) cc_final: 0.7413 (mmm160) REVERT: B 505 GLU cc_start: 0.7950 (pm20) cc_final: 0.6692 (mm-30) REVERT: B 595 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8290 (mtt) REVERT: B 653 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7952 (pp) outliers start: 45 outliers final: 30 residues processed: 207 average time/residue: 0.2615 time to fit residues: 79.3288 Evaluate side-chains 210 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 1.655 ------------------------------------------------------------------------------- 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 672 THR Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain B residue 69 VAL 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 179 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 320 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 627 SER Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain D residue 87 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 89 optimal weight: 0.0570 chunk 153 optimal weight: 3.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 HIS B 148 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.148984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.114537 restraints weight = 17365.637| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.90 r_work: 0.3070 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1709 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= 0.122 Angle : 0.479 9.180 19199 Z= 0.250 Chirality : 0.040 0.157 2113 Planarity : 0.004 0.043 2444 Dihedral : 6.090 67.126 1931 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.01 % Allowed : 18.41 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.21), residues: 1676 helix: 2.20 (0.17), residues: 935 sheet: -0.13 (0.44), residues: 143 loop : 0.41 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 245 HIS 0.006 0.001 HIS A 89 PHE 0.012 0.001 PHE C 30 TYR 0.015 0.001 TYR B 406 ARG 0.003 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 772) hydrogen bonds : angle 4.15881 ( 2247) metal coordination : bond 0.00355 ( 4) covalent geometry : bond 0.00278 (14191) covalent geometry : angle 0.47944 (19199) ********************** 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 213 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 167 time to evaluate : 1.573 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6394 (OUTLIER) cc_final: 0.4936 (ptp) REVERT: A 136 PHE cc_start: 0.8574 (m-80) cc_final: 0.8250 (m-80) REVERT: A 151 LYS cc_start: 0.7862 (mmtt) cc_final: 0.7017 (mtmm) REVERT: A 188 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7829 (ptmm) REVERT: A 314 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8342 (mt-10) REVERT: A 316 ASN cc_start: 0.8230 (t0) cc_final: 0.7894 (t0) REVERT: A 367 ASP cc_start: 0.8322 (t0) cc_final: 0.7949 (t0) REVERT: A 398 ASP cc_start: 0.7227 (t70) cc_final: 0.6983 (t70) REVERT: A 465 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7403 (tp30) REVERT: A 539 LYS cc_start: 0.8148 (mttm) cc_final: 0.7884 (mmtp) REVERT: A 557 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8518 (mtt180) REVERT: B 57 GLU cc_start: 0.6593 (pp20) cc_final: 0.6062 (pp20) REVERT: B 133 GLU cc_start: 0.8240 (pt0) cc_final: 0.7980 (pt0) REVERT: B 151 LYS cc_start: 0.7720 (pttt) cc_final: 0.6977 (mttp) REVERT: B 170 LYS cc_start: 0.7935 (mmtp) cc_final: 0.7475 (mmmt) REVERT: B 177 LYS cc_start: 0.6315 (OUTLIER) cc_final: 0.5982 (mttp) REVERT: B 397 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7514 (mt-10) REVERT: B 408 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.8019 (ttp-170) REVERT: B 418 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7620 (m-30) REVERT: B 502 ARG cc_start: 0.7552 (mmm160) cc_final: 0.7285 (mmm160) REVERT: B 505 GLU cc_start: 0.7861 (pm20) cc_final: 0.6563 (mm-30) REVERT: B 595 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8293 (mtt) REVERT: B 653 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7874 (pp) outliers start: 46 outliers final: 32 residues processed: 202 average time/residue: 0.2614 time to fit residues: 77.4932 Evaluate side-chains 205 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 1.614 ------------------------------------------------------------------------------- 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 672 THR Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain B residue 69 VAL 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 320 ILE 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 627 SER Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain D residue 87 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 47 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 95 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 77 optimal weight: 0.0570 chunk 155 optimal weight: 0.7980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 148 HIS B 89 HIS B 148 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.150901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.116548 restraints weight = 17461.302| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.91 r_work: 0.3188 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14195 Z= 0.107 Angle : 0.464 8.745 19199 Z= 0.244 Chirality : 0.039 0.154 2113 Planarity : 0.003 0.042 2444 Dihedral : 6.055 67.917 1931 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.95 % Allowed : 18.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.21), residues: 1676 helix: 2.21 (0.17), residues: 939 sheet: -0.09 (0.44), residues: 143 loop : 0.45 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 245 HIS 0.005 0.000 HIS A 89 PHE 0.012 0.001 PHE C 30 TYR 0.015 0.001 TYR B 406 ARG 0.003 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 772) hydrogen bonds : angle 4.10137 ( 2247) metal coordination : bond 0.00229 ( 4) covalent geometry : bond 0.00235 (14191) covalent geometry : angle 0.46385 (19199) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8253.94 seconds wall clock time: 143 minutes 11.82 seconds (8591.82 seconds total)