Starting phenix.real_space_refine on Thu Jul 31 22:50:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cxh_45991/07_2025/9cxh_45991.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cxh_45991/07_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_45991/07_2025/9cxh_45991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cxh_45991/07_2025/9cxh_45991.map" model { file = "/net/cci-nas-00/data/ceres_data/9cxh_45991/07_2025/9cxh_45991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cxh_45991/07_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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, '5GP%rna3p': 1, 'PCG': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {' MG': 1, ' ZN': 1, '5GP%rna3p': 1, 'PCG': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 8.76, 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: 3.46 Conformation dependent library (CDL) restraints added in 2.0 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: 1.38 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: 4.88 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4327 1.34 - 1.46: 2079 1.46 - 1.58: 7641 1.58 - 1.70: 6 1.70 - 1.82: 138 Bond restraints: 14191 Sorted by residual: bond pdb=" C1' PCG B 901 " pdb=" O4' PCG B 901 " ideal model delta sigma weight residual 1.409 1.601 -0.192 2.00e-02 2.50e+03 9.21e+01 bond pdb=" C1' PCG A 901 " pdb=" O4' PCG A 901 " ideal model delta sigma weight residual 1.409 1.599 -0.190 2.00e-02 2.50e+03 9.03e+01 bond pdb=" C6 PCG A 901 " pdb=" O6 PCG A 901 " ideal model delta sigma weight residual 1.219 1.398 -0.179 2.00e-02 2.50e+03 7.97e+01 bond pdb=" C6 PCG B 901 " pdb=" O6 PCG B 901 " ideal model delta sigma weight residual 1.219 1.396 -0.177 2.00e-02 2.50e+03 7.86e+01 bond pdb=" C5 PCG A 901 " pdb=" N7 PCG A 901 " ideal model delta sigma weight residual 1.370 1.525 -0.155 2.00e-02 2.50e+03 6.00e+01 ... (remaining 14186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 19030 2.79 - 5.57: 115 5.57 - 8.36: 34 8.36 - 11.15: 18 11.15 - 13.93: 2 Bond angle restraints: 19199 Sorted by residual: angle pdb=" C4 PCG A 901 " pdb=" N9 PCG A 901 " pdb=" C8 PCG A 901 " ideal model delta sigma weight residual 106.51 120.44 -13.93 3.00e+00 1.11e-01 2.16e+01 angle pdb=" C4 PCG B 901 " pdb=" N9 PCG B 901 " pdb=" C8 PCG B 901 " ideal model delta sigma weight residual 106.51 120.33 -13.82 3.00e+00 1.11e-01 2.12e+01 angle pdb=" N GLN A 776 " pdb=" CA GLN A 776 " pdb=" CB GLN A 776 " ideal model delta sigma weight residual 110.16 116.64 -6.48 1.48e+00 4.57e-01 1.92e+01 angle pdb=" N SER A 49 " pdb=" CA SER A 49 " pdb=" CB SER A 49 " ideal model delta sigma weight residual 114.17 109.63 4.54 1.14e+00 7.69e-01 1.58e+01 angle pdb=" O3' PCG A 901 " pdb=" PA PCG A 901 " pdb=" O5' PCG A 901 " ideal model delta sigma weight residual 103.94 114.81 -10.87 3.00e+00 1.11e-01 1.31e+01 ... (remaining 19194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 7493 17.88 - 35.77: 833 35.77 - 53.65: 206 53.65 - 71.54: 87 71.54 - 89.42: 15 Dihedral angle restraints: 8634 sinusoidal: 3665 harmonic: 4969 Sorted by residual: dihedral pdb=" CA MET A 48 " pdb=" C MET A 48 " pdb=" N SER A 49 " pdb=" CA SER A 49 " ideal model delta harmonic sigma weight residual 180.00 159.93 20.07 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA TYR A 406 " pdb=" C TYR A 406 " pdb=" N ASN A 407 " pdb=" CA ASN A 407 " ideal model delta harmonic sigma weight residual -180.00 -160.38 -19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA TYR B 406 " pdb=" C TYR B 406 " pdb=" N ASN B 407 " pdb=" CA ASN B 407 " ideal model delta harmonic sigma weight residual -180.00 -161.94 -18.06 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 8631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1739 0.053 - 0.105: 323 0.105 - 0.158: 47 0.158 - 0.210: 2 0.210 - 0.263: 2 Chirality restraints: 2113 Sorted by residual: chirality pdb=" C2' PCG B 901 " pdb=" C1' PCG B 901 " pdb=" C3' PCG B 901 " pdb=" O2' PCG B 901 " both_signs ideal model delta sigma weight residual False -2.74 -2.48 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C2' PCG A 901 " pdb=" C1' PCG A 901 " pdb=" C3' PCG A 901 " pdb=" O2' PCG A 901 " both_signs ideal model delta sigma weight residual False -2.74 -2.50 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" C1' 5GP A 904 " pdb=" C2' 5GP A 904 " pdb=" N9 5GP A 904 " pdb=" O4' 5GP A 904 " both_signs ideal model delta sigma weight residual False 2.29 2.46 -0.16 2.00e-01 2.50e+01 6.71e-01 ... (remaining 2110 not shown) Planarity restraints: 2444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 219 " -0.013 2.00e-02 2.50e+03 1.53e-02 4.12e+00 pdb=" CG PHE A 219 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 219 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 219 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 219 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 219 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 219 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 118 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO A 119 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 772 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A 773 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 773 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 773 " -0.021 5.00e-02 4.00e+02 ... (remaining 2441 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 50 2.51 - 3.11: 10169 3.11 - 3.71: 21123 3.71 - 4.30: 29804 4.30 - 4.90: 51124 Nonbonded interactions: 112270 Sorted by model distance: nonbonded pdb="ZN ZN A 902 " pdb=" O3P 5GP A 904 " model vdw 1.914 2.230 nonbonded pdb="MG MG A 903 " pdb=" O2P 5GP A 904 " model vdw 1.928 2.170 nonbonded pdb=" OD2 ASP A 603 " pdb="ZN ZN A 902 " model vdw 1.946 2.230 nonbonded pdb="ZN ZN B 902 " pdb=" O3P 5GP B 904 " model vdw 1.969 2.230 nonbonded pdb=" OD2 ASP B 603 " pdb="ZN ZN B 902 " model vdw 1.983 2.230 ... (remaining 112265 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 823 or resid 901 through 904)) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 26 through 49 or resid 52 through 87)) selection = (chain 'D' and (resid 26 through 63 or resid 72 through 87)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 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: 36.550 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.192 14195 Z= 0.324 Angle : 0.666 13.934 19199 Z= 0.305 Chirality : 0.041 0.263 2113 Planarity : 0.004 0.040 2444 Dihedral : 16.887 89.423 5408 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 17.43 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 0.00658 (14191) covalent geometry : angle 0.66630 (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 : 1.562 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: 0.2772 time to fit residues: 78.0755 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 : 1.573 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.4586 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.145512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.110317 restraints weight = 17240.146| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.04 r_work: 0.3152 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0888 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= 0.155 Angle : 0.505 7.578 19199 Z= 0.267 Chirality : 0.042 0.183 2113 Planarity : 0.004 0.043 2444 Dihedral : 5.971 56.655 1931 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.69 % Allowed : 16.64 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.21), residues: 1676 helix: 1.89 (0.17), residues: 932 sheet: -0.22 (0.41), residues: 145 loop : 0.55 (0.26), residues: 599 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 0.012 0.001 PHE B 568 TYR 0.016 0.001 TYR B 406 ARG 0.003 0.000 ARG A 809 Details of bonding type rmsd hydrogen bonds : bond 0.05055 ( 772) hydrogen bonds : angle 4.57519 ( 2247) metal coordination : bond 0.00451 ( 4) covalent geometry : bond 0.00360 (14191) covalent geometry : angle 0.50535 (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 217 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 176 time to evaluate : 1.545 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6505 (OUTLIER) cc_final: 0.5118 (ptm) REVERT: A 82 ARG cc_start: 0.7656 (ttm110) cc_final: 0.6959 (mtm180) REVERT: A 136 PHE cc_start: 0.8671 (m-80) cc_final: 0.8384 (m-80) REVERT: A 151 LYS cc_start: 0.7809 (mmtt) cc_final: 0.6977 (mtmm) REVERT: A 293 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7712 (mt-10) REVERT: A 326 HIS cc_start: 0.8172 (p90) cc_final: 0.7903 (p90) REVERT: A 367 ASP cc_start: 0.8275 (t0) cc_final: 0.7831 (t0) REVERT: A 440 ASP cc_start: 0.7972 (m-30) cc_final: 0.7628 (t70) REVERT: A 465 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7394 (tp30) REVERT: B 48 MET cc_start: 0.4072 (mmp) cc_final: 0.3540 (mmp) REVERT: B 133 GLU cc_start: 0.8248 (pt0) cc_final: 0.8034 (pt0) REVERT: B 151 LYS cc_start: 0.7551 (pttt) cc_final: 0.6978 (pptt) REVERT: B 170 LYS cc_start: 0.7946 (mmtp) cc_final: 0.7446 (mmmt) REVERT: B 232 MET cc_start: 0.8980 (mmt) cc_final: 0.8758 (mmm) REVERT: B 273 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.8130 (t0) REVERT: B 324 ILE cc_start: 0.8047 (mm) cc_final: 0.7815 (mm) REVERT: B 340 ASP cc_start: 0.7599 (t0) cc_final: 0.7030 (m-30) REVERT: B 369 TYR cc_start: 0.8150 (t80) cc_final: 0.7843 (t80) REVERT: B 397 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7625 (mt-10) REVERT: B 415 ASP cc_start: 0.8236 (m-30) cc_final: 0.7920 (m-30) REVERT: B 418 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7547 (m-30) REVERT: B 653 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7964 (pp) REVERT: B 694 MET cc_start: 0.7169 (mtt) cc_final: 0.6453 (mtt) outliers start: 41 outliers final: 21 residues processed: 206 average time/residue: 0.2489 time to fit residues: 77.2081 Evaluate side-chains 191 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 1.553 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 58 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 HIS A 316 ASN B 435 ASN B 569 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.109332 restraints weight = 17324.948| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.04 r_work: 0.3138 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14195 Z= 0.159 Angle : 0.491 7.142 19199 Z= 0.261 Chirality : 0.041 0.172 2113 Planarity : 0.004 0.042 2444 Dihedral : 5.925 56.355 1931 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.08 % Allowed : 16.84 % Favored : 80.08 % 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: 1.79 (0.21), residues: 1676 helix: 1.91 (0.17), residues: 932 sheet: -0.16 (0.42), residues: 143 loop : 0.53 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 145 HIS 0.008 0.001 HIS A 89 PHE 0.012 0.001 PHE B 568 TYR 0.016 0.001 TYR B 406 ARG 0.005 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.04887 ( 772) hydrogen bonds : angle 4.44376 ( 2247) metal coordination : bond 0.00507 ( 4) covalent geometry : bond 0.00375 (14191) covalent geometry : angle 0.49116 (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 221 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.6501 (OUTLIER) cc_final: 0.5174 (ptp) REVERT: A 82 ARG cc_start: 0.7636 (ttm110) cc_final: 0.6930 (mtm180) REVERT: A 136 PHE cc_start: 0.8733 (m-80) cc_final: 0.8407 (m-80) REVERT: A 151 LYS cc_start: 0.7833 (mmtt) cc_final: 0.6976 (mtmm) REVERT: A 293 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7709 (mt-10) REVERT: A 367 ASP cc_start: 0.8326 (t0) cc_final: 0.7894 (t0) REVERT: A 440 ASP cc_start: 0.7997 (m-30) cc_final: 0.7650 (t70) REVERT: A 442 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7601 (mtp) REVERT: A 465 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7366 (tp30) REVERT: B 48 MET cc_start: 0.4073 (mmp) cc_final: 0.3869 (mmp) REVERT: B 133 GLU cc_start: 0.8272 (pt0) cc_final: 0.8050 (pt0) REVERT: B 151 LYS cc_start: 0.7609 (pttt) cc_final: 0.6994 (mttp) REVERT: B 170 LYS cc_start: 0.7952 (mmtp) cc_final: 0.7460 (mmmt) REVERT: B 273 ASN cc_start: 0.8364 (t0) cc_final: 0.8155 (t0) REVERT: B 340 ASP cc_start: 0.7641 (t0) cc_final: 0.7054 (m-30) REVERT: B 369 TYR cc_start: 0.8279 (t80) cc_final: 0.8075 (t80) REVERT: B 418 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7619 (m-30) REVERT: B 595 MET cc_start: 0.8654 (mmm) cc_final: 0.8350 (mtt) REVERT: B 653 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7955 (pp) REVERT: B 694 MET cc_start: 0.7206 (mtt) cc_final: 0.6647 (mtt) outliers start: 47 outliers final: 28 residues processed: 209 average time/residue: 0.2533 time to fit residues: 79.9673 Evaluate side-chains 200 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 442 MET 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 96 CYS 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 309 THR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 785 THR Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain D residue 87 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 130 optimal weight: 0.0370 chunk 154 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- 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 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.141477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106024 restraints weight = 17468.181| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.05 r_work: 0.3092 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14195 Z= 0.216 Angle : 0.537 6.945 19199 Z= 0.283 Chirality : 0.043 0.170 2113 Planarity : 0.004 0.045 2444 Dihedral : 6.047 57.253 1931 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.60 % Allowed : 16.58 % Favored : 79.82 % 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: 1.59 (0.20), residues: 1676 helix: 1.79 (0.17), residues: 932 sheet: -0.24 (0.42), residues: 144 loop : 0.36 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 145 HIS 0.008 0.001 HIS A 89 PHE 0.014 0.001 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 0.05227 ( 772) hydrogen bonds : angle 4.48603 ( 2247) metal coordination : bond 0.00746 ( 4) covalent geometry : bond 0.00526 (14191) covalent geometry : angle 0.53725 (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 234 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 179 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.6443 (OUTLIER) cc_final: 0.5086 (ptm) REVERT: A 82 ARG cc_start: 0.7728 (ttm110) cc_final: 0.7006 (mtm180) REVERT: A 136 PHE cc_start: 0.8755 (m-80) cc_final: 0.8468 (m-80) REVERT: A 151 LYS cc_start: 0.7880 (mmtt) cc_final: 0.7015 (mtmm) REVERT: A 314 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8365 (mt-10) REVERT: A 367 ASP cc_start: 0.8326 (t0) cc_final: 0.7918 (t0) REVERT: A 440 ASP cc_start: 0.8052 (m-30) cc_final: 0.7683 (t70) REVERT: A 442 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7595 (mtp) REVERT: A 465 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7408 (tp30) REVERT: A 483 ASP cc_start: 0.6171 (m-30) cc_final: 0.5121 (t0) REVERT: A 557 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8564 (mtt180) REVERT: B 133 GLU cc_start: 0.8342 (pt0) cc_final: 0.8100 (pt0) REVERT: B 170 LYS cc_start: 0.8026 (mmtp) cc_final: 0.7538 (mmmt) REVERT: B 177 LYS cc_start: 0.6151 (OUTLIER) cc_final: 0.5383 (mttp) REVERT: B 225 ARG cc_start: 0.7724 (ttp80) cc_final: 0.7492 (ttp80) REVERT: B 273 ASN cc_start: 0.8446 (OUTLIER) cc_final: 0.8117 (t0) REVERT: B 340 ASP cc_start: 0.7687 (t0) cc_final: 0.7053 (m-30) REVERT: B 369 TYR cc_start: 0.8356 (t80) cc_final: 0.8141 (t80) REVERT: B 397 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7601 (mt-10) REVERT: B 415 ASP cc_start: 0.8317 (m-30) cc_final: 0.7945 (m-30) REVERT: B 418 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7712 (m-30) REVERT: B 442 MET cc_start: 0.8244 (tpp) cc_final: 0.7997 (ttm) REVERT: B 595 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8419 (mtt) REVERT: B 653 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.7978 (pp) outliers start: 55 outliers final: 33 residues processed: 219 average time/residue: 0.2539 time to fit residues: 83.1333 Evaluate side-chains 211 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 314 GLU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 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 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 739 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 785 THR Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain D residue 87 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 116 optimal weight: 0.7980 chunk 166 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 11 optimal weight: 0.0070 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 HIS A 316 ASN A 734 GLN B 234 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.145825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110552 restraints weight = 17419.113| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.07 r_work: 0.3140 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1446 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= 0.108 Angle : 0.456 7.045 19199 Z= 0.242 Chirality : 0.040 0.154 2113 Planarity : 0.003 0.042 2444 Dihedral : 5.979 62.738 1931 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.62 % Allowed : 17.89 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.86 (0.21), residues: 1676 helix: 2.04 (0.17), residues: 931 sheet: -0.21 (0.42), residues: 143 loop : 0.43 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 67 HIS 0.006 0.001 HIS A 89 PHE 0.011 0.001 PHE A 219 TYR 0.017 0.001 TYR B 406 ARG 0.005 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 772) hydrogen bonds : angle 4.23222 ( 2247) metal coordination : bond 0.00284 ( 4) covalent geometry : bond 0.00231 (14191) covalent geometry : angle 0.45640 (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 211 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 1.622 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6482 (mmp) cc_final: 0.4998 (ptm) REVERT: A 82 ARG cc_start: 0.7712 (ttm110) cc_final: 0.7007 (mtm180) REVERT: A 86 ARG cc_start: 0.6540 (tpp-160) cc_final: 0.6292 (tpp-160) REVERT: A 136 PHE cc_start: 0.8691 (m-80) cc_final: 0.8374 (m-80) REVERT: A 145 TRP cc_start: 0.7441 (t-100) cc_final: 0.6237 (t60) REVERT: A 151 LYS cc_start: 0.7833 (mmtt) cc_final: 0.6992 (mtmm) REVERT: A 367 ASP cc_start: 0.8334 (t0) cc_final: 0.7915 (t0) REVERT: A 398 ASP cc_start: 0.7367 (t70) cc_final: 0.7105 (t70) REVERT: A 442 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7598 (mtp) REVERT: A 465 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7356 (tp30) REVERT: B 58 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6912 (tt0) REVERT: B 133 GLU cc_start: 0.8220 (pt0) cc_final: 0.7972 (pt0) REVERT: B 151 LYS cc_start: 0.7633 (pttt) cc_final: 0.6990 (mttp) REVERT: B 170 LYS cc_start: 0.7988 (mmtp) cc_final: 0.7507 (mmmt) REVERT: B 177 LYS cc_start: 0.6247 (OUTLIER) cc_final: 0.5583 (mttp) REVERT: B 273 ASN cc_start: 0.8390 (t0) cc_final: 0.8141 (t0) REVERT: B 369 TYR cc_start: 0.8315 (t80) cc_final: 0.8066 (t80) REVERT: B 397 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7864 (mm-30) REVERT: B 418 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7599 (m-30) REVERT: B 595 MET cc_start: 0.8646 (mmm) cc_final: 0.8334 (mtt) REVERT: B 653 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7852 (pp) outliers start: 40 outliers final: 26 residues processed: 201 average time/residue: 0.2564 time to fit residues: 77.0031 Evaluate side-chains 197 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 336 THR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 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 69 VAL 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 195 MET Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 386 ASN 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 665 PHE 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: 0.9980 chunk 46 optimal weight: 20.0000 chunk 58 optimal weight: 0.1980 chunk 135 optimal weight: 0.8980 chunk 123 optimal weight: 0.0040 chunk 59 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 HIS A 316 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.147149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112054 restraints weight = 17481.346| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.05 r_work: 0.3159 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14195 Z= 0.104 Angle : 0.451 6.814 19199 Z= 0.238 Chirality : 0.039 0.153 2113 Planarity : 0.003 0.042 2444 Dihedral : 5.817 63.477 1931 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.82 % Allowed : 18.22 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.97 (0.21), residues: 1676 helix: 2.15 (0.17), residues: 934 sheet: -0.15 (0.43), residues: 143 loop : 0.45 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 548 HIS 0.005 0.001 HIS A 89 PHE 0.010 0.001 PHE C 30 TYR 0.016 0.001 TYR B 406 ARG 0.004 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.04138 ( 772) hydrogen bonds : angle 4.13210 ( 2247) metal coordination : bond 0.00247 ( 4) covalent geometry : bond 0.00222 (14191) covalent geometry : angle 0.45130 (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 214 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 1.654 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6403 (OUTLIER) cc_final: 0.4939 (ptm) REVERT: A 82 ARG cc_start: 0.7660 (ttm110) cc_final: 0.6985 (mtm180) REVERT: A 136 PHE cc_start: 0.8621 (m-80) cc_final: 0.8327 (m-80) REVERT: A 151 LYS cc_start: 0.7848 (mmtt) cc_final: 0.6979 (mtmm) REVERT: A 188 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7948 (ptmm) REVERT: A 367 ASP cc_start: 0.8336 (t0) cc_final: 0.7938 (t0) REVERT: A 398 ASP cc_start: 0.7339 (t70) cc_final: 0.7099 (t70) REVERT: A 442 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7558 (mtp) REVERT: A 465 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7350 (tp30) REVERT: A 557 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8547 (mtt180) REVERT: B 57 GLU cc_start: 0.6149 (pp20) cc_final: 0.5927 (pp20) REVERT: B 133 GLU cc_start: 0.8203 (pt0) cc_final: 0.7962 (pt0) REVERT: B 151 LYS cc_start: 0.7702 (pttt) cc_final: 0.7030 (mttp) REVERT: B 170 LYS cc_start: 0.7971 (mmtp) cc_final: 0.7501 (mmmt) REVERT: B 340 ASP cc_start: 0.7578 (t0) cc_final: 0.7050 (m-30) REVERT: B 397 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7636 (mt-10) REVERT: B 408 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.8007 (ttp-170) REVERT: B 595 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8333 (mtt) REVERT: B 653 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7809 (pp) outliers start: 43 outliers final: 26 residues processed: 204 average time/residue: 0.2769 time to fit residues: 83.3468 Evaluate side-chains 198 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain B residue 69 VAL 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 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 739 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: 0.0030 chunk 130 optimal weight: 0.0060 chunk 128 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 160 optimal weight: 0.7980 overall best weight: 0.5406 ------------------------------------------------------------------------------- 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 A 316 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.147995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.113011 restraints weight = 17413.289| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.05 r_work: 0.3173 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1567 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= 0.103 Angle : 0.456 8.846 19199 Z= 0.239 Chirality : 0.039 0.150 2113 Planarity : 0.003 0.043 2444 Dihedral : 5.779 64.538 1931 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.01 % Allowed : 18.15 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.06 (0.21), residues: 1676 helix: 2.24 (0.17), residues: 934 sheet: -0.22 (0.43), residues: 145 loop : 0.49 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 67 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 0.004 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 772) hydrogen bonds : angle 4.06742 ( 2247) metal coordination : bond 0.00215 ( 4) covalent geometry : bond 0.00221 (14191) covalent geometry : angle 0.45567 (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 220 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 174 time to evaluate : 1.916 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6434 (OUTLIER) cc_final: 0.5006 (ptp) REVERT: A 82 ARG cc_start: 0.7724 (ttm110) cc_final: 0.7094 (mtm180) REVERT: A 136 PHE cc_start: 0.8580 (m-80) cc_final: 0.8295 (m-80) REVERT: A 151 LYS cc_start: 0.7874 (mmtt) cc_final: 0.6997 (mtmm) REVERT: A 188 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7948 (ptmm) REVERT: A 367 ASP cc_start: 0.8332 (t0) cc_final: 0.7922 (t0) REVERT: A 465 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7397 (tp30) REVERT: A 539 LYS cc_start: 0.8190 (mttm) cc_final: 0.7919 (mmtp) REVERT: A 557 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8534 (mtt180) REVERT: B 57 GLU cc_start: 0.6022 (pp20) cc_final: 0.5587 (pp20) REVERT: B 86 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7554 (tpt-90) REVERT: B 133 GLU cc_start: 0.8210 (pt0) cc_final: 0.7978 (pt0) REVERT: B 151 LYS cc_start: 0.7754 (pttt) cc_final: 0.7057 (mttp) REVERT: B 170 LYS cc_start: 0.7947 (mmtp) cc_final: 0.7485 (mmmt) REVERT: B 177 LYS cc_start: 0.6352 (OUTLIER) cc_final: 0.5905 (mttp) REVERT: B 340 ASP cc_start: 0.7448 (t0) cc_final: 0.6957 (m-30) REVERT: B 397 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7765 (mm-30) REVERT: B 505 GLU cc_start: 0.7783 (pm20) cc_final: 0.6385 (mm-30) REVERT: B 595 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8281 (mtt) REVERT: B 653 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7747 (pp) outliers start: 46 outliers final: 27 residues processed: 211 average time/residue: 0.3806 time to fit residues: 119.8097 Evaluate side-chains 204 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 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 86 ARG Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 751 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 2 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 44 optimal weight: 0.0770 chunk 30 optimal weight: 4.9990 chunk 63 optimal weight: 0.2980 chunk 92 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 160 optimal weight: 9.9990 overall best weight: 1.8542 ------------------------------------------------------------------------------- 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 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.146304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112898 restraints weight = 17351.312| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.96 r_work: 0.3011 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14195 Z= 0.175 Angle : 0.518 9.116 19199 Z= 0.271 Chirality : 0.042 0.157 2113 Planarity : 0.004 0.043 2444 Dihedral : 6.104 67.105 1931 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.15 % Allowed : 18.09 % Favored : 78.77 % 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: 1.86 (0.21), residues: 1676 helix: 2.09 (0.17), residues: 932 sheet: -0.21 (0.43), residues: 144 loop : 0.33 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 67 HIS 0.007 0.001 HIS A 89 PHE 0.024 0.001 PHE C 30 TYR 0.016 0.002 TYR B 406 ARG 0.006 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.04772 ( 772) hydrogen bonds : angle 4.28650 ( 2247) metal coordination : bond 0.00713 ( 4) covalent geometry : bond 0.00418 (14191) covalent geometry : angle 0.51833 (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 214 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 166 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.6378 (OUTLIER) cc_final: 0.4959 (ptp) REVERT: A 136 PHE cc_start: 0.8547 (m-80) cc_final: 0.8221 (m-80) REVERT: A 151 LYS cc_start: 0.7863 (mmtt) cc_final: 0.6993 (mtmm) REVERT: A 188 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7816 (ptmm) REVERT: A 367 ASP cc_start: 0.8307 (t0) cc_final: 0.7919 (t0) REVERT: A 465 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7340 (tp30) REVERT: A 557 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8531 (mtt180) REVERT: B 133 GLU cc_start: 0.8309 (pt0) cc_final: 0.8057 (pt0) REVERT: B 151 LYS cc_start: 0.7685 (pttt) cc_final: 0.6959 (mttp) REVERT: B 170 LYS cc_start: 0.7975 (mmtp) cc_final: 0.7510 (mmmt) REVERT: B 177 LYS cc_start: 0.6289 (OUTLIER) cc_final: 0.5861 (mttp) REVERT: B 340 ASP cc_start: 0.7500 (t0) cc_final: 0.6931 (m-30) REVERT: B 397 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7534 (mt-10) REVERT: B 418 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7591 (m-30) REVERT: B 595 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8344 (mtt) REVERT: B 653 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7816 (pp) outliers start: 48 outliers final: 32 residues processed: 204 average time/residue: 0.2861 time to fit residues: 86.9533 Evaluate side-chains 201 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 1.710 ------------------------------------------------------------------------------- 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 283 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 674 LEU 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 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 255 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 386 ASN 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: 0.6980 chunk 89 optimal weight: 0.0670 chunk 79 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 28 optimal weight: 0.0770 chunk 116 optimal weight: 1.9990 chunk 113 optimal weight: 0.0000 chunk 53 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 overall best weight: 0.3080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.151609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119014 restraints weight = 17329.305| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.98 r_work: 0.3274 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1683 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= 0.100 Angle : 0.460 7.746 19199 Z= 0.242 Chirality : 0.039 0.147 2113 Planarity : 0.003 0.043 2444 Dihedral : 5.940 67.793 1931 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.16 % Allowed : 19.20 % 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: 2.07 (0.21), residues: 1676 helix: 2.28 (0.17), residues: 935 sheet: -0.21 (0.43), residues: 145 loop : 0.43 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 245 HIS 0.005 0.000 HIS A 89 PHE 0.019 0.001 PHE C 30 TYR 0.015 0.001 TYR B 406 ARG 0.005 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 772) hydrogen bonds : angle 4.06863 ( 2247) metal coordination : bond 0.00136 ( 4) covalent geometry : bond 0.00209 (14191) covalent geometry : angle 0.46005 (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 203 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 2.136 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6439 (OUTLIER) cc_final: 0.5065 (ptp) REVERT: A 82 ARG cc_start: 0.7842 (ttm170) cc_final: 0.7275 (mtm180) REVERT: A 136 PHE cc_start: 0.8734 (m-80) cc_final: 0.8478 (m-80) REVERT: A 151 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7303 (mtmm) REVERT: A 188 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8034 (ptmm) REVERT: A 367 ASP cc_start: 0.8325 (t0) cc_final: 0.7994 (t0) REVERT: A 539 LYS cc_start: 0.8335 (mttm) cc_final: 0.8128 (mmtp) REVERT: A 557 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8466 (mtt180) REVERT: B 86 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7977 (tpt-90) REVERT: B 151 LYS cc_start: 0.7904 (pttt) cc_final: 0.7234 (mttp) REVERT: B 170 LYS cc_start: 0.8048 (mmtp) cc_final: 0.7614 (mmmt) REVERT: B 340 ASP cc_start: 0.7561 (t0) cc_final: 0.7145 (m-30) REVERT: B 397 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7657 (mt-10) REVERT: B 505 GLU cc_start: 0.8088 (pm20) cc_final: 0.6905 (mm-30) REVERT: B 595 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8294 (mtt) REVERT: B 653 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8019 (pp) outliers start: 33 outliers final: 24 residues processed: 197 average time/residue: 0.3439 time to fit residues: 99.6437 Evaluate side-chains 196 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 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 86 ARG 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 255 THR Chi-restraints excluded: chain B residue 320 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 653 LEU Chi-restraints excluded: chain B residue 751 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 89 optimal weight: 0.0970 chunk 153 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.150728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.118136 restraints weight = 17352.456| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.02 r_work: 0.3198 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14195 Z= 0.108 Angle : 0.467 7.890 19199 Z= 0.245 Chirality : 0.040 0.149 2113 Planarity : 0.003 0.043 2444 Dihedral : 5.896 68.071 1931 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.23 % Allowed : 19.00 % Favored : 78.77 % 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: 2.08 (0.21), residues: 1676 helix: 2.27 (0.17), residues: 934 sheet: -0.12 (0.43), residues: 143 loop : 0.43 (0.27), residues: 599 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 0.017 0.001 PHE C 30 TYR 0.015 0.001 TYR B 406 ARG 0.005 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 772) hydrogen bonds : angle 4.07830 ( 2247) metal coordination : bond 0.00270 ( 4) covalent geometry : bond 0.00237 (14191) covalent geometry : angle 0.46665 (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 200 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 1.707 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.6416 (OUTLIER) cc_final: 0.4985 (ptp) REVERT: A 82 ARG cc_start: 0.7763 (ttm170) cc_final: 0.7199 (mtm180) REVERT: A 136 PHE cc_start: 0.8617 (m-80) cc_final: 0.8350 (m-80) REVERT: A 151 LYS cc_start: 0.7944 (mmtt) cc_final: 0.7099 (mtmm) REVERT: A 188 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7982 (ptmm) REVERT: A 367 ASP cc_start: 0.8344 (t0) cc_final: 0.7979 (t0) REVERT: A 398 ASP cc_start: 0.7257 (t70) cc_final: 0.7025 (t70) REVERT: A 539 LYS cc_start: 0.8242 (mttm) cc_final: 0.8004 (mmtp) REVERT: A 557 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8532 (mtt180) REVERT: B 132 LYS cc_start: 0.8168 (mmtp) cc_final: 0.7843 (mmmt) REVERT: B 151 LYS cc_start: 0.7821 (pttt) cc_final: 0.7085 (mttp) REVERT: B 170 LYS cc_start: 0.7917 (mmtp) cc_final: 0.7475 (mmmt) REVERT: B 177 LYS cc_start: 0.6419 (OUTLIER) cc_final: 0.6137 (mttp) REVERT: B 271 TYR cc_start: 0.8817 (m-80) cc_final: 0.8448 (m-80) REVERT: B 340 ASP cc_start: 0.7495 (t0) cc_final: 0.7007 (m-30) REVERT: B 397 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7573 (mt-10) REVERT: B 505 GLU cc_start: 0.7963 (pm20) cc_final: 0.6572 (mm-30) REVERT: B 653 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7921 (pp) outliers start: 34 outliers final: 25 residues processed: 194 average time/residue: 0.2819 time to fit residues: 79.3579 Evaluate side-chains 193 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 665 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 47 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.149103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.115926 restraints weight = 17494.190| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.02 r_work: 0.3190 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14195 Z= 0.129 Angle : 0.489 8.201 19199 Z= 0.255 Chirality : 0.040 0.150 2113 Planarity : 0.004 0.042 2444 Dihedral : 5.990 68.498 1931 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.29 % Allowed : 18.48 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.21), residues: 1676 helix: 2.23 (0.17), residues: 934 sheet: -0.11 (0.43), residues: 141 loop : 0.41 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 67 HIS 0.006 0.001 HIS A 89 PHE 0.016 0.001 PHE C 30 TYR 0.015 0.001 TYR B 406 ARG 0.006 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.04236 ( 772) hydrogen bonds : angle 4.14952 ( 2247) metal coordination : bond 0.00411 ( 4) covalent geometry : bond 0.00299 (14191) covalent geometry : angle 0.48930 (19199) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9551.34 seconds wall clock time: 171 minutes 52.61 seconds (10312.61 seconds total)