Starting phenix.real_space_refine on Wed Mar 4 05:33:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e21_30949/03_2026/7e21_30949.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e21_30949/03_2026/7e21_30949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e21_30949/03_2026/7e21_30949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e21_30949/03_2026/7e21_30949.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e21_30949/03_2026/7e21_30949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e21_30949/03_2026/7e21_30949.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 P 5 5.49 5 Mg 1 5.21 5 S 58 5.16 5 Na 4 4.78 5 C 6871 2.51 5 N 1720 2.21 5 O 1977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10636 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7575 Classifications: {'peptide': 976} Link IDs: {'PTRANS': 43, 'TRANS': 932} Chain breaks: 1 Chain: "B" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2404 Classifications: {'peptide': 294} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 273} Chain: "C" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 256 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 230 Unusual residues: {' MG': 1, ' NA': 4, 'AGS': 1, 'PC1': 1, 'Y01': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "B" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'NAG': 1, 'PC1': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 2.76, per 1000 atoms: 0.26 Number of scatterers: 10636 At special positions: 0 Unit cell: (89.134, 96.743, 181.529, 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) S 58 16.00 P 5 15.00 Mg 1 11.99 Na 4 11.00 O 1977 8.00 N 1720 7.00 C 6871 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 249 " distance=2.05 Simple disulfide: pdb=" SG CYS A 518 " - pdb=" SG CYS A 556 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=1.97 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG B 403 " - " ASN B 265 " " NAG D 1 " - " ASN B 158 " Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 510.3 milliseconds 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2410 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 9 sheets defined 42.5% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 64 through 75 removed outlier: 3.957A pdb=" N ALA A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 97 removed outlier: 3.651A pdb=" N LYS A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 122 removed outlier: 3.522A pdb=" N TRP A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 159 removed outlier: 3.791A pdb=" N GLY A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 removed outlier: 4.056A pdb=" N ILE A 270 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 311 removed outlier: 3.580A pdb=" N ILE A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 294 " --> pdb=" O HIS A 290 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 332 removed outlier: 3.657A pdb=" N VAL A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.761A pdb=" N THR A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 4.102A pdb=" N GLU A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 428 removed outlier: 4.122A pdb=" N LEU A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 458 removed outlier: 4.423A pdb=" N LEU A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 510 through 515 Processing helix chain 'A' and resid 531 through 547 Processing helix chain 'A' and resid 598 through 609 removed outlier: 3.625A pdb=" N GLY A 604 " --> pdb=" O PRO A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 632 Processing helix chain 'A' and resid 640 through 648 removed outlier: 3.938A pdb=" N ILE A 644 " --> pdb=" O THR A 640 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 680 removed outlier: 3.901A pdb=" N ASP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP A 680 " --> pdb=" O GLU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 685 removed outlier: 3.778A pdb=" N TYR A 684 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N HIS A 685 " --> pdb=" O ILE A 681 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 680 through 685' Processing helix chain 'A' and resid 697 through 707 removed outlier: 3.644A pdb=" N ILE A 701 " --> pdb=" O GLN A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 726 Processing helix chain 'A' and resid 754 through 780 removed outlier: 3.977A pdb=" N ILE A 758 " --> pdb=" O ASN A 754 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 759 " --> pdb=" O PHE A 755 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE A 768 " --> pdb=" O GLU A 764 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP A 770 " --> pdb=" O ARG A 766 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 775 " --> pdb=" O ASN A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 796 Proline residue: A 789 - end of helix Processing helix chain 'A' and resid 803 through 822 Proline residue: A 818 - end of helix removed outlier: 3.824A pdb=" N LEU A 822 " --> pdb=" O PRO A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.622A pdb=" N LYS A 833 " --> pdb=" O ASP A 830 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG A 834 " --> pdb=" O ILE A 831 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 830 through 834' Processing helix chain 'A' and resid 846 through 854 removed outlier: 3.824A pdb=" N ILE A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 877 removed outlier: 3.634A pdb=" N ILE A 860 " --> pdb=" O GLN A 856 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR A 868 " --> pdb=" O GLY A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 907 through 937 removed outlier: 3.624A pdb=" N ILE A 913 " --> pdb=" O GLU A 909 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 971 removed outlier: 3.883A pdb=" N ILE A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 969 " --> pdb=" O ALA A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 988 Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.525A pdb=" N LYS A1006 " --> pdb=" O ASP A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1022 removed outlier: 3.824A pdb=" N TYR A1022 " --> pdb=" O GLU A1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 58 removed outlier: 3.519A pdb=" N PHE B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 113 through 117 removed outlier: 3.594A pdb=" N GLN B 117 " --> pdb=" O ASP B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.636A pdb=" N TRP B 155 " --> pdb=" O LYS B 152 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY B 157 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.942A pdb=" N GLY B 172 " --> pdb=" O TYR B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 removed outlier: 4.393A pdb=" N LEU B 250 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 46 removed outlier: 3.690A pdb=" N GLY C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 169 through 171 Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 193 removed outlier: 6.934A pdb=" N CYS A 249 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL A 213 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU A 251 " --> pdb=" O CYS A 211 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N CYS A 211 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE A 257 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE A 205 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL A 259 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU A 203 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 358 removed outlier: 6.173A pdb=" N GLY A 731 " --> pdb=" O MET A 748 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU A 750 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA A 733 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL A 712 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL A 732 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL A 714 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N MET A 734 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLY A 716 " --> pdb=" O MET A 734 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE A 373 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL A 616 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N SER A 375 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL A 613 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N PHE A 690 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N CYS A 663 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ALA A 691 " --> pdb=" O CYS A 663 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 665 " --> pdb=" O ALA A 691 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 392 removed outlier: 3.579A pdb=" N THR A 387 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 590 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N MET A 391 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU A 588 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE A 585 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N HIS A 557 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY A 587 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL A 478 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 898 through 899 Processing sheet with id=AA6, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 90 removed outlier: 3.542A pdb=" N PHE B 90 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 123 through 124 400 hydrogen bonds defined for protein. 1161 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: 1.58 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 2206 1.33 - 1.47: 3741 1.47 - 1.62: 4789 1.62 - 1.76: 41 1.76 - 1.91: 85 Bond restraints: 10862 Sorted by residual: bond pdb=" C3' AGS A1106 " pdb=" C4' AGS A1106 " ideal model delta sigma weight residual 1.526 1.280 0.246 1.10e-02 8.26e+03 4.99e+02 bond pdb=" C1' AGS A1106 " pdb=" C2' AGS A1106 " ideal model delta sigma weight residual 1.530 1.307 0.223 1.30e-02 5.92e+03 2.94e+02 bond pdb=" C4 AGS A1106 " pdb=" N3 AGS A1106 " ideal model delta sigma weight residual 1.340 1.482 -0.142 1.00e-02 1.00e+04 2.01e+02 bond pdb=" C2 AGS A1106 " pdb=" N3 AGS A1106 " ideal model delta sigma weight residual 1.335 1.463 -0.128 1.00e-02 1.00e+04 1.63e+02 bond pdb=" C5 AGS A1106 " pdb=" C6 AGS A1106 " ideal model delta sigma weight residual 1.409 1.524 -0.115 1.00e-02 1.00e+04 1.33e+02 ... (remaining 10857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.32: 14638 6.32 - 12.63: 96 12.63 - 18.95: 1 18.95 - 25.27: 4 25.27 - 31.58: 1 Bond angle restraints: 14740 Sorted by residual: angle pdb=" N1 AGS A1106 " pdb=" C2 AGS A1106 " pdb=" N3 AGS A1106 " ideal model delta sigma weight residual 128.80 119.83 8.97 8.41e-01 1.41e+00 1.14e+02 angle pdb=" CAD Y01 A1107 " pdb=" CBH Y01 A1107 " pdb=" CBF Y01 A1107 " ideal model delta sigma weight residual 111.82 80.24 31.58 3.00e+00 1.11e-01 1.11e+02 angle pdb=" C5 AGS A1106 " pdb=" N7 AGS A1106 " pdb=" C8 AGS A1106 " ideal model delta sigma weight residual 103.67 108.00 -4.33 4.26e-01 5.51e+00 1.03e+02 angle pdb=" C5 AGS A1106 " pdb=" C4 AGS A1106 " pdb=" N3 AGS A1106 " ideal model delta sigma weight residual 126.80 120.07 6.73 7.41e-01 1.82e+00 8.24e+01 angle pdb=" N7 AGS A1106 " pdb=" C8 AGS A1106 " pdb=" N9 AGS A1106 " ideal model delta sigma weight residual 114.03 108.06 5.97 6.99e-01 2.05e+00 7.29e+01 ... (remaining 14735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 6506 35.38 - 70.77: 226 70.77 - 106.15: 48 106.15 - 141.53: 110 141.53 - 176.91: 13 Dihedral angle restraints: 6903 sinusoidal: 3151 harmonic: 3752 Sorted by residual: dihedral pdb=" CB CYS A 518 " pdb=" SG CYS A 518 " pdb=" SG CYS A 556 " pdb=" CB CYS A 556 " ideal model delta sinusoidal sigma weight residual 93.00 23.32 69.68 1 1.00e+01 1.00e-02 6.27e+01 dihedral pdb=" CA THR A 316 " pdb=" C THR A 316 " pdb=" N TRP A 317 " pdb=" CA TRP A 317 " ideal model delta harmonic sigma weight residual 180.00 -150.20 -29.80 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA THR A 85 " pdb=" C THR A 85 " pdb=" N THR A 86 " pdb=" CA THR A 86 " ideal model delta harmonic sigma weight residual 180.00 152.34 27.66 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 6900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.195: 1636 1.195 - 2.390: 0 2.390 - 3.584: 0 3.584 - 4.779: 1 4.779 - 5.974: 29 Chirality restraints: 1666 Sorted by residual: chirality pdb=" CBI Y01 A1107 " pdb=" CAU Y01 A1107 " pdb=" CBE Y01 A1107 " pdb=" CBG Y01 A1107 " both_signs ideal model delta sigma weight residual False 2.94 -3.04 5.97 2.00e-01 2.50e+01 8.92e+02 chirality pdb=" CBI Y01 C1501 " pdb=" CAU Y01 C1501 " pdb=" CBE Y01 C1501 " pdb=" CBG Y01 C1501 " both_signs ideal model delta sigma weight residual False 2.94 -3.04 5.97 2.00e-01 2.50e+01 8.92e+02 chirality pdb=" CBI Y01 A1110 " pdb=" CAU Y01 A1110 " pdb=" CBE Y01 A1110 " pdb=" CBG Y01 A1110 " both_signs ideal model delta sigma weight residual False 2.94 -3.03 5.97 2.00e-01 2.50e+01 8.90e+02 ... (remaining 1663 not shown) Planarity restraints: 1847 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 440 " -0.077 5.00e-02 4.00e+02 1.18e-01 2.22e+01 pdb=" N PRO A 441 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO A 441 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 441 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 81 " 0.061 5.00e-02 4.00e+02 9.28e-02 1.38e+01 pdb=" N PRO A 82 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 132 " 0.049 5.00e-02 4.00e+02 7.33e-02 8.59e+00 pdb=" N PRO B 133 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 133 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 133 " 0.040 5.00e-02 4.00e+02 ... (remaining 1844 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 161 2.64 - 3.21: 9054 3.21 - 3.77: 15621 3.77 - 4.34: 22126 4.34 - 4.90: 36703 Nonbonded interactions: 83665 Sorted by model distance: nonbonded pdb=" O TYR B 242 " pdb=" O TYR B 243 " model vdw 2.077 3.040 nonbonded pdb=" OD1 ASN A 174 " pdb=" N GLY A 175 " model vdw 2.119 3.120 nonbonded pdb=" NH1 ARG A 551 " pdb=" O1B AGS A1106 " model vdw 2.205 3.120 nonbonded pdb=" CAI Y01 A1109 " pdb=" CAD Y01 B 401 " model vdw 2.223 3.760 nonbonded pdb=" OE2 GLU A 875 " pdb=" OAG Y01 A1108 " model vdw 2.230 3.040 ... (remaining 83660 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.490 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.870 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 : 0.014 0.246 10870 Z= 0.752 Angle : 1.393 41.776 14759 Z= 0.677 Chirality : 0.724 5.974 1666 Planarity : 0.008 0.118 1845 Dihedral : 27.997 176.914 4478 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.81 % Favored : 91.34 % Rotamer: Outliers : 0.89 % Allowed : 6.70 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.81 (0.18), residues: 1294 helix: -2.62 (0.16), residues: 526 sheet: -1.12 (0.36), residues: 151 loop : -2.78 (0.21), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 150 TYR 0.045 0.003 TYR A 315 PHE 0.033 0.003 PHE A 793 TRP 0.013 0.002 TRP A 890 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.01416 (10862) covalent geometry : angle 1.34625 (14740) SS BOND : bond 0.02926 ( 5) SS BOND : angle 13.33359 ( 10) hydrogen bonds : bond 0.16445 ( 400) hydrogen bonds : angle 5.97521 ( 1161) link_BETA1-4 : bond 0.00226 ( 1) link_BETA1-4 : angle 2.63078 ( 3) link_NAG-ASN : bond 0.00522 ( 2) link_NAG-ASN : angle 4.45381 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 43 ASP cc_start: 0.6382 (OUTLIER) cc_final: 0.6157 (p0) REVERT: A 261 THR cc_start: 0.8359 (p) cc_final: 0.8133 (t) REVERT: A 392 TRP cc_start: 0.8269 (t60) cc_final: 0.8028 (t60) REVERT: A 401 ASP cc_start: 0.7192 (t0) cc_final: 0.6755 (t0) REVERT: A 483 ASN cc_start: 0.7334 (p0) cc_final: 0.7062 (p0) REVERT: A 591 MET cc_start: 0.8884 (mtm) cc_final: 0.8648 (mpp) REVERT: A 649 ASN cc_start: 0.8379 (t0) cc_final: 0.8146 (t0) REVERT: A 729 ASP cc_start: 0.8676 (m-30) cc_final: 0.8442 (m-30) REVERT: A 764 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7744 (mm-30) REVERT: B 22 LYS cc_start: 0.8065 (mtmm) cc_final: 0.7481 (tttt) REVERT: C 42 LEU cc_start: 0.8146 (mt) cc_final: 0.7891 (mt) outliers start: 10 outliers final: 3 residues processed: 145 average time/residue: 0.6158 time to fit residues: 95.7124 Evaluate side-chains 89 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain B residue 159 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 437 GLN A 486 ASN A 582 ASN A 638 ASN A 654 GLN A 697 GLN ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 HIS B 18 ASN B 104 ASN B 140 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.130304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.088902 restraints weight = 17236.999| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.15 r_work: 0.3030 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10870 Z= 0.151 Angle : 1.602 34.189 14759 Z= 0.597 Chirality : 0.151 1.888 1666 Planarity : 0.006 0.083 1845 Dihedral : 30.918 178.921 2014 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.50 % Favored : 92.19 % Rotamer: Outliers : 2.50 % Allowed : 11.26 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.21), residues: 1294 helix: -0.75 (0.22), residues: 539 sheet: -1.03 (0.37), residues: 153 loop : -2.42 (0.22), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 430 TYR 0.020 0.001 TYR C 21 PHE 0.027 0.002 PHE A 870 TRP 0.009 0.001 TRP A 931 HIS 0.003 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00340 (10862) covalent geometry : angle 1.60095 (14740) SS BOND : bond 0.00843 ( 5) SS BOND : angle 1.65921 ( 10) hydrogen bonds : bond 0.05586 ( 400) hydrogen bonds : angle 4.52895 ( 1161) link_BETA1-4 : bond 0.00688 ( 1) link_BETA1-4 : angle 2.07192 ( 3) link_NAG-ASN : bond 0.00225 ( 2) link_NAG-ASN : angle 3.39014 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 315 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.7286 (m-10) REVERT: A 362 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8162 (tt0) REVERT: A 392 TRP cc_start: 0.8210 (t60) cc_final: 0.7976 (t60) REVERT: A 401 ASP cc_start: 0.7123 (t0) cc_final: 0.6684 (t0) REVERT: A 483 ASN cc_start: 0.7509 (p0) cc_final: 0.7020 (p0) REVERT: A 591 MET cc_start: 0.9095 (mtm) cc_final: 0.8830 (mpp) REVERT: A 729 ASP cc_start: 0.9098 (m-30) cc_final: 0.8814 (m-30) REVERT: A 764 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8481 (mm-30) REVERT: A 1019 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8537 (mtpt) REVERT: B 21 LYS cc_start: 0.8463 (mtpt) cc_final: 0.8052 (mptt) REVERT: B 22 LYS cc_start: 0.7945 (mtmm) cc_final: 0.7292 (tttt) REVERT: B 118 ARG cc_start: 0.8061 (mmp80) cc_final: 0.7714 (mmp80) REVERT: B 203 LYS cc_start: 0.7679 (tptp) cc_final: 0.7083 (mtpt) REVERT: B 268 MET cc_start: 0.8125 (mmt) cc_final: 0.7783 (mmt) REVERT: C 42 LEU cc_start: 0.7569 (mt) cc_final: 0.7264 (mt) outliers start: 28 outliers final: 3 residues processed: 117 average time/residue: 0.5420 time to fit residues: 68.7371 Evaluate side-chains 93 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 1019 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 0 optimal weight: 40.0000 chunk 93 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 96 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 127 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 331 ASN ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.130889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.089617 restraints weight = 17220.819| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.15 r_work: 0.3041 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10870 Z= 0.140 Angle : 1.560 33.048 14759 Z= 0.575 Chirality : 0.150 1.906 1666 Planarity : 0.005 0.070 1845 Dihedral : 30.779 179.593 2007 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.65 % Favored : 92.12 % Rotamer: Outliers : 2.41 % Allowed : 13.05 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.22), residues: 1294 helix: 0.12 (0.23), residues: 535 sheet: -0.74 (0.39), residues: 143 loop : -2.16 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 430 TYR 0.026 0.002 TYR A 488 PHE 0.018 0.001 PHE A 870 TRP 0.009 0.001 TRP A 317 HIS 0.002 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00324 (10862) covalent geometry : angle 1.55903 (14740) SS BOND : bond 0.00599 ( 5) SS BOND : angle 1.80834 ( 10) hydrogen bonds : bond 0.04850 ( 400) hydrogen bonds : angle 4.21883 ( 1161) link_BETA1-4 : bond 0.00522 ( 1) link_BETA1-4 : angle 1.93535 ( 3) link_NAG-ASN : bond 0.00090 ( 2) link_NAG-ASN : angle 2.92671 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 315 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7329 (m-10) REVERT: A 392 TRP cc_start: 0.8233 (t60) cc_final: 0.8021 (t60) REVERT: A 401 ASP cc_start: 0.7183 (t0) cc_final: 0.6606 (t0) REVERT: A 483 ASN cc_start: 0.7533 (p0) cc_final: 0.7036 (p0) REVERT: A 649 ASN cc_start: 0.8806 (t0) cc_final: 0.8347 (t0) REVERT: A 764 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8424 (mm-30) REVERT: B 21 LYS cc_start: 0.8408 (mtpt) cc_final: 0.7800 (mppt) REVERT: B 22 LYS cc_start: 0.7995 (mtmm) cc_final: 0.7327 (tttt) REVERT: B 23 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7732 (mt-10) REVERT: B 118 ARG cc_start: 0.8153 (mmp80) cc_final: 0.7866 (mmp80) REVERT: B 203 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7242 (mmmt) REVERT: B 268 MET cc_start: 0.8112 (mmt) cc_final: 0.7793 (mmt) outliers start: 27 outliers final: 5 residues processed: 107 average time/residue: 0.5046 time to fit residues: 58.7309 Evaluate side-chains 89 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 203 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 122 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.0040 chunk 41 optimal weight: 20.0000 chunk 5 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.132885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.092265 restraints weight = 17296.662| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.16 r_work: 0.3081 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10870 Z= 0.112 Angle : 1.534 33.119 14759 Z= 0.558 Chirality : 0.150 1.878 1666 Planarity : 0.004 0.062 1845 Dihedral : 30.595 179.792 2007 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.65 % Favored : 93.12 % Rotamer: Outliers : 2.23 % Allowed : 14.57 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.23), residues: 1294 helix: 0.63 (0.24), residues: 534 sheet: -0.57 (0.40), residues: 143 loop : -1.87 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 471 TYR 0.030 0.001 TYR A 488 PHE 0.013 0.001 PHE A 870 TRP 0.010 0.001 TRP A 317 HIS 0.003 0.001 HIS A 503 Details of bonding type rmsd covalent geometry : bond 0.00245 (10862) covalent geometry : angle 1.53394 (14740) SS BOND : bond 0.00127 ( 5) SS BOND : angle 1.41381 ( 10) hydrogen bonds : bond 0.03977 ( 400) hydrogen bonds : angle 4.01313 ( 1161) link_BETA1-4 : bond 0.00225 ( 1) link_BETA1-4 : angle 1.68130 ( 3) link_NAG-ASN : bond 0.00246 ( 2) link_NAG-ASN : angle 2.60396 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6851 (pm20) REVERT: A 178 MET cc_start: 0.8125 (ptp) cc_final: 0.7544 (ptp) REVERT: A 183 GLU cc_start: 0.8394 (pt0) cc_final: 0.7862 (pm20) REVERT: A 315 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7349 (m-10) REVERT: A 392 TRP cc_start: 0.8217 (t60) cc_final: 0.8014 (t60) REVERT: A 483 ASN cc_start: 0.7497 (p0) cc_final: 0.6910 (p0) REVERT: A 544 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: A 649 ASN cc_start: 0.8807 (t0) cc_final: 0.8373 (t0) REVERT: A 764 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8380 (mm-30) REVERT: B 21 LYS cc_start: 0.8393 (mtpt) cc_final: 0.7866 (mppt) REVERT: B 22 LYS cc_start: 0.7982 (mtmm) cc_final: 0.7322 (tttt) REVERT: B 23 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7921 (mt-10) REVERT: B 118 ARG cc_start: 0.8188 (mmp80) cc_final: 0.7948 (mmp80) REVERT: B 203 LYS cc_start: 0.7587 (tptp) cc_final: 0.7259 (mmmt) outliers start: 25 outliers final: 8 residues processed: 106 average time/residue: 0.5816 time to fit residues: 66.4662 Evaluate side-chains 88 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 249 CYS Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain B residue 201 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 38 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.132336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.091974 restraints weight = 17071.743| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.14 r_work: 0.3083 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10870 Z= 0.113 Angle : 1.525 33.148 14759 Z= 0.553 Chirality : 0.150 1.892 1666 Planarity : 0.004 0.060 1845 Dihedral : 30.468 179.893 2007 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.80 % Favored : 93.04 % Rotamer: Outliers : 2.32 % Allowed : 15.64 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.24), residues: 1294 helix: 0.93 (0.24), residues: 532 sheet: -0.48 (0.40), residues: 143 loop : -1.76 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 173 TYR 0.027 0.001 TYR A 488 PHE 0.013 0.001 PHE A 793 TRP 0.006 0.001 TRP A 317 HIS 0.003 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00252 (10862) covalent geometry : angle 1.52480 (14740) SS BOND : bond 0.00652 ( 5) SS BOND : angle 1.46651 ( 10) hydrogen bonds : bond 0.03933 ( 400) hydrogen bonds : angle 3.94759 ( 1161) link_BETA1-4 : bond 0.00334 ( 1) link_BETA1-4 : angle 1.60410 ( 3) link_NAG-ASN : bond 0.00180 ( 2) link_NAG-ASN : angle 2.46206 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7145 (pt0) cc_final: 0.6795 (pm20) REVERT: A 183 GLU cc_start: 0.8330 (pt0) cc_final: 0.7874 (pm20) REVERT: A 289 GLU cc_start: 0.8694 (pt0) cc_final: 0.8271 (tt0) REVERT: A 324 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8442 (tp) REVERT: A 392 TRP cc_start: 0.8154 (t60) cc_final: 0.7950 (t60) REVERT: A 399 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7186 (pt0) REVERT: A 471 ARG cc_start: 0.7119 (mpt-90) cc_final: 0.6874 (mmt180) REVERT: A 483 ASN cc_start: 0.7453 (p0) cc_final: 0.6862 (p0) REVERT: A 544 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: A 649 ASN cc_start: 0.8786 (t0) cc_final: 0.8369 (t0) REVERT: A 764 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8391 (mm-30) REVERT: B 20 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7575 (pm20) REVERT: B 21 LYS cc_start: 0.8455 (mtpt) cc_final: 0.7933 (mppt) REVERT: B 22 LYS cc_start: 0.7975 (mtmm) cc_final: 0.7169 (tttt) REVERT: B 23 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7948 (mt-10) REVERT: B 118 ARG cc_start: 0.8163 (mmp80) cc_final: 0.7936 (mmp80) REVERT: B 203 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.7241 (mmmt) outliers start: 26 outliers final: 11 residues processed: 110 average time/residue: 0.5680 time to fit residues: 67.4532 Evaluate side-chains 98 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 294 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 44 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.130273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.089307 restraints weight = 17328.909| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.15 r_work: 0.3039 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10870 Z= 0.155 Angle : 1.539 33.437 14759 Z= 0.562 Chirality : 0.150 1.897 1666 Planarity : 0.004 0.058 1845 Dihedral : 30.348 179.867 2007 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.65 % Favored : 92.27 % Rotamer: Outliers : 2.14 % Allowed : 16.18 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.24), residues: 1294 helix: 1.01 (0.24), residues: 529 sheet: -0.61 (0.39), residues: 153 loop : -1.78 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 61 TYR 0.019 0.002 TYR B 204 PHE 0.017 0.001 PHE A 793 TRP 0.006 0.001 TRP A 890 HIS 0.003 0.001 HIS A 882 Details of bonding type rmsd covalent geometry : bond 0.00372 (10862) covalent geometry : angle 1.53831 (14740) SS BOND : bond 0.00507 ( 5) SS BOND : angle 1.75405 ( 10) hydrogen bonds : bond 0.04691 ( 400) hydrogen bonds : angle 4.00785 ( 1161) link_BETA1-4 : bond 0.00306 ( 1) link_BETA1-4 : angle 1.58436 ( 3) link_NAG-ASN : bond 0.00092 ( 2) link_NAG-ASN : angle 2.59010 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6820 (pm20) REVERT: A 183 GLU cc_start: 0.8364 (pt0) cc_final: 0.7898 (pm20) REVERT: A 289 GLU cc_start: 0.8714 (pt0) cc_final: 0.8334 (tt0) REVERT: A 324 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8454 (tp) REVERT: A 399 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7228 (pt0) REVERT: A 483 ASN cc_start: 0.7543 (p0) cc_final: 0.6982 (p0) REVERT: A 649 ASN cc_start: 0.8781 (t0) cc_final: 0.8369 (t0) REVERT: A 764 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8578 (mm-30) REVERT: B 21 LYS cc_start: 0.8515 (mtpt) cc_final: 0.8009 (mptt) REVERT: B 22 LYS cc_start: 0.8014 (mtmm) cc_final: 0.7193 (tttp) REVERT: B 203 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7135 (mmmt) outliers start: 24 outliers final: 12 residues processed: 103 average time/residue: 0.5676 time to fit residues: 63.3047 Evaluate side-chains 95 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 294 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 113 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.131915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.091027 restraints weight = 17177.900| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.15 r_work: 0.3070 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10870 Z= 0.115 Angle : 1.527 32.921 14759 Z= 0.554 Chirality : 0.151 1.898 1666 Planarity : 0.004 0.067 1845 Dihedral : 30.254 179.187 2007 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.88 % Favored : 92.97 % Rotamer: Outliers : 1.79 % Allowed : 16.98 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.24), residues: 1294 helix: 1.07 (0.24), residues: 535 sheet: -0.57 (0.40), residues: 153 loop : -1.67 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 118 TYR 0.029 0.001 TYR A 488 PHE 0.013 0.001 PHE A 793 TRP 0.007 0.001 TRP A 317 HIS 0.003 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00261 (10862) covalent geometry : angle 1.52643 (14740) SS BOND : bond 0.00550 ( 5) SS BOND : angle 1.49574 ( 10) hydrogen bonds : bond 0.04066 ( 400) hydrogen bonds : angle 3.93912 ( 1161) link_BETA1-4 : bond 0.00343 ( 1) link_BETA1-4 : angle 1.57066 ( 3) link_NAG-ASN : bond 0.00083 ( 2) link_NAG-ASN : angle 2.36974 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.414 Fit side-chains REVERT: A 88 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6837 (pm20) REVERT: A 118 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7188 (tt0) REVERT: A 183 GLU cc_start: 0.8288 (pt0) cc_final: 0.7819 (pm20) REVERT: A 289 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8323 (tt0) REVERT: A 324 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8461 (tp) REVERT: A 386 MET cc_start: 0.8945 (mtp) cc_final: 0.8691 (mtp) REVERT: A 399 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7263 (pt0) REVERT: A 483 ASN cc_start: 0.7584 (p0) cc_final: 0.7041 (p0) REVERT: A 544 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: A 649 ASN cc_start: 0.8736 (t0) cc_final: 0.8332 (t0) REVERT: A 764 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8491 (mm-30) REVERT: B 21 LYS cc_start: 0.8407 (mtpt) cc_final: 0.7953 (mptt) REVERT: B 22 LYS cc_start: 0.7992 (mtmm) cc_final: 0.7132 (tttt) REVERT: B 23 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7808 (mt-10) REVERT: B 203 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7212 (mmmt) outliers start: 20 outliers final: 9 residues processed: 99 average time/residue: 0.6053 time to fit residues: 64.7055 Evaluate side-chains 93 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 294 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 92 optimal weight: 0.0270 chunk 124 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.7640 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.132741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.092352 restraints weight = 17171.597| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.15 r_work: 0.3083 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 10870 Z= 0.109 Angle : 1.516 32.654 14759 Z= 0.548 Chirality : 0.152 1.891 1666 Planarity : 0.004 0.057 1845 Dihedral : 30.151 179.780 2007 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.49 % Favored : 93.43 % Rotamer: Outliers : 1.79 % Allowed : 17.34 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.24), residues: 1294 helix: 1.28 (0.24), residues: 529 sheet: -0.44 (0.40), residues: 153 loop : -1.54 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 118 TYR 0.020 0.001 TYR B 204 PHE 0.015 0.001 PHE A 578 TRP 0.007 0.001 TRP A 317 HIS 0.004 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00245 (10862) covalent geometry : angle 1.51587 (14740) SS BOND : bond 0.00419 ( 5) SS BOND : angle 1.25374 ( 10) hydrogen bonds : bond 0.03708 ( 400) hydrogen bonds : angle 3.85519 ( 1161) link_BETA1-4 : bond 0.00272 ( 1) link_BETA1-4 : angle 1.50258 ( 3) link_NAG-ASN : bond 0.00176 ( 2) link_NAG-ASN : angle 2.21380 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.398 Fit side-chains REVERT: A 88 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6842 (pm20) REVERT: A 118 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7247 (tt0) REVERT: A 178 MET cc_start: 0.8137 (ptp) cc_final: 0.7482 (ptp) REVERT: A 183 GLU cc_start: 0.8217 (pt0) cc_final: 0.7826 (pm20) REVERT: A 190 LEU cc_start: 0.8080 (tp) cc_final: 0.7830 (tp) REVERT: A 289 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8334 (tt0) REVERT: A 324 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8480 (tp) REVERT: A 386 MET cc_start: 0.8866 (mtp) cc_final: 0.8610 (mtp) REVERT: A 399 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7247 (pt0) REVERT: A 483 ASN cc_start: 0.7595 (p0) cc_final: 0.7057 (p0) REVERT: A 544 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: A 649 ASN cc_start: 0.8714 (t0) cc_final: 0.8302 (t0) REVERT: A 764 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8463 (mm-30) REVERT: B 20 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7456 (pm20) REVERT: B 21 LYS cc_start: 0.8478 (mtpt) cc_final: 0.8173 (mppt) REVERT: B 23 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7997 (mt-10) REVERT: B 203 LYS cc_start: 0.7523 (tptp) cc_final: 0.7212 (mmmt) outliers start: 20 outliers final: 7 residues processed: 97 average time/residue: 0.5400 time to fit residues: 56.8101 Evaluate side-chains 91 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 72 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 1 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 51 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.132240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.090136 restraints weight = 17286.874| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.22 r_work: 0.3057 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10870 Z= 0.124 Angle : 1.522 32.890 14759 Z= 0.551 Chirality : 0.152 1.888 1666 Planarity : 0.004 0.053 1845 Dihedral : 30.099 178.404 2007 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.57 % Favored : 93.35 % Rotamer: Outliers : 1.79 % Allowed : 17.61 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.24), residues: 1294 helix: 1.34 (0.24), residues: 523 sheet: -0.58 (0.41), residues: 143 loop : -1.54 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 118 TYR 0.032 0.001 TYR A 488 PHE 0.014 0.001 PHE A 793 TRP 0.006 0.001 TRP A 894 HIS 0.002 0.000 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00290 (10862) covalent geometry : angle 1.52197 (14740) SS BOND : bond 0.00469 ( 5) SS BOND : angle 1.20617 ( 10) hydrogen bonds : bond 0.04119 ( 400) hydrogen bonds : angle 3.88404 ( 1161) link_BETA1-4 : bond 0.00277 ( 1) link_BETA1-4 : angle 1.51879 ( 3) link_NAG-ASN : bond 0.00078 ( 2) link_NAG-ASN : angle 2.27034 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7259 (pt0) cc_final: 0.7017 (pm20) REVERT: A 118 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: A 183 GLU cc_start: 0.8250 (pt0) cc_final: 0.7845 (pm20) REVERT: A 190 LEU cc_start: 0.8135 (tp) cc_final: 0.7875 (tp) REVERT: A 289 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8370 (tt0) REVERT: A 324 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8481 (tp) REVERT: A 386 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8699 (mtp) REVERT: A 399 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7229 (pt0) REVERT: A 483 ASN cc_start: 0.7605 (p0) cc_final: 0.7104 (p0) REVERT: A 649 ASN cc_start: 0.8724 (t0) cc_final: 0.8312 (t0) REVERT: A 764 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8553 (mm-30) REVERT: B 20 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7608 (pm20) REVERT: B 21 LYS cc_start: 0.8457 (mtpt) cc_final: 0.8054 (mptt) REVERT: B 23 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7987 (mt-10) REVERT: B 203 LYS cc_start: 0.7523 (tptp) cc_final: 0.7168 (mmmt) outliers start: 20 outliers final: 12 residues processed: 92 average time/residue: 0.5714 time to fit residues: 57.0816 Evaluate side-chains 93 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 249 CYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 294 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 118 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 121 optimal weight: 0.0670 chunk 17 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.132356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.091803 restraints weight = 17047.208| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.14 r_work: 0.3086 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10870 Z= 0.110 Angle : 1.518 32.604 14759 Z= 0.549 Chirality : 0.152 1.890 1666 Planarity : 0.004 0.050 1845 Dihedral : 30.097 178.780 2007 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.57 % Favored : 93.35 % Rotamer: Outliers : 1.52 % Allowed : 17.96 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.24), residues: 1294 helix: 1.34 (0.24), residues: 529 sheet: -0.52 (0.42), residues: 143 loop : -1.51 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 118 TYR 0.021 0.001 TYR B 204 PHE 0.015 0.001 PHE A 578 TRP 0.007 0.001 TRP A 317 HIS 0.003 0.000 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00249 (10862) covalent geometry : angle 1.51728 (14740) SS BOND : bond 0.00517 ( 5) SS BOND : angle 1.93701 ( 10) hydrogen bonds : bond 0.03826 ( 400) hydrogen bonds : angle 3.86585 ( 1161) link_BETA1-4 : bond 0.00295 ( 1) link_BETA1-4 : angle 1.48408 ( 3) link_NAG-ASN : bond 0.00138 ( 2) link_NAG-ASN : angle 2.14043 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7234 (pt0) cc_final: 0.7008 (pm20) REVERT: A 118 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7223 (tt0) REVERT: A 183 GLU cc_start: 0.8218 (pt0) cc_final: 0.7829 (pm20) REVERT: A 190 LEU cc_start: 0.8135 (tp) cc_final: 0.7877 (tp) REVERT: A 289 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8348 (tt0) REVERT: A 324 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8474 (tp) REVERT: A 386 MET cc_start: 0.8912 (mtp) cc_final: 0.8684 (mtp) REVERT: A 399 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7251 (pt0) REVERT: A 483 ASN cc_start: 0.7614 (p0) cc_final: 0.7081 (p0) REVERT: A 649 ASN cc_start: 0.8714 (t0) cc_final: 0.8299 (t0) REVERT: A 764 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8463 (mm-30) REVERT: B 20 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.6804 (tm-30) REVERT: B 65 LYS cc_start: 0.9111 (ttpp) cc_final: 0.8810 (ttpp) REVERT: B 203 LYS cc_start: 0.7567 (tptp) cc_final: 0.7229 (mmmt) outliers start: 17 outliers final: 10 residues processed: 91 average time/residue: 0.5876 time to fit residues: 58.0103 Evaluate side-chains 91 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 72 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 118 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 4 optimal weight: 20.0000 chunk 91 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.130664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.089653 restraints weight = 17418.662| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.16 r_work: 0.3049 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10870 Z= 0.145 Angle : 1.534 33.177 14759 Z= 0.559 Chirality : 0.152 1.893 1666 Planarity : 0.004 0.048 1845 Dihedral : 30.097 177.569 2007 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.80 % Favored : 93.12 % Rotamer: Outliers : 1.43 % Allowed : 18.50 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.24), residues: 1294 helix: 1.33 (0.24), residues: 523 sheet: -0.38 (0.41), residues: 153 loop : -1.55 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 118 TYR 0.028 0.002 TYR A 488 PHE 0.016 0.001 PHE A 793 TRP 0.008 0.001 TRP A 894 HIS 0.002 0.001 HIS A 882 Details of bonding type rmsd covalent geometry : bond 0.00348 (10862) covalent geometry : angle 1.53328 (14740) SS BOND : bond 0.00558 ( 5) SS BOND : angle 1.96406 ( 10) hydrogen bonds : bond 0.04525 ( 400) hydrogen bonds : angle 3.93368 ( 1161) link_BETA1-4 : bond 0.00237 ( 1) link_BETA1-4 : angle 1.53084 ( 3) link_NAG-ASN : bond 0.00077 ( 2) link_NAG-ASN : angle 2.34809 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3993.40 seconds wall clock time: 68 minutes 29.75 seconds (4109.75 seconds total)