Starting phenix.real_space_refine on Fri Jul 3 00:44:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e21_30949/07_2026/7e21_30949.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e21_30949/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7e21_30949/07_2026/7e21_30949.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e21_30949/07_2026/7e21_30949.cif" model { file = "/net/cci-nas-00/data/ceres_data/7e21_30949/07_2026/7e21_30949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e21_30949/07_2026/7e21_30949.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e21_30949/07_2026/7e21_30949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e21_30949/07_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-6108/lib/python3.11/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 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 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: 1.81, per 1000 atoms: 0.17 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: 0.76 Conformation dependent library (CDL) restraints added in 337.7 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: 0.18 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: 1.47 Time building geometry restraints manager: 0.98 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 - 31.92: 6188 31.92 - 63.83: 243 63.83 - 95.75: 23 95.75 - 127.67: 7 127.67 - 159.58: 2 Dihedral angle restraints: 6463 sinusoidal: 2711 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 6460 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: 0.480 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: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.140 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 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 : 17.215 159.581 4038 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/Z covalent geometry : bond 0.01416 / 0.75 (10862) covalent geometry : angle 1.34625 / 0.66 (14740) SS BOND : bond 0.02926 / 1.47 ( 5) SS BOND : angle 13.33359 / 6.70 ( 10) hydrogen bonds : bond 0.16445 / 11.91 ( 400) hydrogen bonds : angle 5.97521 / 4.18 ( 1161) link_BETA1-4 : bond 0.00226 / 0.12 ( 1) link_BETA1-4 : angle 2.63078 / 1.37 ( 3) link_NAG-ASN : bond 0.00522 / 0.26 ( 2) link_NAG-ASN : angle 4.45381 / 2.35 ( 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 : 0.289 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: 0.4909 time to fit residues: 76.8156 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 : 0.272 ------------------------------------------------------------------------------- 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... A 248 ASN A 437 GLN A 486 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.131062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.088299 restraints weight = 17237.624| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.23 r_work: 0.3022 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10870 Z= 0.155 Angle : 1.572 32.893 14759 Z= 0.587 Chirality : 0.162 2.025 1666 Planarity : 0.006 0.083 1845 Dihedral : 12.592 116.568 1574 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.42 % Favored : 92.27 % Rotamer: Outliers : 2.50 % Allowed : 11.17 % Favored : 86.33 % 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: -2.33 (0.21), residues: 1294 helix: -0.73 (0.22), residues: 539 sheet: -1.17 (0.38), residues: 143 loop : -2.41 (0.22), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 430 TYR 0.020 0.001 TYR C 21 PHE 0.026 0.002 PHE A 870 TRP 0.008 0.001 TRP A 931 HIS 0.003 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (10862) covalent geometry : angle 1.57100 / 0.59 (14740) SS BOND : bond 0.00427 / 0.22 ( 5) SS BOND : angle 1.41741 / 0.84 ( 10) hydrogen bonds : bond 0.05460 / 3.70 ( 400) hydrogen bonds : angle 4.50534 / 3.18 ( 1161) link_BETA1-4 : bond 0.00557 / 0.29 ( 1) link_BETA1-4 : angle 1.81589 / 0.94 ( 3) link_NAG-ASN : bond 0.00175 / 0.09 ( 2) link_NAG-ASN : angle 3.31673 / 1.78 ( 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 130 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 315 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7296 (m-10) REVERT: A 362 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: A 392 TRP cc_start: 0.8224 (t60) cc_final: 0.7971 (t60) REVERT: A 401 ASP cc_start: 0.7132 (t0) cc_final: 0.6715 (t0) REVERT: A 483 ASN cc_start: 0.7517 (p0) cc_final: 0.7022 (p0) REVERT: A 488 TYR cc_start: 0.7004 (m-80) cc_final: 0.6802 (m-80) REVERT: A 649 ASN cc_start: 0.8447 (t0) cc_final: 0.7805 (t0) REVERT: A 729 ASP cc_start: 0.9106 (m-30) cc_final: 0.8828 (m-30) REVERT: A 764 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8492 (mm-30) REVERT: A 1019 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8547 (mtpt) REVERT: B 21 LYS cc_start: 0.8476 (mtpt) cc_final: 0.8052 (mppt) REVERT: B 22 LYS cc_start: 0.7952 (mtmm) cc_final: 0.7294 (tttt) REVERT: B 118 ARG cc_start: 0.8056 (mmp80) cc_final: 0.7706 (mmp80) REVERT: B 203 LYS cc_start: 0.7710 (tptp) cc_final: 0.7114 (mtpt) REVERT: B 268 MET cc_start: 0.8119 (mmt) cc_final: 0.7779 (mmt) REVERT: C 42 LEU cc_start: 0.7568 (mt) cc_final: 0.7263 (mt) outliers start: 28 outliers final: 3 residues processed: 118 average time/residue: 0.4667 time to fit residues: 59.9675 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 : 0.388 ------------------------------------------------------------------------------- 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: 0.6980 chunk 0 optimal weight: 40.0000 chunk 93 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 ASN A 331 ASN A 649 ASN ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 207 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.130859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.088598 restraints weight = 17251.388| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.20 r_work: 0.3026 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1875 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= 0.149 Angle : 1.544 32.115 14759 Z= 0.571 Chirality : 0.158 2.023 1666 Planarity : 0.005 0.071 1845 Dihedral : 11.561 98.418 1567 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.57 % Favored : 92.19 % Rotamer: Outliers : 2.32 % Allowed : 13.14 % 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: -1.55 (0.23), residues: 1294 helix: 0.12 (0.23), residues: 533 sheet: -0.77 (0.39), residues: 143 loop : -2.17 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 430 TYR 0.019 0.002 TYR B 204 PHE 0.017 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/Z covalent geometry : bond 0.00349 / 0.15 (10862) covalent geometry : angle 1.54319 / 0.57 (14740) SS BOND : bond 0.00708 / 0.37 ( 5) SS BOND : angle 1.71349 / 1.10 ( 10) hydrogen bonds : bond 0.05014 / 3.39 ( 400) hydrogen bonds : angle 4.25138 / 3.01 ( 1161) link_BETA1-4 : bond 0.00502 / 0.26 ( 1) link_BETA1-4 : angle 1.64833 / 0.85 ( 3) link_NAG-ASN : bond 0.00082 / 0.04 ( 2) link_NAG-ASN : angle 2.99638 / 1.59 ( 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 115 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 315 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.7354 (m-10) REVERT: A 392 TRP cc_start: 0.8239 (t60) cc_final: 0.8020 (t60) REVERT: A 401 ASP cc_start: 0.7208 (t0) cc_final: 0.6650 (t0) REVERT: A 483 ASN cc_start: 0.7527 (p0) cc_final: 0.7012 (p0) REVERT: A 488 TYR cc_start: 0.6926 (m-80) cc_final: 0.6684 (m-80) REVERT: A 649 ASN cc_start: 0.8463 (t0) cc_final: 0.7818 (t0) REVERT: A 764 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8450 (mm-30) REVERT: B 21 LYS cc_start: 0.8409 (mtpt) cc_final: 0.7943 (mppt) REVERT: B 22 LYS cc_start: 0.8006 (mtmm) cc_final: 0.7336 (tttt) REVERT: B 118 ARG cc_start: 0.8131 (mmp80) cc_final: 0.7900 (mmp80) REVERT: B 203 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7250 (mmmt) REVERT: B 268 MET cc_start: 0.8107 (mmt) cc_final: 0.7789 (mmt) outliers start: 26 outliers final: 7 residues processed: 107 average time/residue: 0.3972 time to fit residues: 46.5607 Evaluate side-chains 89 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 A residue 440 LEU Chi-restraints excluded: chain A residue 470 MET 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: 5.9990 chunk 0 optimal weight: 40.0000 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 47 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3783 r_free = 0.3783 target = 0.130991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.088889 restraints weight = 17339.071| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.22 r_work: 0.3033 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10870 Z= 0.140 Angle : 1.527 32.339 14759 Z= 0.561 Chirality : 0.158 1.996 1666 Planarity : 0.004 0.062 1845 Dihedral : 11.079 94.671 1567 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.65 % Favored : 92.12 % Rotamer: Outliers : 2.77 % Allowed : 14.30 % Favored : 82.93 % 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: -1.09 (0.23), residues: 1294 helix: 0.58 (0.24), residues: 531 sheet: -0.65 (0.39), residues: 143 loop : -1.95 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 471 TYR 0.020 0.001 TYR B 204 PHE 0.015 0.001 PHE A 793 TRP 0.008 0.001 TRP A 317 HIS 0.002 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (10862) covalent geometry : angle 1.52581 / 0.56 (14740) SS BOND : bond 0.00765 / 0.40 ( 5) SS BOND : angle 1.56318 / 0.99 ( 10) hydrogen bonds : bond 0.04706 / 3.18 ( 400) hydrogen bonds : angle 4.11323 / 2.92 ( 1161) link_BETA1-4 : bond 0.00386 / 0.20 ( 1) link_BETA1-4 : angle 1.47460 / 0.76 ( 3) link_NAG-ASN : bond 0.00126 / 0.07 ( 2) link_NAG-ASN : angle 2.79893 / 1.49 ( 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 112 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6763 (pm20) REVERT: A 183 GLU cc_start: 0.8463 (pt0) cc_final: 0.7945 (pm20) REVERT: A 315 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7357 (m-10) REVERT: A 392 TRP cc_start: 0.8212 (t60) cc_final: 0.7981 (t60) REVERT: A 483 ASN cc_start: 0.7489 (p0) cc_final: 0.6961 (p0) REVERT: A 544 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: A 649 ASN cc_start: 0.8445 (t0) cc_final: 0.7831 (t0) REVERT: A 764 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8519 (mm-30) REVERT: B 21 LYS cc_start: 0.8475 (mtpt) cc_final: 0.7857 (mptt) REVERT: B 22 LYS cc_start: 0.8018 (mtmm) cc_final: 0.7348 (tttt) REVERT: B 118 ARG cc_start: 0.8195 (mmp80) cc_final: 0.7977 (mmp80) REVERT: B 203 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7267 (mmmt) REVERT: B 268 MET cc_start: 0.8189 (mmt) cc_final: 0.7899 (mmt) outliers start: 31 outliers final: 10 residues processed: 104 average time/residue: 0.4673 time to fit residues: 52.7379 Evaluate side-chains 90 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 249 CYS Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 334 GLU 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 B residue 72 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 203 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 38 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 88 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.131622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.090620 restraints weight = 17025.217| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.15 r_work: 0.3058 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10870 Z= 0.121 Angle : 1.519 32.131 14759 Z= 0.555 Chirality : 0.158 1.993 1666 Planarity : 0.004 0.060 1845 Dihedral : 10.776 94.659 1567 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.96 % Favored : 92.81 % Rotamer: Outliers : 2.14 % Allowed : 15.55 % Favored : 82.31 % 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: -0.84 (0.23), residues: 1294 helix: 0.80 (0.24), residues: 536 sheet: -0.58 (0.40), residues: 143 loop : -1.84 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 173 TYR 0.020 0.001 TYR B 204 PHE 0.013 0.001 PHE A 793 TRP 0.008 0.001 TRP A 317 HIS 0.003 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (10862) covalent geometry : angle 1.51878 / 0.55 (14740) SS BOND : bond 0.00509 / 0.27 ( 5) SS BOND : angle 1.67068 / 1.01 ( 10) hydrogen bonds : bond 0.04248 / 2.86 ( 400) hydrogen bonds : angle 4.04359 / 2.87 ( 1161) link_BETA1-4 : bond 0.00359 / 0.19 ( 1) link_BETA1-4 : angle 1.37738 / 0.71 ( 3) link_NAG-ASN : bond 0.00151 / 0.08 ( 2) link_NAG-ASN : angle 2.55531 / 1.36 ( 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 114 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 LEU cc_start: 0.7614 (tm) cc_final: 0.7204 (mm) REVERT: A 88 GLU cc_start: 0.7075 (pt0) cc_final: 0.6742 (pm20) REVERT: A 183 GLU cc_start: 0.8416 (pt0) cc_final: 0.7900 (pm20) REVERT: A 324 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8433 (tp) REVERT: A 392 TRP cc_start: 0.8146 (t60) cc_final: 0.7925 (t60) REVERT: A 399 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7152 (pt0) REVERT: A 483 ASN cc_start: 0.7478 (p0) cc_final: 0.6952 (p0) REVERT: A 544 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: A 649 ASN cc_start: 0.8415 (t0) cc_final: 0.7824 (t0) REVERT: A 748 MET cc_start: 0.9145 (ptp) cc_final: 0.8942 (ttm) REVERT: A 764 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8412 (mm-30) REVERT: A 1019 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8594 (ttpt) REVERT: B 21 LYS cc_start: 0.8440 (mtpt) cc_final: 0.8037 (mppt) REVERT: B 22 LYS cc_start: 0.7989 (mtmm) cc_final: 0.7137 (tttt) REVERT: B 23 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7969 (mt-10) REVERT: B 118 ARG cc_start: 0.8217 (mmp80) cc_final: 0.7963 (mmp80) REVERT: B 203 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7230 (mmmt) outliers start: 24 outliers final: 8 residues processed: 107 average time/residue: 0.4851 time to fit residues: 56.1666 Evaluate side-chains 90 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 324 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 1019 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 203 LYS 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: 0.0020 chunk 70 optimal weight: 3.9990 chunk 67 optimal weight: 0.0470 chunk 62 optimal weight: 0.0020 chunk 103 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.8098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.132296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.091607 restraints weight = 17213.489| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.15 r_work: 0.3075 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 10870 Z= 0.112 Angle : 1.507 32.004 14759 Z= 0.548 Chirality : 0.159 1.989 1666 Planarity : 0.004 0.058 1845 Dihedral : 10.403 93.080 1567 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.80 % Favored : 93.12 % Rotamer: Outliers : 2.06 % Allowed : 16.26 % 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: -0.60 (0.24), residues: 1294 helix: 1.01 (0.24), residues: 534 sheet: -0.46 (0.40), residues: 143 loop : -1.70 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 61 TYR 0.019 0.001 TYR B 204 PHE 0.014 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/Z covalent geometry : bond 0.00249 / 0.11 (10862) covalent geometry : angle 1.50628 / 0.55 (14740) SS BOND : bond 0.00519 / 0.27 ( 5) SS BOND : angle 1.58807 / 0.95 ( 10) hydrogen bonds : bond 0.03889 / 2.62 ( 400) hydrogen bonds : angle 3.95498 / 2.81 ( 1161) link_BETA1-4 : bond 0.00377 / 0.20 ( 1) link_BETA1-4 : angle 1.31343 / 0.68 ( 3) link_NAG-ASN : bond 0.00200 / 0.10 ( 2) link_NAG-ASN : angle 2.36656 / 1.26 ( 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 117 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 59 LEU cc_start: 0.7525 (tm) cc_final: 0.7056 (mm) REVERT: A 88 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6789 (pm20) REVERT: A 118 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7198 (tt0) REVERT: A 183 GLU cc_start: 0.8326 (pt0) cc_final: 0.7894 (pm20) REVERT: A 289 GLU cc_start: 0.8674 (pt0) cc_final: 0.8287 (tt0) REVERT: A 324 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8449 (tp) REVERT: A 392 TRP cc_start: 0.8181 (t60) cc_final: 0.7966 (t60) REVERT: A 399 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7221 (pt0) REVERT: A 483 ASN cc_start: 0.7495 (p0) cc_final: 0.6880 (p0) REVERT: A 488 TYR cc_start: 0.6830 (OUTLIER) cc_final: 0.6588 (m-80) REVERT: A 544 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: A 649 ASN cc_start: 0.8502 (t0) cc_final: 0.7874 (t0) REVERT: A 764 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8364 (mm-30) REVERT: A 1019 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8567 (ttpt) REVERT: B 20 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7531 (pm20) REVERT: B 21 LYS cc_start: 0.8498 (mtpt) cc_final: 0.8099 (mppt) REVERT: B 22 LYS cc_start: 0.7975 (mtmm) cc_final: 0.7154 (tttt) REVERT: B 23 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7905 (mt-10) REVERT: B 118 ARG cc_start: 0.8195 (mmp80) cc_final: 0.7995 (mmp80) REVERT: B 203 LYS cc_start: 0.7483 (tptp) cc_final: 0.7210 (mmmt) outliers start: 23 outliers final: 6 residues processed: 111 average time/residue: 0.4821 time to fit residues: 58.1557 Evaluate side-chains 95 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 324 LEU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 1019 LYS Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 72 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 113 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 90 optimal weight: 0.3980 chunk 74 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.132613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.095589 restraints weight = 17139.759| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.69 r_work: 0.3060 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10870 Z= 0.112 Angle : 1.504 31.756 14759 Z= 0.545 Chirality : 0.159 1.987 1666 Planarity : 0.004 0.066 1845 Dihedral : 10.092 94.159 1567 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.41 % Favored : 93.43 % Rotamer: Outliers : 1.79 % Allowed : 17.52 % Favored : 80.70 % 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: -0.45 (0.24), residues: 1294 helix: 1.19 (0.24), residues: 529 sheet: -0.53 (0.39), residues: 152 loop : -1.62 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 471 TYR 0.019 0.001 TYR B 204 PHE 0.012 0.001 PHE A 793 TRP 0.007 0.001 TRP A 317 HIS 0.004 0.000 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (10862) covalent geometry : angle 1.50375 / 0.55 (14740) SS BOND : bond 0.00451 / 0.24 ( 5) SS BOND : angle 1.34116 / 0.84 ( 10) hydrogen bonds : bond 0.03778 / 2.54 ( 400) hydrogen bonds : angle 3.90294 / 2.77 ( 1161) link_BETA1-4 : bond 0.00375 / 0.20 ( 1) link_BETA1-4 : angle 1.32611 / 0.68 ( 3) link_NAG-ASN : bond 0.00153 / 0.08 ( 2) link_NAG-ASN : angle 2.22012 / 1.18 ( 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 102 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.287 Fit side-chains REVERT: A 88 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6841 (pm20) REVERT: A 118 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: A 183 GLU cc_start: 0.8290 (pt0) cc_final: 0.7834 (pm20) REVERT: A 289 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: A 324 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8455 (tp) REVERT: A 392 TRP cc_start: 0.8134 (t60) cc_final: 0.7921 (t60) REVERT: A 399 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7275 (pt0) REVERT: A 483 ASN cc_start: 0.7563 (p0) cc_final: 0.6996 (p0) REVERT: A 544 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: A 649 ASN cc_start: 0.8496 (t0) cc_final: 0.7883 (t0) REVERT: A 764 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8494 (mm-30) REVERT: B 20 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7449 (pm20) REVERT: B 21 LYS cc_start: 0.8499 (mtpt) cc_final: 0.8111 (mppt) REVERT: B 22 LYS cc_start: 0.8000 (mtmm) cc_final: 0.7131 (tttt) REVERT: B 23 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7938 (mt-10) REVERT: B 118 ARG cc_start: 0.8276 (mmp80) cc_final: 0.8020 (mmp80) REVERT: B 203 LYS cc_start: 0.7543 (tptp) cc_final: 0.7230 (mmmt) outliers start: 20 outliers final: 6 residues processed: 97 average time/residue: 0.5057 time to fit residues: 53.0524 Evaluate side-chains 91 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 811 ASP Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 72 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 26 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 97 optimal weight: 0.0170 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 ASN ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.133113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.096929 restraints weight = 17169.320| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.62 r_work: 0.3072 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 10870 Z= 0.107 Angle : 1.495 31.426 14759 Z= 0.541 Chirality : 0.159 1.985 1666 Planarity : 0.004 0.056 1845 Dihedral : 9.788 92.767 1567 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.41 % Favored : 93.51 % Rotamer: Outliers : 1.43 % Allowed : 17.96 % 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: -0.33 (0.24), residues: 1294 helix: 1.22 (0.24), residues: 535 sheet: -0.43 (0.40), residues: 152 loop : -1.52 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 658 TYR 0.032 0.001 TYR A 488 PHE 0.015 0.001 PHE A 578 TRP 0.007 0.001 TRP A 317 HIS 0.002 0.000 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (10862) covalent geometry : angle 1.49509 / 0.54 (14740) SS BOND : bond 0.00458 / 0.24 ( 5) SS BOND : angle 1.19534 / 0.75 ( 10) hydrogen bonds : bond 0.03601 / 2.42 ( 400) hydrogen bonds : angle 3.85438 / 2.73 ( 1161) link_BETA1-4 : bond 0.00429 / 0.23 ( 1) link_BETA1-4 : angle 1.28670 / 0.67 ( 3) link_NAG-ASN : bond 0.00187 / 0.10 ( 2) link_NAG-ASN : angle 2.12719 / 1.13 ( 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 100 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.300 Fit side-chains REVERT: A 88 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6956 (pm20) REVERT: A 118 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7213 (tt0) REVERT: A 183 GLU cc_start: 0.8265 (pt0) cc_final: 0.7847 (pm20) REVERT: A 289 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8320 (tt0) REVERT: A 324 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8469 (tp) REVERT: A 392 TRP cc_start: 0.8212 (t60) cc_final: 0.7990 (t60) REVERT: A 399 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7215 (pt0) REVERT: A 483 ASN cc_start: 0.7579 (p0) cc_final: 0.7017 (p0) REVERT: A 544 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: A 649 ASN cc_start: 0.8458 (t0) cc_final: 0.7851 (t0) REVERT: A 764 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8471 (mm-30) REVERT: B 20 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7589 (pm20) REVERT: B 21 LYS cc_start: 0.8428 (mtpt) cc_final: 0.7989 (mptt) REVERT: B 23 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7871 (mt-10) REVERT: B 203 LYS cc_start: 0.7528 (tptp) cc_final: 0.7239 (mmmt) outliers start: 16 outliers final: 5 residues processed: 94 average time/residue: 0.4573 time to fit residues: 46.5935 Evaluate side-chains 90 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 51 optimal weight: 30.0000 chunk 56 optimal weight: 6.9990 chunk 97 optimal weight: 0.0470 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.128824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.088069 restraints weight = 17257.616| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.14 r_work: 0.3012 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10870 Z= 0.198 Angle : 1.539 32.543 14759 Z= 0.570 Chirality : 0.160 2.011 1666 Planarity : 0.004 0.054 1845 Dihedral : 10.194 95.666 1567 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.96 % Favored : 92.97 % Rotamer: Outliers : 1.34 % Allowed : 18.50 % Favored : 80.16 % 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: -0.50 (0.24), residues: 1294 helix: 1.08 (0.24), residues: 531 sheet: -0.47 (0.40), residues: 152 loop : -1.62 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 118 TYR 0.022 0.002 TYR B 204 PHE 0.020 0.002 PHE A 793 TRP 0.010 0.001 TRP A 894 HIS 0.003 0.001 HIS A 882 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (10862) covalent geometry : angle 1.53812 / 0.57 (14740) SS BOND : bond 0.00627 / 0.33 ( 5) SS BOND : angle 2.04574 / 1.23 ( 10) hydrogen bonds : bond 0.05216 / 3.55 ( 400) hydrogen bonds : angle 4.06914 / 2.86 ( 1161) link_BETA1-4 : bond 0.00352 / 0.19 ( 1) link_BETA1-4 : angle 1.49944 / 0.76 ( 3) link_NAG-ASN : bond 0.00149 / 0.07 ( 2) link_NAG-ASN : angle 2.60447 / 1.38 ( 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 95 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6927 (pm20) REVERT: A 183 GLU cc_start: 0.8284 (pt0) cc_final: 0.7919 (pm20) REVERT: A 289 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8429 (tt0) REVERT: A 324 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8483 (tp) REVERT: A 399 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7244 (pt0) REVERT: A 483 ASN cc_start: 0.7593 (p0) cc_final: 0.7094 (p0) REVERT: A 649 ASN cc_start: 0.8503 (t0) cc_final: 0.7875 (t0) REVERT: A 764 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8599 (mm-30) REVERT: B 20 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7670 (pm20) REVERT: B 21 LYS cc_start: 0.8481 (mtpt) cc_final: 0.8075 (mptt) REVERT: B 22 LYS cc_start: 0.8056 (mtmm) cc_final: 0.7219 (tttp) outliers start: 15 outliers final: 8 residues processed: 88 average time/residue: 0.5498 time to fit residues: 52.3166 Evaluate side-chains 87 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 334 GLU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 544 GLU 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: 5.9990 chunk 102 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 108 optimal weight: 0.1980 chunk 49 optimal weight: 10.0000 chunk 52 optimal weight: 0.2980 chunk 121 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.132161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.091229 restraints weight = 16969.983| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.17 r_work: 0.3063 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10870 Z= 0.114 Angle : 1.504 31.450 14759 Z= 0.548 Chirality : 0.160 1.974 1666 Planarity : 0.004 0.053 1845 Dihedral : 9.855 92.681 1567 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 : 1.07 % Allowed : 18.95 % Favored : 79.98 % 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: -0.33 (0.24), residues: 1294 helix: 1.20 (0.24), residues: 535 sheet: -0.37 (0.41), residues: 152 loop : -1.52 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 118 TYR 0.029 0.001 TYR A 488 PHE 0.016 0.001 PHE A 578 TRP 0.007 0.001 TRP A 317 HIS 0.003 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (10862) covalent geometry : angle 1.50348 / 0.55 (14740) SS BOND : bond 0.00499 / 0.26 ( 5) SS BOND : angle 1.96631 / 1.15 ( 10) hydrogen bonds : bond 0.03989 / 2.68 ( 400) hydrogen bonds : angle 3.93203 / 2.77 ( 1161) link_BETA1-4 : bond 0.00459 / 0.24 ( 1) link_BETA1-4 : angle 1.28242 / 0.67 ( 3) link_NAG-ASN : bond 0.00180 / 0.09 ( 2) link_NAG-ASN : angle 2.23631 / 1.19 ( 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 89 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.7022 (pm20) REVERT: A 118 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7266 (tt0) REVERT: A 183 GLU cc_start: 0.8190 (pt0) cc_final: 0.7781 (pm20) REVERT: A 190 LEU cc_start: 0.8098 (tp) cc_final: 0.7857 (tp) REVERT: A 289 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8328 (tt0) REVERT: A 324 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8481 (tp) REVERT: A 399 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7186 (pt0) REVERT: A 483 ASN cc_start: 0.7610 (p0) cc_final: 0.7075 (p0) REVERT: A 649 ASN cc_start: 0.8469 (t0) cc_final: 0.7865 (t0) REVERT: A 764 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8469 (mm-30) REVERT: B 20 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7610 (pm20) REVERT: B 21 LYS cc_start: 0.8383 (mtpt) cc_final: 0.7978 (mptt) REVERT: B 203 LYS cc_start: 0.7560 (tptp) cc_final: 0.7328 (mmmt) outliers start: 12 outliers final: 6 residues processed: 86 average time/residue: 0.4810 time to fit residues: 44.7676 Evaluate side-chains 85 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 68 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 chunk 91 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.128952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.087826 restraints weight = 17479.200| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.15 r_work: 0.3017 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10870 Z= 0.188 Angle : 1.530 32.817 14759 Z= 0.564 Chirality : 0.159 2.003 1666 Planarity : 0.004 0.050 1845 Dihedral : 10.175 94.999 1567 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.26 % Favored : 92.66 % Rotamer: Outliers : 1.16 % Allowed : 18.86 % Favored : 79.98 % 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: -0.47 (0.24), residues: 1294 helix: 1.07 (0.24), residues: 535 sheet: -0.18 (0.44), residues: 134 loop : -1.62 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 118 TYR 0.023 0.002 TYR B 204 PHE 0.019 0.001 PHE A 793 TRP 0.008 0.001 TRP A 894 HIS 0.003 0.001 HIS A 882 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (10862) covalent geometry : angle 1.52920 / 0.56 (14740) SS BOND : bond 0.00585 / 0.31 ( 5) SS BOND : angle 1.92292 / 1.15 ( 10) hydrogen bonds : bond 0.05140 / 3.50 ( 400) hydrogen bonds : angle 4.06190 / 2.86 ( 1161) link_BETA1-4 : bond 0.00330 / 0.17 ( 1) link_BETA1-4 : angle 1.48250 / 0.76 ( 3) link_NAG-ASN : bond 0.00144 / 0.07 ( 2) link_NAG-ASN : angle 2.58131 / 1.37 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3215.52 seconds wall clock time: 55 minutes 23.06 seconds (3323.06 seconds total)