Starting phenix.real_space_refine on Sat Sep 12 22:27:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qd6_13909/09_2026/7qd6_13909.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qd6_13909/09_2026/7qd6_13909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qd6_13909/09_2026/7qd6_13909.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qd6_13909/09_2026/7qd6_13909.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qd6_13909/09_2026/7qd6_13909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qd6_13909/09_2026/7qd6_13909.map" } resolution = 3.0 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= 0.003 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: 5 Type Number sf(0) Gaussians P 214 5.49 5 S 46 5.16 5 C 11474 2.51 5 N 3400 2.21 5 O 3978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19112 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 7345 Classifications: {'peptide': 908} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 27, 'TRANS': 880} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1110 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain: "C" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 838 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "G" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 263 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 7345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 7345 Classifications: {'peptide': 908} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 27, 'TRANS': 880} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1110 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain: "F" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 838 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "H" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 263 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Time building chain proxies: 4.17, per 1000 atoms: 0.22 Number of scatterers: 19112 At special positions: 0 Unit cell: (167.96, 136.04, 152.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 214 15.00 O 3978 8.00 N 3400 7.00 C 11474 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 724.0 milliseconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3436 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 70.2% alpha, 2.1% beta 98 base pairs and 183 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'A' and resid 8 through 17 Processing helix chain 'A' and resid 24 through 29 removed outlier: 3.623A pdb=" N THR A 28 " --> pdb=" O TRP A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 42 Processing helix chain 'A' and resid 45 through 61 removed outlier: 4.168A pdb=" N ARG A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 85 removed outlier: 3.628A pdb=" N VAL A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.533A pdb=" N GLU A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 removed outlier: 4.093A pdb=" N TRP A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 136 removed outlier: 4.264A pdb=" N GLN A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 Processing helix chain 'A' and resid 159 through 185 removed outlier: 3.877A pdb=" N ILE A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 Processing helix chain 'A' and resid 206 through 213 Processing helix chain 'A' and resid 219 through 237 Processing helix chain 'A' and resid 246 through 260 Processing helix chain 'A' and resid 261 through 268 removed outlier: 3.553A pdb=" N PHE A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 318 removed outlier: 4.243A pdb=" N GLN A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN A 318 " --> pdb=" O ILE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 343 Processing helix chain 'A' and resid 345 through 354 removed outlier: 3.638A pdb=" N ALA A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 369 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.983A pdb=" N ASN A 382 " --> pdb=" O ASP A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.614A pdb=" N VAL A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 399 Processing helix chain 'A' and resid 407 through 424 Processing helix chain 'A' and resid 441 through 446 removed outlier: 4.118A pdb=" N TYR A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 472 Processing helix chain 'A' and resid 484 through 489 Processing helix chain 'A' and resid 511 through 530 removed outlier: 3.596A pdb=" N ILE A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 570 removed outlier: 4.439A pdb=" N ALA A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 586 Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 602 through 619 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 633 through 645 removed outlier: 3.557A pdb=" N MET A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 664 removed outlier: 3.590A pdb=" N GLN A 664 " --> pdb=" O PHE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 4.394A pdb=" N TRP A 670 " --> pdb=" O LEU A 666 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 666 through 671' Processing helix chain 'A' and resid 728 through 738 removed outlier: 3.545A pdb=" N VAL A 732 " --> pdb=" O ASP A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 766 removed outlier: 3.537A pdb=" N PHE A 760 " --> pdb=" O THR A 756 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA A 761 " --> pdb=" O ASP A 757 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU A 762 " --> pdb=" O GLN A 758 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS A 764 " --> pdb=" O PHE A 760 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 810 Processing helix chain 'A' and resid 810 through 824 Processing helix chain 'A' and resid 827 through 834 removed outlier: 3.599A pdb=" N ILE A 831 " --> pdb=" O SER A 827 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 834 " --> pdb=" O LEU A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 866 removed outlier: 3.746A pdb=" N ALA A 845 " --> pdb=" O GLN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 891 Processing helix chain 'A' and resid 892 through 897 removed outlier: 3.849A pdb=" N GLU A 897 " --> pdb=" O GLY A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 938 Processing helix chain 'D' and resid 8 through 17 Processing helix chain 'D' and resid 24 through 29 removed outlier: 3.582A pdb=" N THR D 28 " --> pdb=" O TRP D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 42 Processing helix chain 'D' and resid 45 through 61 removed outlier: 4.152A pdb=" N ARG D 49 " --> pdb=" O ARG D 45 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 85 removed outlier: 3.623A pdb=" N VAL D 77 " --> pdb=" O PRO D 73 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL D 80 " --> pdb=" O VAL D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 removed outlier: 3.538A pdb=" N GLU D 90 " --> pdb=" O PRO D 87 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU D 92 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 113 removed outlier: 4.131A pdb=" N TRP D 102 " --> pdb=" O GLY D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 136 removed outlier: 4.368A pdb=" N GLN D 131 " --> pdb=" O GLN D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 153 Processing helix chain 'D' and resid 159 through 185 removed outlier: 3.862A pdb=" N ILE D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY D 185 " --> pdb=" O ILE D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 197 Processing helix chain 'D' and resid 201 through 205 removed outlier: 3.569A pdb=" N GLY D 204 " --> pdb=" O THR D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 213 Processing helix chain 'D' and resid 219 through 237 Processing helix chain 'D' and resid 246 through 260 Processing helix chain 'D' and resid 261 through 267 Processing helix chain 'D' and resid 269 through 318 removed outlier: 4.223A pdb=" N GLN D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 343 Processing helix chain 'D' and resid 345 through 354 removed outlier: 3.877A pdb=" N ALA D 349 " --> pdb=" O ASP D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 369 Processing helix chain 'D' and resid 377 through 382 removed outlier: 4.008A pdb=" N ASN D 382 " --> pdb=" O ASP D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 390 removed outlier: 3.543A pdb=" N VAL D 388 " --> pdb=" O ARG D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 399 Processing helix chain 'D' and resid 407 through 424 Processing helix chain 'D' and resid 441 through 446 removed outlier: 4.177A pdb=" N TYR D 446 " --> pdb=" O GLN D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 472 Processing helix chain 'D' and resid 484 through 489 removed outlier: 3.530A pdb=" N TYR D 488 " --> pdb=" O ALA D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 530 Processing helix chain 'D' and resid 557 through 570 removed outlier: 4.445A pdb=" N ALA D 561 " --> pdb=" O GLU D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 586 Processing helix chain 'D' and resid 587 through 592 Processing helix chain 'D' and resid 602 through 619 Processing helix chain 'D' and resid 621 through 629 Processing helix chain 'D' and resid 633 through 645 removed outlier: 3.521A pdb=" N MET D 637 " --> pdb=" O SER D 633 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG D 644 " --> pdb=" O ALA D 640 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET D 645 " --> pdb=" O SER D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 664 removed outlier: 3.654A pdb=" N GLN D 664 " --> pdb=" O PHE D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 671 removed outlier: 4.475A pdb=" N TRP D 670 " --> pdb=" O LEU D 666 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY D 671 " --> pdb=" O SER D 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 666 through 671' Processing helix chain 'D' and resid 728 through 738 removed outlier: 3.590A pdb=" N VAL D 732 " --> pdb=" O ASP D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 766 removed outlier: 3.989A pdb=" N ALA D 761 " --> pdb=" O ASP D 757 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU D 762 " --> pdb=" O GLN D 758 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS D 764 " --> pdb=" O PHE D 760 " (cutoff:3.500A) Processing helix chain 'D' and resid 804 through 824 removed outlier: 5.179A pdb=" N GLU D 812 " --> pdb=" O LYS D 808 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ASP D 813 " --> pdb=" O GLU D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 827 through 834 removed outlier: 3.587A pdb=" N ILE D 831 " --> pdb=" O SER D 827 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS D 834 " --> pdb=" O LEU D 830 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 866 removed outlier: 3.639A pdb=" N ALA D 845 " --> pdb=" O GLN D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 891 Processing helix chain 'D' and resid 902 through 938 Processing helix chain 'D' and resid 945 through 949 Processing sheet with id=AA1, first strand: chain 'A' and resid 401 through 403 Processing sheet with id=AA2, first strand: chain 'A' and resid 573 through 574 removed outlier: 7.333A pdb=" N ILE A 573 " --> pdb=" O ASN A 958 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 679 through 683 removed outlier: 3.580A pdb=" N THR A 705 " --> pdb=" O ILE A 722 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 722 " --> pdb=" O THR A 705 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 748 through 750 Processing sheet with id=AA5, first strand: chain 'D' and resid 401 through 403 Processing sheet with id=AA6, first strand: chain 'D' and resid 573 through 574 removed outlier: 7.372A pdb=" N ILE D 573 " --> pdb=" O ASN D 958 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 679 through 683 removed outlier: 3.559A pdb=" N THR D 705 " --> pdb=" O ILE D 722 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE D 722 " --> pdb=" O THR D 705 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 748 through 750 883 hydrogen bonds defined for protein. 2592 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 244 hydrogen bonds 488 hydrogen bond angles 0 basepair planarities 98 basepair parallelities 183 stacking parallelities Total time for adding SS restraints: 4.45 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4221 1.33 - 1.46: 5924 1.46 - 1.58: 9279 1.58 - 1.71: 424 1.71 - 1.83: 90 Bond restraints: 19938 Sorted by residual: bond pdb=" C3' DG F1062 " pdb=" C2' DG F1062 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.31e+01 bond pdb=" C3' DA B 21 " pdb=" C2' DA B 21 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DG C1062 " pdb=" C2' DG C1062 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DA E 21 " pdb=" C2' DA E 21 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C5' DA B 68 " pdb=" C4' DA B 68 " ideal model delta sigma weight residual 1.512 1.535 -0.023 7.00e-03 2.04e+04 1.11e+01 ... (remaining 19933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 27169 2.56 - 5.13: 607 5.13 - 7.69: 70 7.69 - 10.26: 23 10.26 - 12.82: 3 Bond angle restraints: 27872 Sorted by residual: angle pdb=" C LYS D 425 " pdb=" N ARG D 426 " pdb=" CA ARG D 426 " ideal model delta sigma weight residual 121.54 131.36 -9.82 1.91e+00 2.74e-01 2.64e+01 angle pdb=" O4' DC B 42 " pdb=" C1' DC B 42 " pdb=" N1 DC B 42 " ideal model delta sigma weight residual 108.00 111.48 -3.48 7.00e-01 2.04e+00 2.47e+01 angle pdb=" N GLU D 144 " pdb=" CA GLU D 144 " pdb=" CB GLU D 144 " ideal model delta sigma weight residual 110.28 117.54 -7.26 1.55e+00 4.16e-01 2.20e+01 angle pdb=" O4' DA B 67 " pdb=" C4' DA B 67 " pdb=" C3' DA B 67 " ideal model delta sigma weight residual 106.00 103.22 2.78 6.00e-01 2.78e+00 2.15e+01 angle pdb=" N3 DT G1072 " pdb=" C4 DT G1072 " pdb=" O4 DT G1072 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.07e+01 ... (remaining 27867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 8833 17.88 - 35.76: 1430 35.76 - 53.63: 870 53.63 - 71.51: 202 71.51 - 89.39: 41 Dihedral angle restraints: 11376 sinusoidal: 6062 harmonic: 5314 Sorted by residual: dihedral pdb=" CA ARG D 45 " pdb=" C ARG D 45 " pdb=" N GLY D 46 " pdb=" CA GLY D 46 " ideal model delta harmonic sigma weight residual 180.00 -153.27 -26.73 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA MET D 645 " pdb=" C MET D 645 " pdb=" N TYR D 646 " pdb=" CA TYR D 646 " ideal model delta harmonic sigma weight residual 180.00 155.03 24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA ARG A 45 " pdb=" C ARG A 45 " pdb=" N GLY A 46 " pdb=" CA GLY A 46 " ideal model delta harmonic sigma weight residual -180.00 -155.25 -24.75 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 11373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2652 0.072 - 0.145: 409 0.145 - 0.217: 32 0.217 - 0.290: 2 0.290 - 0.362: 1 Chirality restraints: 3096 Sorted by residual: chirality pdb=" CB ILE D 452 " pdb=" CA ILE D 452 " pdb=" CG1 ILE D 452 " pdb=" CG2 ILE D 452 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA GLN A 172 " pdb=" N GLN A 172 " pdb=" C GLN A 172 " pdb=" CB GLN A 172 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB VAL A 759 " pdb=" CA VAL A 759 " pdb=" CG1 VAL A 759 " pdb=" CG2 VAL A 759 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 3093 not shown) Planarity restraints: 2804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 485 " 0.017 2.00e-02 2.50e+03 2.63e-02 1.21e+01 pdb=" CG PHE A 485 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 485 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 485 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE A 485 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 485 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 485 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 485 " -0.015 2.00e-02 2.50e+03 2.26e-02 8.97e+00 pdb=" CG PHE D 485 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE D 485 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE D 485 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE D 485 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 485 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 485 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 371 " 0.046 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO A 372 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 372 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 372 " 0.038 5.00e-02 4.00e+02 ... (remaining 2801 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4201 2.80 - 3.32: 16701 3.32 - 3.85: 35673 3.85 - 4.37: 40616 4.37 - 4.90: 62985 Nonbonded interactions: 160176 Sorted by model distance: nonbonded pdb=" O MET A 614 " pdb=" OG1 THR A 618 " model vdw 2.270 3.040 nonbonded pdb=" OD1 ASP A 734 " pdb=" OG SER A 828 " model vdw 2.296 3.040 nonbonded pdb=" OE2 GLU D 581 " pdb=" OH TYR D 927 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR A 749 " pdb=" NE ARG A 872 " model vdw 2.317 3.120 nonbonded pdb=" OD1 ASP D 734 " pdb=" OG SER D 828 " model vdw 2.322 3.040 ... (remaining 160171 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 6.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.000 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6131 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 19938 Z= 0.432 Angle : 0.952 12.820 27872 Z= 0.649 Chirality : 0.051 0.362 3096 Planarity : 0.007 0.069 2804 Dihedral : 22.481 89.389 7940 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.18), residues: 1780 helix: -0.40 (0.13), residues: 1154 sheet: 0.12 (0.99), residues: 36 loop : -0.53 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 49 TYR 0.036 0.002 TYR D 141 PHE 0.060 0.003 PHE A 485 TRP 0.029 0.003 TRP D 64 HIS 0.017 0.002 HIS D 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.43 (19938) covalent geometry : angle 0.95186 / 0.65 (27872) hydrogen bonds : bond 0.11752 / 7.46 ( 1127) hydrogen bonds : angle 5.49389 / 3.95 ( 3080) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 872 ARG cc_start: 0.5346 (ttp-170) cc_final: 0.4482 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.5416 time to fit residues: 111.0708 Evaluate side-chains 122 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 50.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 10.0000 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 GLN A 400 HIS A 481 HIS A 639 ASN A 661 GLN ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 ASN D 43 HIS D 127 GLN D 131 GLN D 311 GLN D 639 ASN ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5351 r_free = 0.5351 target = 0.256422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5249 r_free = 0.5249 target = 0.241618 restraints weight = 20539.191| |-----------------------------------------------------------------------------| r_work (start): 0.5045 rms_B_bonded: 0.35 r_work: 0.4727 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.4535 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work: 0.4460 rms_B_bonded: 3.48 restraints_weight: 0.1250 r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 19938 Z= 0.261 Angle : 0.765 10.279 27872 Z= 0.427 Chirality : 0.050 0.275 3096 Planarity : 0.006 0.072 2804 Dihedral : 25.365 94.043 4350 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.00 % Allowed : 9.48 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.19), residues: 1780 helix: 0.29 (0.14), residues: 1182 sheet: -0.15 (0.89), residues: 36 loop : -0.62 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 635 TYR 0.023 0.003 TYR D 263 PHE 0.024 0.003 PHE D 592 TRP 0.022 0.003 TRP D 102 HIS 0.010 0.002 HIS D 748 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.26 (19938) covalent geometry : angle 0.76544 / 0.43 (27872) hydrogen bonds : bond 0.07180 / 4.72 ( 1127) hydrogen bonds : angle 4.48715 / 3.25 ( 3080) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 614 MET cc_start: 0.7800 (ttp) cc_final: 0.7507 (ttp) REVERT: A 760 PHE cc_start: 0.5666 (OUTLIER) cc_final: 0.4592 (t80) REVERT: A 872 ARG cc_start: 0.6216 (OUTLIER) cc_final: 0.5354 (mtm180) REVERT: D 635 ARG cc_start: 0.6947 (tpt90) cc_final: 0.6557 (tmt170) REVERT: D 647 ASP cc_start: 0.6971 (OUTLIER) cc_final: 0.6617 (m-30) outliers start: 31 outliers final: 15 residues processed: 151 average time/residue: 0.6088 time to fit residues: 104.0599 Evaluate side-chains 139 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 872 ARG Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 647 ASP Chi-restraints excluded: chain D residue 760 PHE Chi-restraints excluded: chain D residue 764 HIS Chi-restraints excluded: chain D residue 928 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 34 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 145 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 143 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 193 optimal weight: 9.9990 chunk 188 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 HIS ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5347 r_free = 0.5347 target = 0.256639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.5275 r_free = 0.5275 target = 0.246305 restraints weight = 20603.389| |-----------------------------------------------------------------------------| r_work (start): 0.5293 rms_B_bonded: 0.26 r_work: 0.5160 rms_B_bonded: 0.94 restraints_weight: 0.5000 r_work: 0.5135 rms_B_bonded: 1.35 restraints_weight: 0.2500 r_work (final): 0.5135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5714 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19938 Z= 0.190 Angle : 0.657 8.235 27872 Z= 0.375 Chirality : 0.044 0.257 3096 Planarity : 0.005 0.064 2804 Dihedral : 25.330 97.491 4350 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.13 % Allowed : 13.48 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.19), residues: 1780 helix: 0.77 (0.14), residues: 1182 sheet: -0.14 (0.87), residues: 36 loop : -0.62 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 635 TYR 0.037 0.002 TYR A 141 PHE 0.023 0.002 PHE D 128 TRP 0.023 0.002 TRP D 102 HIS 0.014 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.19 (19938) covalent geometry : angle 0.65662 / 0.38 (27872) hydrogen bonds : bond 0.05494 / 3.62 ( 1127) hydrogen bonds : angle 4.15135 / 3.00 ( 3080) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 569 MET cc_start: 0.5395 (OUTLIER) cc_final: 0.5110 (ptt) REVERT: A 760 PHE cc_start: 0.5513 (OUTLIER) cc_final: 0.4897 (t80) outliers start: 33 outliers final: 12 residues processed: 144 average time/residue: 0.5334 time to fit residues: 88.0343 Evaluate side-chains 137 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 760 PHE Chi-restraints excluded: chain D residue 764 HIS Chi-restraints excluded: chain D residue 851 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 153 optimal weight: 0.0040 chunk 22 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 178 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 chunk 122 optimal weight: 0.5980 chunk 136 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS A 183 HIS A 400 HIS D 104 HIS ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5379 r_free = 0.5379 target = 0.258289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5295 r_free = 0.5295 target = 0.246029 restraints weight = 20618.341| |-----------------------------------------------------------------------------| r_work (start): 0.5303 rms_B_bonded: 0.31 r_work: 0.5180 rms_B_bonded: 1.04 restraints_weight: 0.5000 r_work: 0.5157 rms_B_bonded: 1.41 restraints_weight: 0.2500 r_work (final): 0.5157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5656 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19938 Z= 0.139 Angle : 0.590 9.212 27872 Z= 0.341 Chirality : 0.041 0.231 3096 Planarity : 0.004 0.053 2804 Dihedral : 25.275 102.304 4350 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.81 % Allowed : 14.45 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.20), residues: 1780 helix: 1.29 (0.15), residues: 1174 sheet: 0.06 (0.90), residues: 36 loop : -0.32 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 249 TYR 0.021 0.002 TYR D 492 PHE 0.018 0.002 PHE D 128 TRP 0.022 0.002 TRP A 102 HIS 0.015 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (19938) covalent geometry : angle 0.58984 / 0.34 (27872) hydrogen bonds : bond 0.04392 / 2.88 ( 1127) hydrogen bonds : angle 3.85339 / 2.78 ( 3080) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3033 (ptm) cc_final: 0.2238 (ttp) REVERT: A 359 MET cc_start: 0.5290 (tpt) cc_final: 0.5084 (tpp) REVERT: A 569 MET cc_start: 0.5368 (tmm) cc_final: 0.5069 (ptt) REVERT: A 760 PHE cc_start: 0.5564 (OUTLIER) cc_final: 0.4889 (t80) outliers start: 28 outliers final: 9 residues processed: 157 average time/residue: 0.5582 time to fit residues: 100.4618 Evaluate side-chains 134 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 760 PHE Chi-restraints excluded: chain D residue 764 HIS Chi-restraints excluded: chain D residue 851 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 26 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 121 optimal weight: 0.0170 chunk 23 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS A 400 HIS ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS D 48 ASN D 304 GLN ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 924 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5377 r_free = 0.5377 target = 0.257976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5286 r_free = 0.5286 target = 0.244743 restraints weight = 20617.518| |-----------------------------------------------------------------------------| r_work (start): 0.5078 rms_B_bonded: 0.33 r_work: 0.4746 rms_B_bonded: 0.92 restraints_weight: 0.5000 r_work: 0.4531 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work: 0.4454 rms_B_bonded: 2.82 restraints_weight: 0.1250 r_work (final): 0.4454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19938 Z= 0.142 Angle : 0.586 8.983 27872 Z= 0.338 Chirality : 0.041 0.238 3096 Planarity : 0.004 0.045 2804 Dihedral : 25.233 105.835 4350 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.68 % Allowed : 16.26 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.20), residues: 1780 helix: 1.44 (0.15), residues: 1176 sheet: 0.04 (0.89), residues: 36 loop : -0.32 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 635 TYR 0.030 0.002 TYR A 141 PHE 0.015 0.002 PHE A 892 TRP 0.022 0.001 TRP A 102 HIS 0.016 0.001 HIS D 748 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 (19938) covalent geometry : angle 0.58561 / 0.34 (27872) hydrogen bonds : bond 0.04453 / 2.93 ( 1127) hydrogen bonds : angle 3.81087 / 2.75 ( 3080) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3435 (ptm) cc_final: 0.2285 (ttp) REVERT: A 160 MET cc_start: 0.6985 (mmp) cc_final: 0.6654 (mmt) REVERT: A 359 MET cc_start: 0.5572 (tpt) cc_final: 0.5092 (tpp) REVERT: A 569 MET cc_start: 0.5836 (tmm) cc_final: 0.5598 (ptt) REVERT: A 760 PHE cc_start: 0.5702 (OUTLIER) cc_final: 0.4507 (t80) REVERT: D 832 MET cc_start: 0.5893 (tpp) cc_final: 0.5413 (ttm) REVERT: D 872 ARG cc_start: 0.6202 (ttp-170) cc_final: 0.5881 (tmm-80) outliers start: 26 outliers final: 8 residues processed: 150 average time/residue: 0.5387 time to fit residues: 93.0260 Evaluate side-chains 133 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 760 PHE Chi-restraints excluded: chain D residue 764 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 16 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 123 optimal weight: 0.5980 chunk 0 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 154 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 162 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 HIS A 748 HIS A 810 ASN D 104 HIS D 172 GLN D 304 GLN ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5375 r_free = 0.5375 target = 0.259470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5275 r_free = 0.5275 target = 0.244913 restraints weight = 20388.473| |-----------------------------------------------------------------------------| r_work (start): 0.5069 rms_B_bonded: 0.35 r_work: 0.4753 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.4601 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.4601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19938 Z= 0.143 Angle : 0.588 11.821 27872 Z= 0.338 Chirality : 0.041 0.220 3096 Planarity : 0.004 0.043 2804 Dihedral : 25.207 109.583 4350 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.19 % Allowed : 16.71 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.36 (0.20), residues: 1780 helix: 1.54 (0.15), residues: 1176 sheet: 0.31 (0.90), residues: 36 loop : -0.31 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 60 TYR 0.021 0.002 TYR D 492 PHE 0.014 0.002 PHE A 892 TRP 0.021 0.001 TRP D 102 HIS 0.018 0.001 HIS D 748 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 (19938) covalent geometry : angle 0.58795 / 0.34 (27872) hydrogen bonds : bond 0.04391 / 2.91 ( 1127) hydrogen bonds : angle 3.75010 / 2.71 ( 3080) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3146 (ptm) cc_final: 0.2152 (ttp) REVERT: A 569 MET cc_start: 0.5872 (tmm) cc_final: 0.5662 (ptt) REVERT: A 669 TYR cc_start: 0.5547 (m-10) cc_final: 0.5342 (m-10) REVERT: A 760 PHE cc_start: 0.5720 (OUTLIER) cc_final: 0.4804 (t80) REVERT: D 172 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7471 (mp10) outliers start: 34 outliers final: 15 residues processed: 159 average time/residue: 0.5282 time to fit residues: 96.9118 Evaluate side-chains 142 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 172 GLN Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 663 GLU Chi-restraints excluded: chain D residue 760 PHE Chi-restraints excluded: chain D residue 764 HIS Chi-restraints excluded: chain D residue 851 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 192 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 198 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 748 HIS D 104 HIS D 172 GLN ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5376 r_free = 0.5376 target = 0.259107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.5285 r_free = 0.5285 target = 0.245755 restraints weight = 20513.064| |-----------------------------------------------------------------------------| r_work (start): 0.5291 rms_B_bonded: 0.33 r_work: 0.5166 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.5145 rms_B_bonded: 1.53 restraints_weight: 0.2500 r_work (final): 0.5145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5677 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19938 Z= 0.144 Angle : 0.591 9.393 27872 Z= 0.340 Chirality : 0.041 0.216 3096 Planarity : 0.004 0.041 2804 Dihedral : 25.191 112.287 4350 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.00 % Allowed : 17.94 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.20), residues: 1780 helix: 1.67 (0.15), residues: 1150 sheet: 0.24 (0.89), residues: 36 loop : -0.28 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 872 TYR 0.034 0.002 TYR A 141 PHE 0.025 0.002 PHE A 892 TRP 0.021 0.001 TRP A 102 HIS 0.020 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (19938) covalent geometry : angle 0.59117 / 0.34 (27872) hydrogen bonds : bond 0.04358 / 2.89 ( 1127) hydrogen bonds : angle 3.73982 / 2.70 ( 3080) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2835 (ptm) cc_final: 0.2079 (ttp) REVERT: A 359 MET cc_start: 0.5508 (tpt) cc_final: 0.5199 (tpp) REVERT: A 388 VAL cc_start: 0.7411 (OUTLIER) cc_final: 0.7162 (p) REVERT: D 354 MET cc_start: 0.3691 (ppp) cc_final: 0.2900 (ptp) REVERT: D 832 MET cc_start: 0.5425 (tpp) cc_final: 0.5057 (ttm) outliers start: 31 outliers final: 17 residues processed: 152 average time/residue: 0.5284 time to fit residues: 93.1320 Evaluate side-chains 146 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 663 GLU Chi-restraints excluded: chain D residue 731 HIS Chi-restraints excluded: chain D residue 760 PHE Chi-restraints excluded: chain D residue 764 HIS Chi-restraints excluded: chain D residue 851 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 195 optimal weight: 50.0000 chunk 164 optimal weight: 0.0770 chunk 9 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 71 optimal weight: 30.0000 chunk 117 optimal weight: 0.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 748 HIS D 172 GLN ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5370 r_free = 0.5370 target = 0.258461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.5279 r_free = 0.5279 target = 0.245084 restraints weight = 20518.149| |-----------------------------------------------------------------------------| r_work (start): 0.5283 rms_B_bonded: 0.32 r_work: 0.5147 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.5124 rms_B_bonded: 1.49 restraints_weight: 0.2500 r_work (final): 0.5124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5731 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19938 Z= 0.153 Angle : 0.600 9.479 27872 Z= 0.343 Chirality : 0.041 0.218 3096 Planarity : 0.004 0.041 2804 Dihedral : 25.178 115.053 4350 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.94 % Allowed : 18.19 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.20), residues: 1780 helix: 1.60 (0.15), residues: 1162 sheet: -0.03 (0.83), residues: 36 loop : -0.27 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 872 TYR 0.025 0.002 TYR D 492 PHE 0.025 0.002 PHE A 892 TRP 0.025 0.001 TRP D 102 HIS 0.016 0.001 HIS A 748 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (19938) covalent geometry : angle 0.60011 / 0.34 (27872) hydrogen bonds : bond 0.04573 / 3.03 ( 1127) hydrogen bonds : angle 3.74268 / 2.71 ( 3080) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.3468 (t80) cc_final: 0.2953 (t80) REVERT: A 153 MET cc_start: 0.2890 (ptm) cc_final: 0.2124 (ttp) REVERT: A 359 MET cc_start: 0.5553 (tpt) cc_final: 0.5276 (tpp) REVERT: A 388 VAL cc_start: 0.7433 (OUTLIER) cc_final: 0.7166 (p) REVERT: D 832 MET cc_start: 0.5386 (tpp) cc_final: 0.5065 (ttm) outliers start: 30 outliers final: 17 residues processed: 148 average time/residue: 0.5384 time to fit residues: 91.8677 Evaluate side-chains 142 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 663 GLU Chi-restraints excluded: chain D residue 731 HIS Chi-restraints excluded: chain D residue 760 PHE Chi-restraints excluded: chain D residue 764 HIS Chi-restraints excluded: chain D residue 851 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 6 optimal weight: 0.0470 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 183 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 195 optimal weight: 50.0000 chunk 60 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 ASN ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 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 = 0.5362 r_free = 0.5362 target = 0.258885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5282 r_free = 0.5282 target = 0.247189 restraints weight = 20378.952| |-----------------------------------------------------------------------------| r_work (start): 0.5299 rms_B_bonded: 0.29 r_work: 0.5164 rms_B_bonded: 0.73 restraints_weight: 0.5000 r_work: 0.5111 rms_B_bonded: 1.68 restraints_weight: 0.2500 r_work: 0.5025 rms_B_bonded: 3.52 restraints_weight: 0.1250 r_work (final): 0.5025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5893 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19938 Z= 0.146 Angle : 0.600 13.045 27872 Z= 0.341 Chirality : 0.041 0.210 3096 Planarity : 0.004 0.040 2804 Dihedral : 25.158 118.588 4350 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.00 % Allowed : 18.13 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.20), residues: 1780 helix: 1.69 (0.15), residues: 1160 sheet: -0.18 (0.81), residues: 36 loop : -0.26 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 872 TYR 0.032 0.001 TYR A 141 PHE 0.042 0.002 PHE A 128 TRP 0.022 0.001 TRP A 102 HIS 0.018 0.001 HIS A 748 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (19938) covalent geometry : angle 0.60029 / 0.34 (27872) hydrogen bonds : bond 0.04356 / 2.88 ( 1127) hydrogen bonds : angle 3.72107 / 2.69 ( 3080) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2861 (ptm) cc_final: 0.2085 (ttp) REVERT: A 359 MET cc_start: 0.5543 (tpt) cc_final: 0.5227 (tpp) REVERT: A 388 VAL cc_start: 0.7502 (OUTLIER) cc_final: 0.7237 (p) REVERT: A 454 ARG cc_start: 0.5895 (OUTLIER) cc_final: 0.5038 (mtp180) REVERT: D 354 MET cc_start: 0.3936 (ppp) cc_final: 0.3226 (ptp) REVERT: D 832 MET cc_start: 0.5498 (OUTLIER) cc_final: 0.5192 (ttm) outliers start: 31 outliers final: 16 residues processed: 150 average time/residue: 0.5466 time to fit residues: 94.6603 Evaluate side-chains 143 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 731 HIS Chi-restraints excluded: chain D residue 760 PHE Chi-restraints excluded: chain D residue 764 HIS Chi-restraints excluded: chain D residue 832 MET Chi-restraints excluded: chain D residue 851 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 0.0980 chunk 190 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 HIS D 131 GLN ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5363 r_free = 0.5363 target = 0.258200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.5278 r_free = 0.5278 target = 0.245766 restraints weight = 20476.664| |-----------------------------------------------------------------------------| r_work (start): 0.5282 rms_B_bonded: 0.31 r_work: 0.5136 rms_B_bonded: 0.82 restraints_weight: 0.5000 r_work: 0.5085 rms_B_bonded: 1.67 restraints_weight: 0.2500 r_work: 0.4994 rms_B_bonded: 3.66 restraints_weight: 0.1250 r_work (final): 0.4994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19938 Z= 0.162 Angle : 0.613 10.343 27872 Z= 0.348 Chirality : 0.042 0.218 3096 Planarity : 0.004 0.041 2804 Dihedral : 25.143 120.830 4350 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.61 % Allowed : 18.77 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.20), residues: 1780 helix: 1.50 (0.15), residues: 1176 sheet: -0.52 (0.80), residues: 36 loop : -0.42 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 872 TYR 0.027 0.002 TYR A 492 PHE 0.038 0.002 PHE A 128 TRP 0.023 0.002 TRP D 102 HIS 0.018 0.002 HIS A 748 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (19938) covalent geometry : angle 0.61321 / 0.35 (27872) hydrogen bonds : bond 0.04788 / 3.17 ( 1127) hydrogen bonds : angle 3.80048 / 2.76 ( 3080) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2857 (ptm) cc_final: 0.2069 (ttp) REVERT: A 359 MET cc_start: 0.5538 (tpt) cc_final: 0.5236 (tpp) REVERT: A 388 VAL cc_start: 0.7542 (OUTLIER) cc_final: 0.7270 (p) REVERT: A 454 ARG cc_start: 0.5915 (OUTLIER) cc_final: 0.5082 (mtp180) REVERT: D 354 MET cc_start: 0.3974 (ppp) cc_final: 0.3349 (ptp) REVERT: D 832 MET cc_start: 0.5536 (OUTLIER) cc_final: 0.5242 (ttm) REVERT: D 872 ARG cc_start: 0.5994 (tmm-80) cc_final: 0.5569 (mtm110) outliers start: 25 outliers final: 16 residues processed: 145 average time/residue: 0.5408 time to fit residues: 90.4474 Evaluate side-chains 146 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 731 HIS Chi-restraints excluded: chain D residue 760 PHE Chi-restraints excluded: chain D residue 764 HIS Chi-restraints excluded: chain D residue 832 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 34 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 187 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.0070 chunk 62 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 116 optimal weight: 0.5980 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 HIS ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 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 = 0.5171 r_free = 0.5171 target = 0.225885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.5035 r_free = 0.5035 target = 0.209873 restraints weight = 19000.003| |-----------------------------------------------------------------------------| r_work (start): 0.5025 rms_B_bonded: 0.79 r_work: 0.4490 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4340 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19938 Z= 0.148 Angle : 0.617 13.665 27872 Z= 0.347 Chirality : 0.041 0.212 3096 Planarity : 0.004 0.043 2804 Dihedral : 25.130 122.312 4350 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.94 % Allowed : 18.90 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.20), residues: 1780 helix: 1.63 (0.15), residues: 1164 sheet: -0.55 (0.79), residues: 36 loop : -0.20 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 872 TYR 0.034 0.002 TYR A 141 PHE 0.028 0.002 PHE D 128 TRP 0.024 0.001 TRP D 102 HIS 0.026 0.002 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (19938) covalent geometry : angle 0.61664 / 0.35 (27872) hydrogen bonds : bond 0.04452 / 2.95 ( 1127) hydrogen bonds : angle 3.77342 / 2.74 ( 3080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6508.90 seconds wall clock time: 111 minutes 36.36 seconds (6696.36 seconds total)