Starting phenix.real_space_refine on Sat Sep 12 20:17:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qd5_13908/09_2026/7qd5_13908.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qd5_13908/09_2026/7qd5_13908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qd5_13908/09_2026/7qd5_13908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qd5_13908/09_2026/7qd5_13908.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qd5_13908/09_2026/7qd5_13908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qd5_13908/09_2026/7qd5_13908.map" } resolution = 3.1 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= 1.001 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 180 5.49 5 S 46 5.16 5 C 11122 2.51 5 N 3266 2.21 5 O 3766 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: 18380 Number of models: 1 Model: "" Number of chains: 6 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: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 925 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "C" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 920 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} 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: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 925 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "F" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 920 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Time building chain proxies: 3.50, per 1000 atoms: 0.19 Number of scatterers: 18380 At special positions: 0 Unit cell: (132.172, 161.204, 155.092, 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 180 15.00 O 3766 8.00 N 3266 7.00 C 11122 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: 1.39 Conformation dependent library (CDL) restraints added in 658.6 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 6 sheets defined 69.6% alpha, 1.8% beta 54 base pairs and 153 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 33 through 43 removed outlier: 3.609A pdb=" N HIS A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 61 removed outlier: 3.684A pdb=" N ARG A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 85 removed outlier: 3.657A pdb=" N VAL A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 removed outlier: 3.985A pdb=" N TRP A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 136 removed outlier: 5.049A pdb=" N GLN A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 Processing helix chain 'A' and resid 159 through 185 removed outlier: 3.696A pdb=" N ILE A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 4.396A 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 Processing helix chain 'A' and resid 269 through 317 removed outlier: 4.174A pdb=" N GLN A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 342 removed outlier: 3.549A pdb=" N LEU A 322 " --> pdb=" O ASN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 354 removed outlier: 3.541A pdb=" N MET A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 370 Processing helix chain 'A' and resid 377 through 383 removed outlier: 4.050A pdb=" N ASN A 382 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR A 383 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.527A pdb=" N VAL A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 399 removed outlier: 3.569A pdb=" N LEU A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 424 Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.732A pdb=" N TYR A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 471 Processing helix chain 'A' and resid 484 through 489 removed outlier: 3.643A pdb=" N TYR A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 489' Processing helix chain 'A' and resid 491 through 496 Processing helix chain 'A' and resid 512 through 530 Processing helix chain 'A' and resid 557 through 569 removed outlier: 4.468A pdb=" N ALA A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 587 Processing helix chain 'A' and resid 588 through 592 Processing helix chain 'A' and resid 602 through 619 removed outlier: 3.608A pdb=" N ASN A 619 " --> pdb=" O ALA A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 633 through 644 Processing helix chain 'A' and resid 646 through 663 Processing helix chain 'A' and resid 665 through 669 removed outlier: 3.633A pdb=" N SER A 668 " --> pdb=" O LYS A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 738 removed outlier: 4.304A pdb=" N VAL A 732 " --> pdb=" O ASP A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 765 removed outlier: 3.745A pdb=" N PHE A 760 " --> pdb=" O THR A 756 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA A 761 " --> pdb=" O ASP A 757 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU A 762 " --> pdb=" O GLN A 758 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS A 764 " --> pdb=" O PHE A 760 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 765 " --> pdb=" O ALA A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 823 removed outlier: 5.584A pdb=" N GLU A 812 " --> pdb=" O LYS A 808 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASP A 813 " --> pdb=" O GLU A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 833 Processing helix chain 'A' and resid 841 through 866 removed outlier: 3.755A 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: 3.519A pdb=" N ARG A 895 " --> pdb=" O PHE A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 938 Processing helix chain 'A' and resid 945 through 949 Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 24 through 29 Processing helix chain 'D' and resid 33 through 43 removed outlier: 3.906A pdb=" N HIS D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 61 removed outlier: 3.562A pdb=" N ARG D 49 " --> pdb=" O ARG D 45 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR D 61 " --> pdb=" O VAL D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 85 removed outlier: 3.627A pdb=" N VAL D 77 " --> pdb=" O PRO D 73 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL D 80 " --> pdb=" O VAL D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 113 removed outlier: 3.853A pdb=" N TRP D 102 " --> pdb=" O GLY D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 136 removed outlier: 4.905A pdb=" N GLN D 131 " --> pdb=" O GLN D 127 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN D 132 " --> pdb=" O PHE D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 153 Processing helix chain 'D' and resid 159 through 184 removed outlier: 3.728A pdb=" N ILE D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 197 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 268 Processing helix chain 'D' and resid 269 through 318 removed outlier: 4.168A pdb=" N GLN D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN D 318 " --> pdb=" O ILE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 342 Processing helix chain 'D' and resid 345 through 354 removed outlier: 3.565A pdb=" N MET D 354 " --> pdb=" O LEU D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 369 Processing helix chain 'D' and resid 377 through 383 removed outlier: 4.084A pdb=" N ASN D 382 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR D 383 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 390 Processing helix chain 'D' and resid 391 through 399 removed outlier: 3.576A pdb=" N LEU D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 424 Processing helix chain 'D' and resid 441 through 446 removed outlier: 3.718A 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: 3.660A pdb=" N TYR D 488 " --> pdb=" O ALA D 484 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU D 489 " --> pdb=" O PHE D 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 484 through 489' Processing helix chain 'D' and resid 491 through 496 Processing helix chain 'D' and resid 512 through 530 Processing helix chain 'D' and resid 557 through 569 removed outlier: 4.511A pdb=" N ALA D 561 " --> pdb=" O GLU D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 587 Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 602 through 619 removed outlier: 3.618A pdb=" N ASN D 619 " --> pdb=" O ALA D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 629 Processing helix chain 'D' and resid 633 through 644 Processing helix chain 'D' and resid 646 through 663 Processing helix chain 'D' and resid 665 through 669 removed outlier: 3.527A pdb=" N SER D 668 " --> pdb=" O LYS D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 728 through 738 removed outlier: 4.279A pdb=" N VAL D 732 " --> pdb=" O ASP D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 765 removed outlier: 3.708A pdb=" N PHE D 760 " --> pdb=" O THR D 756 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA D 761 " --> pdb=" O ASP D 757 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU D 762 " --> pdb=" O GLN D 758 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS D 764 " --> pdb=" O PHE D 760 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 765 " --> pdb=" O ALA D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 804 through 823 removed outlier: 5.507A pdb=" N GLU D 812 " --> pdb=" O LYS D 808 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ASP D 813 " --> pdb=" O GLU D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 827 through 833 Processing helix chain 'D' and resid 841 through 866 removed outlier: 3.750A 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 892 through 897 removed outlier: 3.515A pdb=" N ARG D 895 " --> pdb=" O PHE D 892 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 938 Processing helix chain 'D' and resid 945 through 949 removed outlier: 3.510A pdb=" N TYR D 948 " --> pdb=" O LEU D 945 " (cutoff:3.500A) 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: 7.359A 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 Processing sheet with id=AA4, first strand: chain 'D' and resid 401 through 403 Processing sheet with id=AA5, first strand: chain 'D' and resid 573 through 574 removed outlier: 7.338A pdb=" N ILE D 573 " --> pdb=" O ASN D 958 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 679 through 683 880 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 140 hydrogen bonds 280 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 153 stacking parallelities Total time for adding SS restraints: 3.46 Time building geometry restraints manager: 1.87 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: 4224 1.33 - 1.46: 5066 1.46 - 1.58: 9380 1.58 - 1.70: 358 1.70 - 1.82: 90 Bond restraints: 19118 Sorted by residual: bond pdb=" C3' DG C1062 " pdb=" C2' DG C1062 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.33e+01 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 1.32e+01 bond pdb=" C3' DA B 54 " pdb=" C2' DA B 54 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DA E 54 " pdb=" C2' DA E 54 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DC E 65 " pdb=" C2' DC E 65 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 ... (remaining 19113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 25907 2.33 - 4.65: 587 4.65 - 6.98: 80 6.98 - 9.31: 34 9.31 - 11.64: 2 Bond angle restraints: 26610 Sorted by residual: angle pdb=" O4' DG B 33 " pdb=" C4' DG B 33 " pdb=" C3' DG B 33 " ideal model delta sigma weight residual 106.00 103.10 2.90 6.00e-01 2.78e+00 2.33e+01 angle pdb=" O4' DG E 33 " pdb=" C4' DG E 33 " pdb=" C3' DG E 33 " ideal model delta sigma weight residual 106.00 103.18 2.82 6.00e-01 2.78e+00 2.20e+01 angle pdb=" N GLU A 144 " pdb=" CA GLU A 144 " pdb=" CB GLU A 144 " ideal model delta sigma weight residual 110.28 117.45 -7.17 1.55e+00 4.16e-01 2.14e+01 angle pdb=" C LYS D 425 " pdb=" N ARG D 426 " pdb=" CA ARG D 426 " ideal model delta sigma weight residual 121.54 129.85 -8.31 1.91e+00 2.74e-01 1.89e+01 angle pdb=" C LYS A 425 " pdb=" N ARG A 426 " pdb=" CA ARG A 426 " ideal model delta sigma weight residual 121.54 129.75 -8.21 1.91e+00 2.74e-01 1.85e+01 ... (remaining 26605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 8897 17.65 - 35.30: 1338 35.30 - 52.95: 624 52.95 - 70.60: 108 70.60 - 88.25: 17 Dihedral angle restraints: 10984 sinusoidal: 5670 harmonic: 5314 Sorted by residual: dihedral pdb=" CA HIS A 43 " pdb=" C HIS A 43 " pdb=" N ARG A 44 " pdb=" CA ARG A 44 " ideal model delta harmonic sigma weight residual -180.00 -155.38 -24.62 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA PHE A 128 " pdb=" C PHE A 128 " pdb=" N LEU A 129 " pdb=" CA LEU A 129 " ideal model delta harmonic sigma weight residual -180.00 -159.12 -20.88 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA PHE D 128 " pdb=" C PHE D 128 " pdb=" N LEU D 129 " pdb=" CA LEU D 129 " ideal model delta harmonic sigma weight residual -180.00 -162.54 -17.46 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 10981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2223 0.053 - 0.106: 606 0.106 - 0.159: 102 0.159 - 0.212: 18 0.212 - 0.265: 5 Chirality restraints: 2954 Sorted by residual: chirality pdb=" CB THR A 239 " pdb=" CA THR A 239 " pdb=" OG1 THR A 239 " pdb=" CG2 THR A 239 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB THR D 239 " pdb=" CA THR D 239 " pdb=" OG1 THR D 239 " pdb=" CG2 THR D 239 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CG LEU D 952 " pdb=" CB LEU D 952 " pdb=" CD1 LEU D 952 " pdb=" CD2 LEU D 952 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 2951 not shown) Planarity restraints: 2768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 426 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.74e+00 pdb=" C ARG D 426 " 0.051 2.00e-02 2.50e+03 pdb=" O ARG D 426 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS D 427 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 87 " -0.046 5.00e-02 4.00e+02 7.09e-02 8.05e+00 pdb=" N PRO D 88 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO D 88 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 88 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 102 " 0.015 2.00e-02 2.50e+03 1.78e-02 7.90e+00 pdb=" CG TRP D 102 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP D 102 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 102 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 102 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 102 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 102 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 102 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 102 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 102 " 0.000 2.00e-02 2.50e+03 ... (remaining 2765 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3891 2.79 - 3.32: 15620 3.32 - 3.85: 31991 3.85 - 4.37: 37920 4.37 - 4.90: 60273 Nonbonded interactions: 149695 Sorted by model distance: nonbonded pdb=" OH TYR D 47 " pdb=" OP1 DC F1037 " model vdw 2.266 3.040 nonbonded pdb=" OH TYR A 669 " pdb=" OE2 GLU A 943 " model vdw 2.285 3.040 nonbonded pdb=" OG SER A 678 " pdb=" O TYR A 749 " model vdw 2.336 3.040 nonbonded pdb=" OH TYR A 47 " pdb=" OP1 DC C1037 " model vdw 2.338 3.040 nonbonded pdb=" O GLU A 338 " pdb=" OG1 THR A 342 " model vdw 2.373 3.040 ... (remaining 149690 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' } 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: 7.180 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: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 17.580 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 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 0.057 19118 Z= 0.427 Angle : 0.880 11.636 26610 Z= 0.592 Chirality : 0.050 0.265 2954 Planarity : 0.006 0.095 2768 Dihedral : 19.643 88.250 7548 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.13 % Allowed : 0.13 % Favored : 99.74 % 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: -0.83 (0.18), residues: 1780 helix: -0.30 (0.13), residues: 1182 sheet: -0.65 (0.83), residues: 44 loop : -0.77 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 44 TYR 0.035 0.002 TYR A 141 PHE 0.022 0.002 PHE A 892 TRP 0.047 0.002 TRP D 102 HIS 0.016 0.001 HIS D 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.43 (19118) covalent geometry : angle 0.88004 / 0.59 (26610) hydrogen bonds : bond 0.15704 / 10.52 ( 1020) hydrogen bonds : angle 6.17224 / 4.35 ( 2851) *********************** 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 176 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 174 time to evaluate : 0.379 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 174 average time/residue: 0.1382 time to fit residues: 35.2898 Evaluate side-chains 144 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain D residue 858 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 GLN A 318 ASN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN D 188 GLN ** D 914 ASN ** 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 = 0.4524 r_free = 0.4524 target = 0.217222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.199212 restraints weight = 20131.508| |-----------------------------------------------------------------------------| r_work (start): 0.4346 rms_B_bonded: 0.93 r_work: 0.4136 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4098 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 19118 Z= 0.242 Angle : 0.682 9.536 26610 Z= 0.382 Chirality : 0.047 0.229 2954 Planarity : 0.006 0.109 2768 Dihedral : 22.503 88.234 3962 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.65 % Allowed : 5.81 % Favored : 93.55 % 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: 0.76 (0.20), residues: 1780 helix: 1.11 (0.15), residues: 1190 sheet: -0.85 (0.81), residues: 44 loop : -0.58 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 267 TYR 0.023 0.002 TYR D 260 PHE 0.021 0.002 PHE D 892 TRP 0.010 0.002 TRP D 923 HIS 0.010 0.002 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.24 (19118) covalent geometry : angle 0.68238 / 0.38 (26610) hydrogen bonds : bond 0.06097 / 4.03 ( 1020) hydrogen bonds : angle 4.05905 / 2.89 ( 2851) *********************** 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: 10 poor density : 157 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 306 LYS cc_start: 0.8222 (tttt) cc_final: 0.7908 (tttm) REVERT: D 773 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.6334 (ttp80) outliers start: 10 outliers final: 8 residues processed: 161 average time/residue: 0.1483 time to fit residues: 35.9601 Evaluate side-chains 155 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 756 THR Chi-restraints excluded: chain D residue 773 ARG Chi-restraints excluded: chain D residue 932 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 3 optimal weight: 0.0770 chunk 97 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 170 optimal weight: 0.3980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN D 914 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.220091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.203888 restraints weight = 20239.519| |-----------------------------------------------------------------------------| r_work (start): 0.4392 rms_B_bonded: 0.89 r_work: 0.4168 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4131 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19118 Z= 0.134 Angle : 0.539 8.611 26610 Z= 0.314 Chirality : 0.039 0.177 2954 Planarity : 0.004 0.045 2768 Dihedral : 22.690 87.988 3960 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.03 % Allowed : 7.42 % Favored : 91.55 % 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: 1.53 (0.20), residues: 1780 helix: 1.80 (0.15), residues: 1194 sheet: -0.81 (0.81), residues: 44 loop : -0.54 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.025 0.001 TYR A 141 PHE 0.027 0.002 PHE A 52 TRP 0.014 0.001 TRP D 102 HIS 0.006 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 (19118) covalent geometry : angle 0.53883 / 0.31 (26610) hydrogen bonds : bond 0.04678 / 3.09 ( 1020) hydrogen bonds : angle 3.68555 / 2.62 ( 2851) *********************** 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: 16 poor density : 149 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: D 773 ARG cc_start: 0.6614 (OUTLIER) cc_final: 0.6357 (ttp80) outliers start: 16 outliers final: 6 residues processed: 159 average time/residue: 0.1537 time to fit residues: 36.6632 Evaluate side-chains 142 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 773 ARG Chi-restraints excluded: chain D residue 933 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 43 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 173 optimal weight: 7.9990 chunk 185 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 ASN A 435 HIS ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.216309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.199304 restraints weight = 20253.245| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 0.92 r_work: 0.4125 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4090 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 19118 Z= 0.232 Angle : 0.623 8.289 26610 Z= 0.348 Chirality : 0.045 0.208 2954 Planarity : 0.005 0.105 2768 Dihedral : 22.951 88.134 3958 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.35 % Allowed : 8.84 % Favored : 89.81 % 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: 1.53 (0.20), residues: 1780 helix: 1.82 (0.15), residues: 1198 sheet: -1.07 (0.76), residues: 44 loop : -0.61 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 635 TYR 0.018 0.002 TYR A 260 PHE 0.023 0.002 PHE D 117 TRP 0.012 0.002 TRP D 102 HIS 0.008 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.23 (19118) covalent geometry : angle 0.62321 / 0.35 (26610) hydrogen bonds : bond 0.05776 / 3.82 ( 1020) hydrogen bonds : angle 3.85366 / 2.76 ( 2851) *********************** 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: 21 poor density : 146 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: D 773 ARG cc_start: 0.6552 (OUTLIER) cc_final: 0.6265 (ttp80) outliers start: 21 outliers final: 18 residues processed: 158 average time/residue: 0.1431 time to fit residues: 34.7477 Evaluate side-chains 161 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 756 THR Chi-restraints excluded: chain D residue 773 ARG Chi-restraints excluded: chain D residue 914 ASN Chi-restraints excluded: chain D residue 932 VAL Chi-restraints excluded: chain D residue 933 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 175 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 169 optimal weight: 20.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 ASN A 435 HIS ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.218200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.201970 restraints weight = 20089.344| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 0.88 r_work: 0.4146 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4114 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19118 Z= 0.146 Angle : 0.547 8.725 26610 Z= 0.312 Chirality : 0.039 0.148 2954 Planarity : 0.004 0.046 2768 Dihedral : 22.914 88.211 3958 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.23 % Allowed : 9.42 % Favored : 89.35 % 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: 1.88 (0.21), residues: 1780 helix: 2.10 (0.15), residues: 1200 sheet: -1.03 (0.77), residues: 44 loop : -0.51 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 773 TYR 0.010 0.001 TYR A 387 PHE 0.025 0.002 PHE D 117 TRP 0.011 0.001 TRP D 102 HIS 0.008 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (19118) covalent geometry : angle 0.54668 / 0.31 (26610) hydrogen bonds : bond 0.04780 / 3.17 ( 1020) hydrogen bonds : angle 3.65625 / 2.62 ( 2851) *********************** 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 163 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: D 773 ARG cc_start: 0.6521 (OUTLIER) cc_final: 0.6237 (ttp80) outliers start: 19 outliers final: 13 residues processed: 156 average time/residue: 0.1526 time to fit residues: 36.3299 Evaluate side-chains 150 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 773 ARG Chi-restraints excluded: chain D residue 914 ASN Chi-restraints excluded: chain D residue 932 VAL Chi-restraints excluded: chain D residue 933 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 165 optimal weight: 9.9990 chunk 29 optimal weight: 0.1980 chunk 14 optimal weight: 0.7980 chunk 163 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 190 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 HIS ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.218029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.201958 restraints weight = 19946.007| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 0.87 r_work: 0.4159 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.4123 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19118 Z= 0.151 Angle : 0.538 8.075 26610 Z= 0.309 Chirality : 0.039 0.151 2954 Planarity : 0.004 0.051 2768 Dihedral : 22.932 88.284 3958 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.29 % Allowed : 9.94 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.02 (0.21), residues: 1780 helix: 2.22 (0.15), residues: 1200 sheet: -1.03 (0.78), residues: 44 loop : -0.49 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 773 TYR 0.016 0.001 TYR D 141 PHE 0.023 0.002 PHE D 117 TRP 0.012 0.001 TRP D 102 HIS 0.008 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (19118) covalent geometry : angle 0.53824 / 0.31 (26610) hydrogen bonds : bond 0.04703 / 3.12 ( 1020) hydrogen bonds : angle 3.61312 / 2.59 ( 2851) *********************** 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 159 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 129 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8172 (tt) REVERT: D 773 ARG cc_start: 0.6505 (OUTLIER) cc_final: 0.6240 (ttp80) outliers start: 20 outliers final: 15 residues processed: 150 average time/residue: 0.1462 time to fit residues: 33.4932 Evaluate side-chains 154 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 756 THR Chi-restraints excluded: chain D residue 773 ARG Chi-restraints excluded: chain D residue 914 ASN Chi-restraints excluded: chain D residue 932 VAL Chi-restraints excluded: chain D residue 933 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 17 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 185 optimal weight: 0.3980 chunk 119 optimal weight: 0.5980 chunk 190 optimal weight: 10.0000 chunk 179 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 158 optimal weight: 0.9990 chunk 136 optimal weight: 0.0870 chunk 57 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 HIS ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.219487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.203966 restraints weight = 20225.269| |-----------------------------------------------------------------------------| r_work (start): 0.4391 rms_B_bonded: 0.85 r_work: 0.4172 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4138 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19118 Z= 0.123 Angle : 0.510 9.523 26610 Z= 0.295 Chirality : 0.037 0.138 2954 Planarity : 0.003 0.043 2768 Dihedral : 22.917 88.305 3958 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.23 % Allowed : 10.32 % Favored : 88.45 % 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: 2.22 (0.21), residues: 1780 helix: 2.42 (0.15), residues: 1190 sheet: -0.91 (0.79), residues: 44 loop : -0.47 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 773 TYR 0.011 0.001 TYR A 61 PHE 0.020 0.001 PHE A 52 TRP 0.015 0.001 TRP D 102 HIS 0.007 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.12 (19118) covalent geometry : angle 0.50990 / 0.30 (26610) hydrogen bonds : bond 0.04232 / 2.81 ( 1020) hydrogen bonds : angle 3.48042 / 2.49 ( 2851) *********************** 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 158 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 6 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6940 (pp) REVERT: A 129 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8212 (tt) REVERT: D 6 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6879 (pp) REVERT: D 773 ARG cc_start: 0.6485 (OUTLIER) cc_final: 0.6226 (ttp80) outliers start: 19 outliers final: 12 residues processed: 149 average time/residue: 0.1448 time to fit residues: 33.1854 Evaluate side-chains 154 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 756 THR Chi-restraints excluded: chain D residue 773 ARG Chi-restraints excluded: chain D residue 933 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 12 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 120 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 141 optimal weight: 0.1980 chunk 195 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 118 optimal weight: 0.0020 chunk 22 optimal weight: 0.7980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 HIS ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.219760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.204553 restraints weight = 20204.684| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 0.83 r_work: 0.4180 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.4148 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19118 Z= 0.124 Angle : 0.498 8.804 26610 Z= 0.290 Chirality : 0.038 0.164 2954 Planarity : 0.003 0.046 2768 Dihedral : 22.919 88.304 3958 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.48 % Allowed : 10.19 % Favored : 88.32 % 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: 2.37 (0.21), residues: 1780 helix: 2.53 (0.15), residues: 1190 sheet: -0.85 (0.79), residues: 44 loop : -0.42 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 773 TYR 0.010 0.001 TYR D 927 PHE 0.020 0.001 PHE A 52 TRP 0.023 0.001 TRP D 102 HIS 0.006 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.12 (19118) covalent geometry : angle 0.49771 / 0.29 (26610) hydrogen bonds : bond 0.04103 / 2.73 ( 1020) hydrogen bonds : angle 3.39888 / 2.43 ( 2851) *********************** 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 165 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 6 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6889 (pp) REVERT: A 129 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8152 (tt) REVERT: A 952 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8897 (mt) REVERT: D 6 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6919 (pp) REVERT: D 773 ARG cc_start: 0.6476 (OUTLIER) cc_final: 0.6205 (ttp80) REVERT: D 952 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8912 (mt) outliers start: 23 outliers final: 14 residues processed: 154 average time/residue: 0.1247 time to fit residues: 29.6687 Evaluate side-chains 162 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 756 THR Chi-restraints excluded: chain D residue 773 ARG Chi-restraints excluded: chain D residue 914 ASN Chi-restraints excluded: chain D residue 932 VAL Chi-restraints excluded: chain D residue 933 GLU Chi-restraints excluded: chain D residue 952 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 108 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 134 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 188 optimal weight: 8.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 435 HIS ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.218921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.202513 restraints weight = 20132.381| |-----------------------------------------------------------------------------| r_work (start): 0.4377 rms_B_bonded: 0.89 r_work: 0.4156 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4122 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19118 Z= 0.143 Angle : 0.518 8.538 26610 Z= 0.296 Chirality : 0.038 0.158 2954 Planarity : 0.004 0.046 2768 Dihedral : 22.938 88.309 3958 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.35 % Allowed : 10.32 % Favored : 88.32 % 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: 2.34 (0.21), residues: 1780 helix: 2.51 (0.15), residues: 1190 sheet: -0.79 (0.79), residues: 44 loop : -0.43 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 773 TYR 0.010 0.001 TYR A 387 PHE 0.017 0.001 PHE A 52 TRP 0.031 0.001 TRP D 102 HIS 0.007 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (19118) covalent geometry : angle 0.51777 / 0.30 (26610) hydrogen bonds : bond 0.04296 / 2.85 ( 1020) hydrogen bonds : angle 3.42857 / 2.46 ( 2851) *********************** 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 163 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 6 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6933 (pp) REVERT: A 129 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8213 (tt) REVERT: A 952 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8905 (mt) REVERT: D 6 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6957 (pp) REVERT: D 773 ARG cc_start: 0.6476 (OUTLIER) cc_final: 0.6195 (ttp80) REVERT: D 952 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8929 (mt) outliers start: 21 outliers final: 12 residues processed: 154 average time/residue: 0.1419 time to fit residues: 33.4671 Evaluate side-chains 160 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 756 THR Chi-restraints excluded: chain D residue 773 ARG Chi-restraints excluded: chain D residue 932 VAL Chi-restraints excluded: chain D residue 933 GLU Chi-restraints excluded: chain D residue 952 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 184 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 86 optimal weight: 0.0050 chunk 49 optimal weight: 8.9990 chunk 174 optimal weight: 8.9990 chunk 192 optimal weight: 40.0000 chunk 121 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 182 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 HIS ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.219386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.203097 restraints weight = 20114.434| |-----------------------------------------------------------------------------| r_work (start): 0.4382 rms_B_bonded: 0.89 r_work: 0.4161 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4125 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19118 Z= 0.130 Angle : 0.510 9.151 26610 Z= 0.292 Chirality : 0.038 0.156 2954 Planarity : 0.003 0.046 2768 Dihedral : 22.913 88.259 3958 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.23 % Allowed : 10.58 % Favored : 88.19 % 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: 2.39 (0.21), residues: 1780 helix: 2.55 (0.15), residues: 1190 sheet: -0.77 (0.79), residues: 44 loop : -0.43 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 773 TYR 0.010 0.001 TYR A 61 PHE 0.018 0.001 PHE D 898 TRP 0.029 0.001 TRP D 102 HIS 0.007 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.13 (19118) covalent geometry : angle 0.50999 / 0.29 (26610) hydrogen bonds : bond 0.04113 / 2.73 ( 1020) hydrogen bonds : angle 3.38525 / 2.43 ( 2851) ********************** 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 165 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 6 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6970 (pp) REVERT: A 129 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8199 (tt) REVERT: A 952 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8894 (mt) REVERT: D 6 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6974 (pp) REVERT: D 773 ARG cc_start: 0.6496 (OUTLIER) cc_final: 0.6221 (ttp80) REVERT: D 952 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8913 (mt) outliers start: 19 outliers final: 12 residues processed: 156 average time/residue: 0.1436 time to fit residues: 34.8314 Evaluate side-chains 160 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 756 THR Chi-restraints excluded: chain D residue 773 ARG Chi-restraints excluded: chain D residue 914 ASN Chi-restraints excluded: chain D residue 932 VAL Chi-restraints excluded: chain D residue 933 GLU Chi-restraints excluded: chain D residue 952 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 149 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 93 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 141 optimal weight: 0.0370 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 166 optimal weight: 7.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 HIS ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.219354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.203624 restraints weight = 20142.428| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 0.86 r_work: 0.4168 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.4136 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.206 19118 Z= 0.174 Angle : 0.708 59.200 26610 Z= 0.426 Chirality : 0.038 0.195 2954 Planarity : 0.003 0.045 2768 Dihedral : 22.914 88.259 3958 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.29 % Allowed : 10.90 % Favored : 87.81 % Cbeta Deviations : 0.06 % 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: 2.37 (0.21), residues: 1780 helix: 2.53 (0.15), residues: 1190 sheet: -0.77 (0.79), residues: 44 loop : -0.42 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 773 TYR 0.023 0.001 TYR D 121 PHE 0.018 0.001 PHE D 898 TRP 0.025 0.001 TRP D 102 HIS 0.006 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (19118) covalent geometry : angle 0.70756 / 0.43 (26610) hydrogen bonds : bond 0.04114 / 2.74 ( 1020) hydrogen bonds : angle 3.39211 / 2.43 ( 2851) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4612.06 seconds wall clock time: 79 minutes 35.94 seconds (4775.94 seconds total)