Starting phenix.real_space_refine on Thu Mar 5 01:45:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qd5_13908/03_2026/7qd5_13908.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qd5_13908/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7qd5_13908/03_2026/7qd5_13908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qd5_13908/03_2026/7qd5_13908.map" model { file = "/net/cci-nas-00/data/ceres_data/7qd5_13908/03_2026/7qd5_13908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qd5_13908/03_2026/7qd5_13908.cif" } 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-dev-5986/lib/python3.9/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: 3.82, per 1000 atoms: 0.21 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: 1.45 Conformation dependent library (CDL) restraints added in 583.0 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 6 sheets defined 69.6% alpha, 1.8% beta 54 base pairs and 153 stacking pairs defined. Time for finding SS restraints: 2.76 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: 4.02 Time building geometry restraints manager: 1.95 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=" N ILE D 854 " pdb=" CA ILE D 854 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.59e+00 bond pdb=" N ILE A 854 " pdb=" CA ILE A 854 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.34e+00 bond pdb=" N ILE A 802 " pdb=" CA ILE A 802 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.24e-02 6.50e+03 7.11e+00 bond pdb=" N ILE D 802 " pdb=" CA ILE D 802 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.24e-02 6.50e+03 7.07e+00 bond pdb=" N THR D 857 " pdb=" CA THR D 857 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.19e+00 ... (remaining 19113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 26045 2.33 - 4.65: 449 4.65 - 6.98: 80 6.98 - 9.31: 34 9.31 - 11.64: 2 Bond angle restraints: 26610 Sorted by residual: 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 angle pdb=" CB GLU D 933 " pdb=" CG GLU D 933 " pdb=" CD GLU D 933 " ideal model delta sigma weight residual 112.60 119.51 -6.91 1.70e+00 3.46e-01 1.65e+01 angle pdb=" CB LYS A 306 " pdb=" CG LYS A 306 " pdb=" CD LYS A 306 " ideal model delta sigma weight residual 111.30 120.34 -9.04 2.30e+00 1.89e-01 1.55e+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: 2397 0.053 - 0.106: 450 0.106 - 0.159: 86 0.159 - 0.212: 16 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: 0.02 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: 7.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.740 Find NCS groups from input model: 0.220 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 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 : 0.005 0.057 19118 Z= 0.248 Angle : 0.824 11.636 26610 Z= 0.456 Chirality : 0.045 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 covalent geometry : bond 0.00493 (19118) covalent geometry : angle 0.82441 (26610) hydrogen bonds : bond 0.15704 ( 1020) hydrogen bonds : angle 6.17224 ( 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 : 0.644 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 174 average time/residue: 0.1533 time to fit residues: 38.9414 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 : 0.578 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN A 318 ASN A 914 ASN D 137 ASN D 188 GLN D 368 GLN D 914 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.219451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.203048 restraints weight = 20298.366| |-----------------------------------------------------------------------------| r_work (start): 0.4377 rms_B_bonded: 0.92 r_work: 0.4161 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4127 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19118 Z= 0.187 Angle : 0.567 7.971 26610 Z= 0.319 Chirality : 0.039 0.157 2954 Planarity : 0.005 0.094 2768 Dihedral : 22.271 87.955 3962 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.71 % Allowed : 5.35 % Favored : 93.94 % 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: 0.92 (0.20), residues: 1780 helix: 1.23 (0.15), residues: 1196 sheet: -0.61 (0.84), residues: 44 loop : -0.55 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 267 TYR 0.024 0.001 TYR A 141 PHE 0.020 0.002 PHE D 892 TRP 0.014 0.001 TRP D 102 HIS 0.006 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00424 (19118) covalent geometry : angle 0.56701 (26610) hydrogen bonds : bond 0.05121 ( 1020) hydrogen bonds : angle 3.82866 ( 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 168 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 306 LYS cc_start: 0.8211 (tttt) cc_final: 0.7903 (tttm) outliers start: 11 outliers final: 7 residues processed: 163 average time/residue: 0.1589 time to fit residues: 38.4417 Evaluate side-chains 146 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 756 THR Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 932 VAL Chi-restraints excluded: chain D residue 933 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 3 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 170 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN D 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.217302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.200910 restraints weight = 20187.525| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 0.88 r_work: 0.4134 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4098 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19118 Z= 0.213 Angle : 0.574 9.067 26610 Z= 0.319 Chirality : 0.039 0.161 2954 Planarity : 0.005 0.092 2768 Dihedral : 22.464 87.455 3958 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.03 % Allowed : 7.68 % Favored : 91.29 % 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: 1.75 (0.15), residues: 1186 sheet: -0.85 (0.79), residues: 44 loop : -0.53 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 942 TYR 0.027 0.002 TYR A 141 PHE 0.022 0.002 PHE D 52 TRP 0.012 0.001 TRP D 102 HIS 0.007 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00490 (19118) covalent geometry : angle 0.57397 (26610) hydrogen bonds : bond 0.05283 ( 1020) hydrogen bonds : angle 3.76927 ( 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 164 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 426 ARG cc_start: 0.6817 (tpp80) cc_final: 0.6593 (ttt90) outliers start: 16 outliers final: 12 residues processed: 159 average time/residue: 0.1523 time to fit residues: 36.4328 Evaluate side-chains 152 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 756 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain D residue 125 LEU 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 932 VAL 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: 3.9990 chunk 122 optimal weight: 0.8980 chunk 143 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 173 optimal weight: 6.9990 chunk 185 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 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 = 0.4537 r_free = 0.4537 target = 0.218658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.201962 restraints weight = 20228.858| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 0.90 r_work: 0.4151 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4112 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1707 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= 0.155 Angle : 0.515 7.612 26610 Z= 0.292 Chirality : 0.036 0.138 2954 Planarity : 0.004 0.052 2768 Dihedral : 22.424 87.445 3958 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.90 % Allowed : 9.81 % Favored : 89.29 % 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: 1.84 (0.20), residues: 1780 helix: 2.07 (0.15), residues: 1202 sheet: -0.89 (0.78), residues: 44 loop : -0.54 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.022 0.001 TYR A 141 PHE 0.026 0.002 PHE D 128 TRP 0.014 0.001 TRP D 102 HIS 0.006 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00344 (19118) covalent geometry : angle 0.51499 (26610) hydrogen bonds : bond 0.04469 ( 1020) hydrogen bonds : angle 3.57944 ( 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 160 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.596 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 155 average time/residue: 0.1523 time to fit residues: 35.8718 Evaluate side-chains 150 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 182 LEU Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 756 THR 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: 0.6980 chunk 7 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 169 optimal weight: 20.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 914 ASN D 914 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.219538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.202861 restraints weight = 20215.630| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 0.93 r_work: 0.4157 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.4118 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19118 Z= 0.150 Angle : 0.503 7.928 26610 Z= 0.285 Chirality : 0.036 0.142 2954 Planarity : 0.004 0.048 2768 Dihedral : 22.443 87.484 3958 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.23 % Allowed : 9.61 % Favored : 89.16 % 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: 2.06 (0.21), residues: 1780 helix: 2.25 (0.15), residues: 1202 sheet: -0.89 (0.78), residues: 44 loop : -0.48 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.024 0.001 TYR A 141 PHE 0.022 0.002 PHE D 117 TRP 0.014 0.001 TRP D 102 HIS 0.005 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00331 (19118) covalent geometry : angle 0.50287 (26610) hydrogen bonds : bond 0.04321 ( 1020) hydrogen bonds : angle 3.50868 ( 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 169 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.627 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 16 residues processed: 159 average time/residue: 0.1440 time to fit residues: 34.9391 Evaluate side-chains 157 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 239 THR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 914 ASN 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 335 THR Chi-restraints excluded: chain D residue 756 THR 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: 5.9990 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 165 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 163 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN A 435 HIS A 914 ASN D 914 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.218403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.201633 restraints weight = 19955.850| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 0.90 r_work: 0.4152 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4119 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19118 Z= 0.159 Angle : 0.506 8.028 26610 Z= 0.286 Chirality : 0.036 0.142 2954 Planarity : 0.004 0.052 2768 Dihedral : 22.467 87.519 3958 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.29 % Allowed : 10.26 % 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: 2.14 (0.21), residues: 1780 helix: 2.32 (0.15), residues: 1200 sheet: -0.94 (0.77), residues: 44 loop : -0.47 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 44 TYR 0.021 0.001 TYR A 141 PHE 0.022 0.002 PHE D 117 TRP 0.016 0.001 TRP D 102 HIS 0.007 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00356 (19118) covalent geometry : angle 0.50583 (26610) hydrogen bonds : bond 0.04379 ( 1020) hydrogen bonds : angle 3.49270 ( 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 167 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: D 6 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6927 (pp) outliers start: 20 outliers final: 15 residues processed: 158 average time/residue: 0.1479 time to fit residues: 35.6355 Evaluate side-chains 157 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 144 GLU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 914 ASN 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 239 THR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 756 THR 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: 0.8980 chunk 125 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 chunk 119 optimal weight: 0.5980 chunk 190 optimal weight: 2.9990 chunk 179 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 914 ASN D 914 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.219472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.203114 restraints weight = 20229.139| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 0.89 r_work: 0.4163 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4132 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19118 Z= 0.133 Angle : 0.486 9.586 26610 Z= 0.276 Chirality : 0.035 0.148 2954 Planarity : 0.004 0.049 2768 Dihedral : 22.425 87.458 3958 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.16 % Allowed : 10.45 % Favored : 88.39 % 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: 2.29 (0.21), residues: 1780 helix: 2.45 (0.15), residues: 1200 sheet: -0.80 (0.79), residues: 44 loop : -0.44 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 773 TYR 0.011 0.001 TYR D 863 PHE 0.019 0.001 PHE A 52 TRP 0.021 0.001 TRP D 102 HIS 0.005 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00283 (19118) covalent geometry : angle 0.48639 (26610) hydrogen bonds : bond 0.04001 ( 1020) hydrogen bonds : angle 3.39078 ( 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 164 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 6 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6938 (pp) outliers start: 18 outliers final: 15 residues processed: 155 average time/residue: 0.1456 time to fit residues: 34.4495 Evaluate side-chains 160 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 144 GLU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 914 ASN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 12 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 120 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 141 optimal weight: 0.4980 chunk 195 optimal weight: 1.9990 chunk 168 optimal weight: 8.9990 chunk 180 optimal weight: 0.4980 chunk 138 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN A 374 ASN A 435 HIS A 914 ASN D 914 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.219569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.202180 restraints weight = 20198.146| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 0.94 r_work: 0.4162 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4125 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19118 Z= 0.134 Angle : 0.485 8.672 26610 Z= 0.274 Chirality : 0.035 0.157 2954 Planarity : 0.003 0.043 2768 Dihedral : 22.422 87.368 3958 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % 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: 2.51 (0.15), residues: 1200 sheet: -0.77 (0.79), residues: 44 loop : -0.44 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 773 TYR 0.021 0.001 TYR A 141 PHE 0.017 0.001 PHE D 892 TRP 0.027 0.001 TRP D 102 HIS 0.005 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00288 (19118) covalent geometry : angle 0.48549 (26610) hydrogen bonds : bond 0.03950 ( 1020) hydrogen bonds : angle 3.35952 ( 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 169 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6977 (pp) REVERT: D 6 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6950 (pp) REVERT: D 952 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8900 (mt) outliers start: 23 outliers final: 17 residues processed: 158 average time/residue: 0.1460 time to fit residues: 35.0091 Evaluate side-chains 163 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 140 LEU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 933 GLU 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 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 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: 4.9990 chunk 112 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 914 ASN D 374 ASN D 914 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.218684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.202851 restraints weight = 20141.498| |-----------------------------------------------------------------------------| r_work (start): 0.4382 rms_B_bonded: 0.86 r_work: 0.4168 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4135 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2105 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= 0.155 Angle : 0.512 15.897 26610 Z= 0.284 Chirality : 0.036 0.159 2954 Planarity : 0.004 0.048 2768 Dihedral : 22.444 87.288 3958 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.42 % Allowed : 10.58 % Favored : 88.00 % 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: 2.32 (0.21), residues: 1780 helix: 2.47 (0.15), residues: 1200 sheet: -0.86 (0.78), residues: 44 loop : -0.46 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 901 TYR 0.013 0.001 TYR A 141 PHE 0.018 0.002 PHE D 128 TRP 0.022 0.001 TRP D 102 HIS 0.005 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00345 (19118) covalent geometry : angle 0.51183 (26610) hydrogen bonds : bond 0.04187 ( 1020) hydrogen bonds : angle 3.41124 ( 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 164 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6972 (pp) REVERT: D 952 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8909 (mt) outliers start: 22 outliers final: 17 residues processed: 153 average time/residue: 0.1450 time to fit residues: 33.9561 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 : 0.646 ------------------------------------------------------------------------------- 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 140 LEU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 933 GLU 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 239 THR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 756 THR 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 184 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 86 optimal weight: 0.1980 chunk 49 optimal weight: 5.9990 chunk 174 optimal weight: 0.0470 chunk 192 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 182 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 118 optimal weight: 0.1980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN A 914 ASN D 914 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.215011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.193681 restraints weight = 20291.601| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 1.11 r_work: 0.3950 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3905 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19118 Z= 0.122 Angle : 0.488 15.780 26610 Z= 0.273 Chirality : 0.035 0.158 2954 Planarity : 0.003 0.043 2768 Dihedral : 22.351 87.042 3958 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.16 % Allowed : 10.77 % Favored : 88.06 % 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: 2.44 (0.21), residues: 1780 helix: 2.57 (0.15), residues: 1202 sheet: -0.77 (0.78), residues: 44 loop : -0.42 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 901 TYR 0.011 0.001 TYR D 863 PHE 0.015 0.001 PHE D 892 TRP 0.030 0.001 TRP D 102 HIS 0.004 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00252 (19118) covalent geometry : angle 0.48759 (26610) hydrogen bonds : bond 0.03678 ( 1020) hydrogen bonds : angle 3.30453 ( 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 159 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 6 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.7067 (pp) REVERT: A 933 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7516 (mm-30) REVERT: D 952 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8852 (mt) outliers start: 18 outliers final: 13 residues processed: 150 average time/residue: 0.1406 time to fit residues: 32.6452 Evaluate side-chains 156 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 144 GLU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 933 GLU 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 239 THR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 756 THR Chi-restraints excluded: chain D residue 914 ASN 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: 0.7980 chunk 93 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 141 optimal weight: 0.0020 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 166 optimal weight: 9.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 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 = 0.4470 r_free = 0.4470 target = 0.214112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.192633 restraints weight = 20281.234| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 1.12 r_work: 0.3937 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3893 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19118 Z= 0.136 Angle : 0.496 15.345 26610 Z= 0.276 Chirality : 0.035 0.165 2954 Planarity : 0.003 0.043 2768 Dihedral : 22.373 86.905 3958 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.10 % Allowed : 10.97 % Favored : 87.94 % 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: 2.42 (0.21), residues: 1780 helix: 2.56 (0.15), residues: 1204 sheet: -0.75 (0.78), residues: 44 loop : -0.46 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 773 TYR 0.027 0.001 TYR D 141 PHE 0.020 0.002 PHE A 128 TRP 0.029 0.001 TRP D 102 HIS 0.004 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00296 (19118) covalent geometry : angle 0.49571 (26610) hydrogen bonds : bond 0.03867 ( 1020) hydrogen bonds : angle 3.32567 ( 2851) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4793.83 seconds wall clock time: 82 minutes 38.00 seconds (4958.00 seconds total)