Starting phenix.real_space_refine on Mon Jun 16 03:56:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qd5_13908/06_2025/7qd5_13908.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qd5_13908/06_2025/7qd5_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_13908/06_2025/7qd5_13908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qd5_13908/06_2025/7qd5_13908.map" model { file = "/net/cci-nas-00/data/ceres_data/7qd5_13908/06_2025/7qd5_13908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qd5_13908/06_2025/7qd5_13908.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 4} 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: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 4} 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: 11.47, per 1000 atoms: 0.62 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: 4.54 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 6.89 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: 8.40 Time building geometry restraints manager: 5.41 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: 0.08 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: 3.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 49.350 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.100 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.470 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.047 0.002 TRP D 102 HIS 0.016 0.001 HIS D 435 PHE 0.022 0.002 PHE A 892 TYR 0.035 0.002 TYR A 141 ARG 0.021 0.001 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.15704 ( 1020) hydrogen bonds : angle 6.17224 ( 2851) covalent geometry : bond 0.00493 (19118) covalent geometry : angle 0.82441 (26610) *********************** 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 : 1.843 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 174 average time/residue: 0.3581 time to fit residues: 91.4895 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 : 1.715 ------------------------------------------------------------------------------- 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 165 optimal weight: 0.9990 chunk 148 optimal weight: 40.0000 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 30.0000 chunk 100 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 114 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4555 r_free = 0.4555 target = 0.220606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.204492 restraints weight = 20417.051| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 0.92 r_work: 0.4175 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4137 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19118 Z= 0.164 Angle : 0.539 8.173 26610 Z= 0.307 Chirality : 0.037 0.145 2954 Planarity : 0.004 0.066 2768 Dihedral : 22.186 87.801 3962 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.45 % Allowed : 5.42 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.20), residues: 1780 helix: 1.29 (0.15), residues: 1196 sheet: -0.55 (0.85), residues: 44 loop : -0.52 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 102 HIS 0.006 0.001 HIS A 43 PHE 0.020 0.002 PHE D 52 TYR 0.022 0.001 TYR A 141 ARG 0.004 0.000 ARG D 267 Details of bonding type rmsd hydrogen bonds : bond 0.04777 ( 1020) hydrogen bonds : angle 3.77525 ( 2851) covalent geometry : bond 0.00359 (19118) covalent geometry : angle 0.53934 (26610) *********************** 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 165 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 158 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 306 LYS cc_start: 0.8224 (tttt) cc_final: 0.7910 (tttm) REVERT: D 773 ARG cc_start: 0.6610 (OUTLIER) cc_final: 0.6353 (ttp80) outliers start: 7 outliers final: 4 residues processed: 161 average time/residue: 0.3387 time to fit residues: 80.8532 Evaluate side-chains 143 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 138 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain D residue 137 ASN 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 75 optimal weight: 9.9990 chunk 144 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 178 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.217908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.201085 restraints weight = 20042.239| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 0.90 r_work: 0.4137 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4103 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19118 Z= 0.198 Angle : 0.560 9.245 26610 Z= 0.312 Chirality : 0.039 0.156 2954 Planarity : 0.005 0.100 2768 Dihedral : 22.418 87.315 3958 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.16 % Allowed : 7.74 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.20), residues: 1780 helix: 1.84 (0.15), residues: 1186 sheet: -0.78 (0.80), residues: 44 loop : -0.49 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 102 HIS 0.006 0.001 HIS A 43 PHE 0.024 0.002 PHE A 52 TYR 0.021 0.002 TYR A 141 ARG 0.003 0.001 ARG A 942 Details of bonding type rmsd hydrogen bonds : bond 0.05061 ( 1020) hydrogen bonds : angle 3.70654 ( 2851) covalent geometry : bond 0.00453 (19118) covalent geometry : angle 0.55987 (26610) *********************** 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: 18 poor density : 147 time to evaluate : 1.791 Fit side-chains revert: symmetry clash REVERT: A 145 ILE cc_start: 0.7415 (mm) cc_final: 0.7140 (mm) REVERT: A 426 ARG cc_start: 0.6792 (tpp80) cc_final: 0.6591 (ttt90) REVERT: D 773 ARG cc_start: 0.6566 (OUTLIER) cc_final: 0.6279 (ttp80) outliers start: 18 outliers final: 12 residues processed: 158 average time/residue: 0.3590 time to fit residues: 86.1100 Evaluate side-chains 155 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 1.609 ------------------------------------------------------------------------------- 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 945 LEU Chi-restraints excluded: chain D residue 125 LEU 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 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 2 optimal weight: 0.0980 chunk 42 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 134 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4542 r_free = 0.4542 target = 0.219219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.203067 restraints weight = 20165.562| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 0.88 r_work: 0.4161 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4122 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.1747 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= 0.154 Angle : 0.505 7.521 26610 Z= 0.287 Chirality : 0.036 0.142 2954 Planarity : 0.004 0.053 2768 Dihedral : 22.431 87.412 3958 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.10 % Allowed : 9.23 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.20), residues: 1780 helix: 2.15 (0.15), residues: 1202 sheet: -0.80 (0.79), residues: 44 loop : -0.48 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 102 HIS 0.005 0.001 HIS A 43 PHE 0.026 0.002 PHE D 128 TYR 0.010 0.001 TYR A 260 ARG 0.005 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.04300 ( 1020) hydrogen bonds : angle 3.52382 ( 2851) covalent geometry : bond 0.00341 (19118) covalent geometry : angle 0.50545 (26610) *********************** 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 168 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 1.602 Fit side-chains revert: symmetry clash REVERT: A 145 ILE cc_start: 0.7350 (mm) cc_final: 0.7110 (mm) REVERT: D 773 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.6254 (ttp80) outliers start: 17 outliers final: 12 residues processed: 161 average time/residue: 0.3253 time to fit residues: 78.6882 Evaluate side-chains 156 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 1.768 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 181 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 172 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 180 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4543 r_free = 0.4543 target = 0.219330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.202358 restraints weight = 20218.371| |-----------------------------------------------------------------------------| r_work (start): 0.4376 rms_B_bonded: 0.92 r_work: 0.4160 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4128 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19118 Z= 0.145 Angle : 0.496 7.915 26610 Z= 0.282 Chirality : 0.036 0.154 2954 Planarity : 0.004 0.045 2768 Dihedral : 22.446 87.432 3958 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.16 % Allowed : 9.61 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.21), residues: 1780 helix: 2.34 (0.15), residues: 1190 sheet: -0.81 (0.79), residues: 44 loop : -0.41 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 102 HIS 0.006 0.001 HIS A 43 PHE 0.021 0.002 PHE D 117 TYR 0.014 0.001 TYR D 141 ARG 0.004 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 1020) hydrogen bonds : angle 3.46128 ( 2851) covalent geometry : bond 0.00317 (19118) covalent geometry : angle 0.49599 (26610) *********************** 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: 18 poor density : 151 time to evaluate : 1.632 Fit side-chains revert: symmetry clash REVERT: A 145 ILE cc_start: 0.7320 (mm) cc_final: 0.7116 (mm) REVERT: D 773 ARG cc_start: 0.6519 (OUTLIER) cc_final: 0.6241 (ttp80) outliers start: 18 outliers final: 14 residues processed: 160 average time/residue: 0.3052 time to fit residues: 75.0743 Evaluate side-chains 158 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 1.745 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 67 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 153 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 182 optimal weight: 0.5980 chunk 164 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 = 0.4514 r_free = 0.4514 target = 0.216365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.199868 restraints weight = 20158.568| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 0.87 r_work: 0.4132 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.4092 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 19118 Z= 0.228 Angle : 0.566 8.868 26610 Z= 0.313 Chirality : 0.040 0.159 2954 Planarity : 0.004 0.087 2768 Dihedral : 22.586 87.586 3958 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.29 % Allowed : 10.13 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.21), residues: 1780 helix: 2.18 (0.15), residues: 1196 sheet: -1.11 (0.75), residues: 44 loop : -0.48 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 102 HIS 0.010 0.001 HIS A 43 PHE 0.022 0.002 PHE A 52 TYR 0.015 0.002 TYR A 260 ARG 0.006 0.001 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.05151 ( 1020) hydrogen bonds : angle 3.65957 ( 2851) covalent geometry : bond 0.00531 (19118) covalent geometry : angle 0.56606 (26610) *********************** 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 164 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 1.850 Fit side-chains revert: symmetry clash REVERT: D 773 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.6220 (ttp80) outliers start: 20 outliers final: 15 residues processed: 155 average time/residue: 0.3173 time to fit residues: 75.8165 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 : 1.837 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 86 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN 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 = 0.4517 r_free = 0.4517 target = 0.216585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.199637 restraints weight = 19978.611| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 0.90 r_work: 0.4130 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4098 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 19118 Z= 0.197 Angle : 0.541 8.064 26610 Z= 0.302 Chirality : 0.038 0.146 2954 Planarity : 0.004 0.071 2768 Dihedral : 22.579 87.550 3958 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.42 % Allowed : 10.32 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.21), residues: 1780 helix: 2.22 (0.15), residues: 1198 sheet: -1.15 (0.75), residues: 44 loop : -0.51 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 102 HIS 0.006 0.001 HIS A 43 PHE 0.018 0.002 PHE A 52 TYR 0.013 0.001 TYR A 387 ARG 0.005 0.000 ARG A 773 Details of bonding type rmsd hydrogen bonds : bond 0.04887 ( 1020) hydrogen bonds : angle 3.61348 ( 2851) covalent geometry : bond 0.00454 (19118) covalent geometry : angle 0.54069 (26610) *********************** 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 162 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.610 Fit side-chains revert: symmetry clash REVERT: A 6 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.7052 (pp) REVERT: D 773 ARG cc_start: 0.6495 (OUTLIER) cc_final: 0.6203 (ttp80) outliers start: 22 outliers final: 15 residues processed: 152 average time/residue: 0.3126 time to fit residues: 72.8336 Evaluate side-chains 156 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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 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 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 104 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 136 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4526 r_free = 0.4526 target = 0.217601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.201089 restraints weight = 20041.252| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 0.88 r_work: 0.4146 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4113 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2150 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 : 0.517 8.346 26610 Z= 0.290 Chirality : 0.036 0.138 2954 Planarity : 0.004 0.049 2768 Dihedral : 22.528 87.413 3958 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.42 % Allowed : 10.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.21), residues: 1780 helix: 2.32 (0.15), residues: 1204 sheet: -1.03 (0.75), residues: 44 loop : -0.49 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 102 HIS 0.005 0.001 HIS A 43 PHE 0.018 0.002 PHE D 892 TYR 0.011 0.001 TYR D 863 ARG 0.005 0.000 ARG A 773 Details of bonding type rmsd hydrogen bonds : bond 0.04463 ( 1020) hydrogen bonds : angle 3.51937 ( 2851) covalent geometry : bond 0.00356 (19118) covalent geometry : angle 0.51688 (26610) *********************** 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 162 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.7055 (pp) REVERT: A 901 ARG cc_start: 0.5767 (OUTLIER) cc_final: 0.5500 (mtm-85) REVERT: D 773 ARG cc_start: 0.6454 (OUTLIER) cc_final: 0.6180 (ttp80) REVERT: D 952 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8968 (mt) outliers start: 22 outliers final: 16 residues processed: 152 average time/residue: 0.3149 time to fit residues: 73.2105 Evaluate side-chains 157 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 1.792 ------------------------------------------------------------------------------- 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 756 THR Chi-restraints excluded: chain A residue 901 ARG 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 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 62 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 141 optimal weight: 0.0970 chunk 159 optimal weight: 0.3980 chunk 123 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 182 optimal weight: 0.5980 chunk 181 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4539 r_free = 0.4539 target = 0.219007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.203196 restraints weight = 20244.925| |-----------------------------------------------------------------------------| r_work (start): 0.4384 rms_B_bonded: 0.86 r_work: 0.4168 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4134 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2189 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= 0.132 Angle : 0.493 8.387 26610 Z= 0.279 Chirality : 0.035 0.137 2954 Planarity : 0.003 0.044 2768 Dihedral : 22.453 87.218 3958 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.35 % Allowed : 10.52 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.21), residues: 1780 helix: 2.46 (0.15), residues: 1204 sheet: -0.92 (0.76), residues: 44 loop : -0.46 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 102 HIS 0.004 0.001 HIS A 43 PHE 0.018 0.001 PHE D 892 TYR 0.011 0.001 TYR D 863 ARG 0.006 0.000 ARG D 901 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 1020) hydrogen bonds : angle 3.40472 ( 2851) covalent geometry : bond 0.00281 (19118) covalent geometry : angle 0.49344 (26610) *********************** 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 162 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 901 ARG cc_start: 0.5788 (OUTLIER) cc_final: 0.5493 (mtm-85) REVERT: D 773 ARG cc_start: 0.6452 (OUTLIER) cc_final: 0.6211 (ttp80) REVERT: D 952 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8925 (mt) outliers start: 21 outliers final: 16 residues processed: 153 average time/residue: 0.3212 time to fit residues: 75.6103 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 : 1.791 ------------------------------------------------------------------------------- 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 144 GLU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 901 ARG 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 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 26 optimal weight: 0.0980 chunk 141 optimal weight: 0.0070 chunk 73 optimal weight: 9.9990 chunk 124 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 = 0.4552 r_free = 0.4552 target = 0.220443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.205852 restraints weight = 20297.770| |-----------------------------------------------------------------------------| r_work (start): 0.4401 rms_B_bonded: 0.81 r_work: 0.4195 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4155 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19118 Z= 0.128 Angle : 0.491 8.728 26610 Z= 0.277 Chirality : 0.035 0.137 2954 Planarity : 0.003 0.043 2768 Dihedral : 22.406 87.012 3958 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.23 % Allowed : 10.65 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.21), residues: 1780 helix: 2.56 (0.15), residues: 1204 sheet: -0.90 (0.77), residues: 44 loop : -0.48 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 102 HIS 0.004 0.001 HIS A 43 PHE 0.016 0.001 PHE D 892 TYR 0.022 0.001 TYR D 141 ARG 0.006 0.000 ARG D 901 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 1020) hydrogen bonds : angle 3.34520 ( 2851) covalent geometry : bond 0.00269 (19118) covalent geometry : angle 0.49135 (26610) ********************** 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 164 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 901 ARG cc_start: 0.5755 (OUTLIER) cc_final: 0.5445 (mtm-85) REVERT: D 773 ARG cc_start: 0.6432 (OUTLIER) cc_final: 0.6196 (ttp80) REVERT: D 952 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8897 (mt) outliers start: 19 outliers final: 14 residues processed: 155 average time/residue: 0.3386 time to fit residues: 81.6824 Evaluate side-chains 158 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 1.731 ------------------------------------------------------------------------------- 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 144 GLU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 901 ARG 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 773 ARG 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 37 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 111 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 174 optimal weight: 0.0570 chunk 87 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 overall best weight: 0.7698 ------------------------------------------------------------------------------- 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 = 0.218769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.202470 restraints weight = 20147.613| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 0.88 r_work: 0.4167 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.4135 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19118 Z= 0.146 Angle : 0.504 8.839 26610 Z= 0.282 Chirality : 0.036 0.187 2954 Planarity : 0.003 0.043 2768 Dihedral : 22.428 86.904 3958 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.42 % Allowed : 10.71 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.21), residues: 1780 helix: 2.53 (0.15), residues: 1202 sheet: -0.90 (0.75), residues: 44 loop : -0.46 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 102 HIS 0.004 0.001 HIS A 43 PHE 0.017 0.001 PHE D 892 TYR 0.011 0.001 TYR D 863 ARG 0.006 0.000 ARG A 773 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 1020) hydrogen bonds : angle 3.38622 ( 2851) covalent geometry : bond 0.00323 (19118) covalent geometry : angle 0.50428 (26610) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10133.50 seconds wall clock time: 173 minutes 35.49 seconds (10415.49 seconds total)