Starting phenix.real_space_refine on Sun Mar 17 16:35:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd5_13908/03_2024/7qd5_13908.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd5_13908/03_2024/7qd5_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd5_13908/03_2024/7qd5_13908.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd5_13908/03_2024/7qd5_13908.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd5_13908/03_2024/7qd5_13908.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd5_13908/03_2024/7qd5_13908.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9.27, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 6.70 Conformation dependent library (CDL) restraints added in 2.4 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: 6.43 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: 8.96 Time building geometry restraints manager: 7.24 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: 96.87 - 104.31: 771 104.31 - 111.75: 9051 111.75 - 119.19: 6796 119.19 - 126.63: 9231 126.63 - 134.07: 761 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 2.440 nonbonded pdb=" OH TYR A 669 " pdb=" OE2 GLU A 943 " model vdw 2.285 2.440 nonbonded pdb=" OG SER A 678 " pdb=" O TYR A 749 " model vdw 2.336 2.440 nonbonded pdb=" OH TYR A 47 " pdb=" OP1 DC C1037 " model vdw 2.338 2.440 nonbonded pdb=" O GLU A 338 " pdb=" OG1 THR A 342 " model vdw 2.373 2.440 ... (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 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: 3.210 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: 0.020 Extract box with map and model: 17.220 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 52.460 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.100 ------------------------------------------------------------------------------- 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= 0.304 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 *********************** 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 fitting. rotamer outliers: 2 poor density : 174 time to evaluate : 1.586 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 174 average time/residue: 0.3462 time to fit residues: 88.3734 Evaluate side-chains 144 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 1.694 ------------------------------------------------------------------------------- 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: 0.9980 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: 2.9990 chunk 153 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 114 optimal weight: 0.4980 chunk 177 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19118 Z= 0.209 Angle : 0.533 7.719 26610 Z= 0.303 Chirality : 0.037 0.134 2954 Planarity : 0.004 0.063 2768 Dihedral : 22.186 87.758 3962 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.65 % Allowed : 5.23 % 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: 1.03 (0.20), residues: 1780 helix: 1.32 (0.15), residues: 1194 sheet: -0.58 (0.83), residues: 44 loop : -0.53 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 102 HIS 0.004 0.001 HIS A 104 PHE 0.017 0.002 PHE D 892 TYR 0.022 0.001 TYR A 141 ARG 0.004 0.000 ARG A 454 *********************** 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 fitting. rotamer outliers: 10 poor density : 155 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 306 LYS cc_start: 0.8103 (tttt) cc_final: 0.7792 (tttm) outliers start: 10 outliers final: 6 residues processed: 159 average time/residue: 0.3476 time to fit residues: 81.4616 Evaluate side-chains 145 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 139 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 423 THR 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 98 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 148 optimal weight: 40.0000 chunk 121 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 60 optimal weight: 0.0970 chunk 143 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 368 GLN ** D 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19118 Z= 0.281 Angle : 0.560 8.723 26610 Z= 0.311 Chirality : 0.039 0.164 2954 Planarity : 0.005 0.111 2768 Dihedral : 22.493 87.276 3958 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.23 % Allowed : 8.06 % Favored : 90.71 % 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: 1.56 (0.20), residues: 1780 helix: 1.79 (0.15), residues: 1198 sheet: -0.82 (0.78), residues: 44 loop : -0.48 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 102 HIS 0.005 0.001 HIS A 43 PHE 0.024 0.002 PHE D 52 TYR 0.020 0.002 TYR D 141 ARG 0.005 0.001 ARG A 942 *********************** 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 171 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 162 average time/residue: 0.3205 time to fit residues: 77.6340 Evaluate side-chains 157 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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 379 ASP Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain D residue 31 THR 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 933 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 169 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19118 Z= 0.297 Angle : 0.550 7.628 26610 Z= 0.308 Chirality : 0.039 0.160 2954 Planarity : 0.004 0.085 2768 Dihedral : 22.530 87.618 3958 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.42 % Allowed : 9.48 % Favored : 89.10 % 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: 1.74 (0.20), residues: 1780 helix: 2.00 (0.15), residues: 1196 sheet: -1.12 (0.73), residues: 44 loop : -0.55 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 102 HIS 0.006 0.001 HIS A 43 PHE 0.025 0.002 PHE D 128 TYR 0.015 0.001 TYR A 260 ARG 0.009 0.000 ARG A 44 *********************** 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 178 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 1.934 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 18 residues processed: 171 average time/residue: 0.3246 time to fit residues: 83.5691 Evaluate side-chains 166 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 1.855 ------------------------------------------------------------------------------- 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 379 ASP Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 618 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.5980 chunk 107 optimal weight: 10.0000 chunk 2 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 161 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 914 ASN D 914 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.2043 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= 0.288 Angle : 0.544 7.512 26610 Z= 0.304 Chirality : 0.039 0.149 2954 Planarity : 0.004 0.081 2768 Dihedral : 22.560 87.485 3958 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.68 % Allowed : 10.39 % 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 (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: 1.88 (0.20), residues: 1780 helix: 2.12 (0.15), residues: 1196 sheet: -1.31 (0.70), residues: 44 loop : -0.52 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 102 HIS 0.005 0.001 HIS A 43 PHE 0.027 0.002 PHE A 117 TYR 0.014 0.001 TYR A 260 ARG 0.007 0.001 ARG A 773 *********************** 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 174 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 148 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 944 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7517 (p0) outliers start: 26 outliers final: 22 residues processed: 163 average time/residue: 0.3190 time to fit residues: 79.1120 Evaluate side-chains 166 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 143 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR 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 239 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 944 ASP Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 618 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 63 optimal weight: 0.5980 chunk 170 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 62 optimal weight: 0.0870 chunk 99 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN A 435 HIS A 914 ASN D 914 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2107 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= 0.180 Angle : 0.489 7.791 26610 Z= 0.278 Chirality : 0.035 0.137 2954 Planarity : 0.003 0.037 2768 Dihedral : 22.453 87.262 3958 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.74 % Allowed : 11.42 % Favored : 86.84 % 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: 2.16 (0.21), residues: 1780 helix: 2.34 (0.15), residues: 1208 sheet: -1.06 (0.72), residues: 44 loop : -0.51 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 102 HIS 0.005 0.001 HIS A 43 PHE 0.028 0.002 PHE D 128 TYR 0.010 0.001 TYR A 456 ARG 0.005 0.000 ARG A 773 *********************** 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 171 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 144 time to evaluate : 1.886 Fit side-chains revert: symmetry clash REVERT: D 6 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.7021 (pp) outliers start: 27 outliers final: 16 residues processed: 162 average time/residue: 0.3040 time to fit residues: 76.0916 Evaluate side-chains 158 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 1.654 ------------------------------------------------------------------------------- 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 153 MET Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 618 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 159 optimal weight: 0.3980 chunk 105 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 118 optimal weight: 0.0570 chunk 115 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19118 Z= 0.162 Angle : 0.473 10.315 26610 Z= 0.268 Chirality : 0.034 0.149 2954 Planarity : 0.003 0.036 2768 Dihedral : 22.370 86.876 3958 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.55 % Allowed : 11.74 % Favored : 86.71 % 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: 2.39 (0.21), residues: 1780 helix: 2.53 (0.15), residues: 1212 sheet: -0.80 (0.75), residues: 44 loop : -0.49 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 102 HIS 0.005 0.001 HIS A 43 PHE 0.027 0.001 PHE D 117 TYR 0.009 0.001 TYR D 927 ARG 0.007 0.000 ARG A 773 *********************** 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 175 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 952 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8854 (mt) outliers start: 24 outliers final: 14 residues processed: 165 average time/residue: 0.3166 time to fit residues: 78.8325 Evaluate side-chains 156 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 141 time to evaluate : 1.711 ------------------------------------------------------------------------------- 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 239 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 933 GLU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain D residue 31 THR 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 618 THR Chi-restraints excluded: chain D residue 773 ARG Chi-restraints excluded: chain D residue 933 GLU Chi-restraints excluded: chain D residue 952 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 148 optimal weight: 30.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN A 435 HIS A 914 ASN D 374 ASN D 914 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 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 0.039 19118 Z= 0.206 Angle : 0.500 8.599 26610 Z= 0.281 Chirality : 0.036 0.158 2954 Planarity : 0.004 0.063 2768 Dihedral : 22.429 86.769 3958 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.68 % Allowed : 12.00 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.39 (0.21), residues: 1780 helix: 2.51 (0.15), residues: 1208 sheet: -0.77 (0.74), residues: 44 loop : -0.44 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 102 HIS 0.004 0.001 HIS A 43 PHE 0.035 0.002 PHE D 128 TYR 0.019 0.001 TYR A 141 ARG 0.009 0.000 ARG D 901 *********************** 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 168 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 142 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 952 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8871 (mt) REVERT: D 952 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8876 (mt) outliers start: 26 outliers final: 18 residues processed: 159 average time/residue: 0.3156 time to fit residues: 75.6094 Evaluate side-chains 160 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 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 239 THR Chi-restraints excluded: chain A residue 379 ASP 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 A residue 952 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 618 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 171 optimal weight: 6.9990 chunk 180 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 159 optimal weight: 0.6980 chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19118 Z= 0.238 Angle : 0.529 17.557 26610 Z= 0.291 Chirality : 0.037 0.160 2954 Planarity : 0.004 0.059 2768 Dihedral : 22.448 86.709 3958 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.68 % Allowed : 12.32 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.27 (0.21), residues: 1780 helix: 2.43 (0.15), residues: 1206 sheet: -0.78 (0.73), residues: 44 loop : -0.49 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 102 HIS 0.004 0.001 HIS A 43 PHE 0.028 0.002 PHE D 117 TYR 0.021 0.001 TYR D 141 ARG 0.008 0.000 ARG A 901 *********************** 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 166 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 952 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8892 (mt) REVERT: D 773 ARG cc_start: 0.6188 (OUTLIER) cc_final: 0.5967 (ttp80) REVERT: D 952 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8888 (mt) outliers start: 26 outliers final: 19 residues processed: 156 average time/residue: 0.3111 time to fit residues: 73.9389 Evaluate side-chains 159 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 379 ASP 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 A residue 952 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 37 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 379 ASP Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 756 THR Chi-restraints excluded: chain D residue 773 ARG Chi-restraints excluded: chain D residue 932 VAL Chi-restraints excluded: chain D residue 933 GLU Chi-restraints excluded: chain D residue 952 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.7980 chunk 186 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 129 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 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 435 HIS A 914 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19118 Z= 0.191 Angle : 0.505 13.201 26610 Z= 0.281 Chirality : 0.036 0.156 2954 Planarity : 0.004 0.042 2768 Dihedral : 22.401 86.611 3958 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.55 % Allowed : 12.45 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.37 (0.21), residues: 1780 helix: 2.49 (0.15), residues: 1208 sheet: -0.62 (0.73), residues: 44 loop : -0.44 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 102 HIS 0.003 0.001 HIS A 43 PHE 0.029 0.002 PHE D 117 TYR 0.011 0.001 TYR D 863 ARG 0.008 0.000 ARG A 901 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 952 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8878 (mt) REVERT: D 773 ARG cc_start: 0.6153 (OUTLIER) cc_final: 0.5928 (ttp80) REVERT: D 952 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8871 (mt) outliers start: 24 outliers final: 19 residues processed: 155 average time/residue: 0.2951 time to fit residues: 70.9313 Evaluate side-chains 161 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 139 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 379 ASP 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 A residue 952 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 37 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 379 ASP Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 756 THR Chi-restraints excluded: chain D residue 773 ARG Chi-restraints excluded: chain D residue 932 VAL Chi-restraints excluded: chain D residue 933 GLU Chi-restraints excluded: chain D residue 952 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 159 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.218542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.202834 restraints weight = 20124.059| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 0.84 r_work: 0.4181 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4148 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19118 Z= 0.189 Angle : 0.503 11.840 26610 Z= 0.280 Chirality : 0.036 0.161 2954 Planarity : 0.004 0.040 2768 Dihedral : 22.382 86.522 3958 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.42 % Allowed : 12.52 % Favored : 86.06 % 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: 2.40 (0.21), residues: 1780 helix: 2.51 (0.15), residues: 1208 sheet: -0.51 (0.74), residues: 44 loop : -0.43 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 102 HIS 0.003 0.001 HIS A 43 PHE 0.028 0.002 PHE D 117 TYR 0.012 0.001 TYR D 141 ARG 0.007 0.000 ARG A 901 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3827.42 seconds wall clock time: 70 minutes 54.86 seconds (4254.86 seconds total)