Starting phenix.real_space_refine on Thu Mar 5 03:37:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qd4_13906/03_2026/7qd4_13906.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qd4_13906/03_2026/7qd4_13906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qd4_13906/03_2026/7qd4_13906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qd4_13906/03_2026/7qd4_13906.map" model { file = "/net/cci-nas-00/data/ceres_data/7qd4_13906/03_2026/7qd4_13906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qd4_13906/03_2026/7qd4_13906.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.002 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 216 5.49 5 S 46 5.16 5 C 11474 2.51 5 N 3400 2.21 5 O 3982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19118 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 7345 Classifications: {'peptide': 908} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 27, 'TRANS': 880} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1110 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain: "C" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1104 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain: "E" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1110 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain: "F" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1104 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain: "D" Number of atoms: 7345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 7345 Classifications: {'peptide': 908} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 27, 'TRANS': 880} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 4.09, per 1000 atoms: 0.21 Number of scatterers: 19118 At special positions: 0 Unit cell: (108.006, 187.67, 152.434, 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 216 15.00 O 3982 8.00 N 3400 7.00 C 11474 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 680.0 milliseconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3436 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 69.7% alpha, 2.2% beta 102 base pairs and 175 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 Processing helix chain 'A' and resid 24 through 29 removed outlier: 3.736A pdb=" N THR A 28 " --> pdb=" O TRP A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 41 Processing helix chain 'A' and resid 45 through 61 removed outlier: 3.900A pdb=" N ARG A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 85 removed outlier: 3.519A pdb=" N VAL A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 removed outlier: 3.751A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 113 removed outlier: 4.254A pdb=" N LEU A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 136 removed outlier: 3.506A pdb=" N LYS A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.549A pdb=" N MET A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 184 removed outlier: 3.730A pdb=" N ILE A 163 " --> pdb=" O ALA A 159 " (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 318 removed outlier: 3.924A pdb=" N GLN A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 343 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 355 through 370 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.864A pdb=" N ASN A 382 " --> pdb=" O ASP A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.558A pdb=" N VAL A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 399 Processing helix chain 'A' and resid 407 through 424 Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.917A 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: 3.506A pdb=" N TYR A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) removed outlier: 3.541A 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 494 through 499 removed outlier: 3.677A pdb=" N VAL A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 530 Processing helix chain 'A' and resid 557 through 569 removed outlier: 4.344A 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 618 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 633 through 645 removed outlier: 3.557A pdb=" N MET A 645 " --> pdb=" O SER A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 664 removed outlier: 3.593A pdb=" N GLN A 664 " --> pdb=" O PHE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 4.132A pdb=" N TRP A 670 " --> pdb=" O LEU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 738 removed outlier: 4.285A pdb=" N VAL A 732 " --> pdb=" O ASP A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 766 removed outlier: 3.510A pdb=" N ALA A 761 " --> pdb=" O ASP A 757 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU A 762 " --> pdb=" O GLN A 758 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS A 764 " --> pdb=" O PHE A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 823 removed outlier: 5.339A pdb=" N GLU A 812 " --> pdb=" O LYS A 808 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ASP A 813 " --> pdb=" O GLU A 809 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG A 816 " --> pdb=" O GLU A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 834 removed outlier: 4.004A pdb=" N LYS A 834 " --> pdb=" O LEU A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 841 through 866 removed outlier: 3.850A 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 902 through 938 Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 24 through 29 removed outlier: 3.713A pdb=" N THR D 28 " --> pdb=" O TRP D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 41 Processing helix chain 'D' and resid 45 through 61 removed outlier: 3.655A pdb=" N ARG D 49 " --> pdb=" O ARG D 45 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 85 removed outlier: 3.741A pdb=" N VAL D 80 " --> pdb=" O VAL D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 94 removed outlier: 3.712A pdb=" N VAL D 93 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 113 removed outlier: 4.265A pdb=" N LEU D 101 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TRP D 102 " --> pdb=" O GLY D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 136 removed outlier: 4.433A pdb=" N GLN D 131 " --> pdb=" O GLN D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 153 removed outlier: 3.545A pdb=" N MET D 153 " --> pdb=" O THR D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 184 removed outlier: 3.790A 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: 3.922A pdb=" N GLN D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 343 Processing helix chain 'D' and resid 345 through 354 Processing helix chain 'D' and resid 355 through 370 Processing helix chain 'D' and resid 377 through 382 removed outlier: 3.868A pdb=" N ASN D 382 " --> pdb=" O ASP D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 390 removed outlier: 3.544A pdb=" N VAL D 388 " --> pdb=" O ARG D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 399 Processing helix chain 'D' and resid 407 through 424 Processing helix chain 'D' and resid 441 through 446 removed outlier: 3.907A pdb=" N TYR D 446 " --> pdb=" O GLN D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 471 Processing helix chain 'D' and resid 484 through 489 removed outlier: 3.632A pdb=" N TYR D 488 " --> pdb=" O ALA D 484 " (cutoff:3.500A) removed outlier: 3.643A 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 494 through 499 removed outlier: 3.658A pdb=" N VAL D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 530 Processing helix chain 'D' and resid 557 through 569 removed outlier: 4.358A 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 618 Processing helix chain 'D' and resid 621 through 629 Processing helix chain 'D' and resid 633 through 645 removed outlier: 3.558A pdb=" N MET D 645 " --> pdb=" O SER D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 664 removed outlier: 3.576A pdb=" N GLN D 664 " --> pdb=" O PHE D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 671 removed outlier: 4.198A pdb=" N TRP D 670 " --> pdb=" O LEU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 728 through 738 removed outlier: 4.263A pdb=" N VAL D 732 " --> pdb=" O ASP D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 766 removed outlier: 3.659A pdb=" N ALA D 761 " --> pdb=" O ASP D 757 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 762 " --> pdb=" O GLN D 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 804 through 823 removed outlier: 5.420A pdb=" N GLU D 812 " --> pdb=" O LYS D 808 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ASP D 813 " --> pdb=" O GLU D 809 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG D 816 " --> pdb=" O GLU D 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 827 through 834 removed outlier: 4.001A pdb=" N LYS D 834 " --> pdb=" O LEU D 830 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 837 No H-bonds generated for 'chain 'D' and resid 835 through 837' Processing helix chain 'D' and resid 841 through 866 removed outlier: 3.843A pdb=" N ALA D 845 " --> pdb=" O GLN D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 891 Processing helix chain 'D' and resid 902 through 938 Processing 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: 7.067A 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 'A' and resid 748 through 750 removed outlier: 6.358A pdb=" N HIS A 748 " --> pdb=" O ALA A 771 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 401 through 403 Processing sheet with id=AA6, first strand: chain 'D' and resid 573 through 574 removed outlier: 7.068A pdb=" N ILE D 573 " --> pdb=" O ASN D 958 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 679 through 683 Processing sheet with id=AA8, first strand: chain 'D' and resid 748 through 750 removed outlier: 6.387A pdb=" N HIS D 748 " --> pdb=" O ALA D 771 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 883 hydrogen bonds defined for protein. 2607 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 256 hydrogen bonds 512 hydrogen bond angles 0 basepair planarities 102 basepair parallelities 175 stacking parallelities Total time for adding SS restraints: 3.86 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4435 1.34 - 1.46: 5382 1.46 - 1.58: 9611 1.58 - 1.70: 428 1.70 - 1.82: 90 Bond restraints: 19946 Sorted by residual: bond pdb=" CG1 ILE A 145 " pdb=" CD1 ILE A 145 " ideal model delta sigma weight residual 1.513 1.434 0.079 3.90e-02 6.57e+02 4.09e+00 bond pdb=" N ARG A 426 " pdb=" CA ARG A 426 " ideal model delta sigma weight residual 1.459 1.480 -0.021 1.15e-02 7.56e+03 3.34e+00 bond pdb=" N GLU A 144 " pdb=" CA GLU A 144 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.23e-02 6.61e+03 3.18e+00 bond pdb=" CB ASN D 914 " pdb=" CG ASN D 914 " ideal model delta sigma weight residual 1.516 1.474 0.042 2.50e-02 1.60e+03 2.81e+00 bond pdb=" CB ASN A 914 " pdb=" CG ASN A 914 " ideal model delta sigma weight residual 1.516 1.475 0.041 2.50e-02 1.60e+03 2.66e+00 ... (remaining 19941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 27147 2.19 - 4.39: 620 4.39 - 6.58: 86 6.58 - 8.78: 29 8.78 - 10.97: 6 Bond angle restraints: 27888 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 110.16 118.82 -8.66 1.48e+00 4.57e-01 3.42e+01 angle pdb=" CA MET A 153 " pdb=" C MET A 153 " pdb=" O MET A 153 " ideal model delta sigma weight residual 119.59 113.62 5.97 1.23e+00 6.61e-01 2.36e+01 angle pdb=" N GLU D 144 " pdb=" CA GLU D 144 " pdb=" CB GLU D 144 " ideal model delta sigma weight residual 110.30 117.39 -7.09 1.54e+00 4.22e-01 2.12e+01 angle pdb=" CA GLU A 144 " pdb=" CB GLU A 144 " pdb=" CG GLU A 144 " ideal model delta sigma weight residual 114.10 122.20 -8.10 2.00e+00 2.50e-01 1.64e+01 angle pdb=" C LYS D 425 " pdb=" N ARG D 426 " pdb=" CA ARG D 426 " ideal model delta sigma weight residual 122.08 127.51 -5.43 1.47e+00 4.63e-01 1.37e+01 ... (remaining 27883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 8854 17.61 - 35.23: 1432 35.23 - 52.84: 840 52.84 - 70.45: 226 70.45 - 88.06: 32 Dihedral angle restraints: 11384 sinusoidal: 6070 harmonic: 5314 Sorted by residual: dihedral pdb=" CA ARG D 942 " pdb=" C ARG D 942 " pdb=" N GLU D 943 " pdb=" CA GLU D 943 " ideal model delta harmonic sigma weight residual -180.00 -157.18 -22.82 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ARG A 942 " pdb=" C ARG A 942 " pdb=" N GLU A 943 " pdb=" CA GLU A 943 " ideal model delta harmonic sigma weight residual -180.00 -158.20 -21.80 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA VAL D 719 " pdb=" C VAL D 719 " pdb=" N LYS D 720 " pdb=" CA LYS D 720 " ideal model delta harmonic sigma weight residual 180.00 162.11 17.89 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 11381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2462 0.053 - 0.105: 523 0.105 - 0.158: 93 0.158 - 0.210: 17 0.210 - 0.263: 3 Chirality restraints: 3098 Sorted by residual: chirality pdb=" CB ILE A 452 " pdb=" CA ILE A 452 " pdb=" CG1 ILE A 452 " pdb=" CG2 ILE A 452 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB ILE D 452 " pdb=" CA ILE D 452 " pdb=" CG1 ILE D 452 " pdb=" CG2 ILE D 452 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA GLU A 419 " pdb=" N GLU A 419 " pdb=" C GLU A 419 " pdb=" CB GLU A 419 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 3095 not shown) Planarity restraints: 2804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 371 " 0.047 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO D 372 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO D 372 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 372 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 371 " -0.046 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO A 372 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 372 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 372 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 426 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C ARG A 426 " -0.041 2.00e-02 2.50e+03 pdb=" O ARG A 426 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS A 427 " 0.014 2.00e-02 2.50e+03 ... (remaining 2801 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2515 2.76 - 3.30: 17100 3.30 - 3.83: 35764 3.83 - 4.37: 41648 4.37 - 4.90: 65199 Nonbonded interactions: 162226 Sorted by model distance: nonbonded pdb=" O MET A 614 " pdb=" OG1 THR A 618 " model vdw 2.227 3.040 nonbonded pdb=" O MET D 614 " pdb=" OG1 THR D 618 " model vdw 2.235 3.040 nonbonded pdb=" OP1 DC F1037 " pdb=" OH TYR D 47 " model vdw 2.285 3.040 nonbonded pdb=" O ILE A 145 " pdb=" OG1 THR A 149 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR A 47 " pdb=" OP1 DC C1037 " model vdw 2.307 3.040 ... (remaining 162221 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.790 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 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 : 0.004 0.079 19946 Z= 0.216 Angle : 0.823 10.974 27888 Z= 0.453 Chirality : 0.046 0.263 3098 Planarity : 0.006 0.070 2804 Dihedral : 22.058 88.065 7948 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.18), residues: 1780 helix: -0.35 (0.13), residues: 1164 sheet: -0.45 (0.84), residues: 44 loop : -0.51 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 872 TYR 0.031 0.002 TYR A 707 PHE 0.036 0.003 PHE A 128 TRP 0.012 0.001 TRP D 670 HIS 0.005 0.001 HIS D 567 Details of bonding type rmsd covalent geometry : bond 0.00446 (19946) covalent geometry : angle 0.82270 (27888) hydrogen bonds : bond 0.09968 ( 1139) hydrogen bonds : angle 5.26449 ( 3119) *********************** 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 184 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.636 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.8255 time to fit residues: 166.0635 Evaluate side-chains 130 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN A 368 GLN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 975 ASN D 318 ASN D 368 GLN ** D 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 GLN D 914 ASN D 958 ASN D 975 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.213757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.174976 restraints weight = 22741.334| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.06 r_work: 0.3569 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 19946 Z= 0.219 Angle : 0.583 8.496 27888 Z= 0.329 Chirality : 0.039 0.164 3098 Planarity : 0.005 0.065 2804 Dihedral : 24.993 87.377 4358 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.42 % Allowed : 8.39 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.20), residues: 1780 helix: 1.07 (0.15), residues: 1166 sheet: -0.20 (0.88), residues: 44 loop : -0.31 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 942 TYR 0.018 0.002 TYR D 488 PHE 0.017 0.002 PHE A 965 TRP 0.009 0.001 TRP A 670 HIS 0.005 0.001 HIS D 418 Details of bonding type rmsd covalent geometry : bond 0.00497 (19946) covalent geometry : angle 0.58326 (27888) hydrogen bonds : bond 0.04619 ( 1139) hydrogen bonds : angle 4.02751 ( 3119) *********************** 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 166 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.7574 (mp-120) cc_final: 0.7182 (mp10) REVERT: D 314 ILE cc_start: 0.8774 (tt) cc_final: 0.8489 (pt) REVERT: D 681 MET cc_start: 0.4052 (OUTLIER) cc_final: 0.3807 (ptp) REVERT: D 844 LEU cc_start: 0.6656 (tp) cc_final: 0.6317 (mm) outliers start: 22 outliers final: 8 residues processed: 152 average time/residue: 0.7320 time to fit residues: 123.0056 Evaluate side-chains 130 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 681 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 175 optimal weight: 0.0670 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 252 GLN A 368 GLN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 GLN D 368 GLN ** D 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.214639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.175554 restraints weight = 22852.378| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 2.06 r_work: 0.3569 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19946 Z= 0.170 Angle : 0.530 8.249 27888 Z= 0.304 Chirality : 0.037 0.154 3098 Planarity : 0.004 0.043 2804 Dihedral : 24.874 86.175 4358 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.42 % Allowed : 11.23 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.20), residues: 1780 helix: 1.65 (0.15), residues: 1168 sheet: -0.11 (0.89), residues: 44 loop : -0.12 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 390 TYR 0.015 0.001 TYR D 634 PHE 0.013 0.002 PHE D 965 TRP 0.007 0.001 TRP A 643 HIS 0.003 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00379 (19946) covalent geometry : angle 0.52958 (27888) hydrogen bonds : bond 0.04078 ( 1139) hydrogen bonds : angle 3.73866 ( 3119) *********************** 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 152 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.7562 (mp-120) cc_final: 0.7099 (mp10) REVERT: A 603 GLN cc_start: 0.7706 (tp-100) cc_final: 0.7286 (mp10) REVERT: A 762 LEU cc_start: 0.8692 (mt) cc_final: 0.8474 (tt) REVERT: D 150 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6410 (mm) REVERT: D 844 LEU cc_start: 0.6559 (tp) cc_final: 0.6168 (mm) outliers start: 22 outliers final: 8 residues processed: 138 average time/residue: 0.7310 time to fit residues: 111.9640 Evaluate side-chains 121 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 874 GLN Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 655 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 192 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 6 optimal weight: 0.1980 chunk 130 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN D 368 GLN ** D 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 878 ASN ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.215049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.178642 restraints weight = 22729.762| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 1.93 r_work: 0.3610 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19946 Z= 0.154 Angle : 0.512 7.696 27888 Z= 0.294 Chirality : 0.036 0.145 3098 Planarity : 0.004 0.042 2804 Dihedral : 24.754 86.033 4358 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.87 % Allowed : 12.77 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.20), residues: 1780 helix: 1.92 (0.15), residues: 1172 sheet: 0.05 (0.89), residues: 44 loop : 0.01 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 390 TYR 0.019 0.001 TYR A 141 PHE 0.018 0.002 PHE A 128 TRP 0.007 0.001 TRP A 643 HIS 0.005 0.001 HIS D 525 Details of bonding type rmsd covalent geometry : bond 0.00342 (19946) covalent geometry : angle 0.51240 (27888) hydrogen bonds : bond 0.03873 ( 1139) hydrogen bonds : angle 3.58196 ( 3119) *********************** 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 152 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.7599 (mp-120) cc_final: 0.7163 (mp10) REVERT: A 603 GLN cc_start: 0.7705 (tp-100) cc_final: 0.7311 (mp10) REVERT: A 906 GLN cc_start: 0.8769 (mm110) cc_final: 0.8492 (mm-40) REVERT: D 150 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6415 (mm) REVERT: D 844 LEU cc_start: 0.6648 (tp) cc_final: 0.6268 (mm) outliers start: 29 outliers final: 12 residues processed: 137 average time/residue: 0.7187 time to fit residues: 109.2125 Evaluate side-chains 127 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 874 GLN Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 655 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 41 optimal weight: 0.9980 chunk 40 optimal weight: 0.0670 chunk 185 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 88 optimal weight: 0.1980 chunk 109 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN D 368 GLN D 444 HIS ** D 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.215272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.176714 restraints weight = 22728.110| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 2.08 r_work: 0.3581 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19946 Z= 0.145 Angle : 0.503 7.218 27888 Z= 0.290 Chirality : 0.035 0.141 3098 Planarity : 0.003 0.041 2804 Dihedral : 24.697 86.305 4358 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.61 % Allowed : 13.87 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.20), residues: 1780 helix: 2.09 (0.15), residues: 1172 sheet: 0.07 (0.87), residues: 44 loop : 0.05 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 942 TYR 0.031 0.001 TYR D 141 PHE 0.013 0.001 PHE D 892 TRP 0.006 0.001 TRP A 643 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00319 (19946) covalent geometry : angle 0.50316 (27888) hydrogen bonds : bond 0.03772 ( 1139) hydrogen bonds : angle 3.51484 ( 3119) *********************** 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 147 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.7588 (mp-120) cc_final: 0.7164 (mp10) REVERT: A 134 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.6728 (mpp) REVERT: A 150 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6322 (mm) REVERT: A 603 GLN cc_start: 0.7788 (tp-100) cc_final: 0.7282 (mp10) REVERT: A 906 GLN cc_start: 0.8814 (mm110) cc_final: 0.8511 (mm110) REVERT: D 150 LEU cc_start: 0.6695 (OUTLIER) cc_final: 0.6412 (mm) outliers start: 25 outliers final: 9 residues processed: 138 average time/residue: 0.7227 time to fit residues: 110.5350 Evaluate side-chains 126 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 367 LYS Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 655 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 158 optimal weight: 0.0980 chunk 57 optimal weight: 0.9980 chunk 117 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 159 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN A 444 HIS ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN D 368 GLN ** D 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.215167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.176684 restraints weight = 22630.804| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.04 r_work: 0.3576 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19946 Z= 0.150 Angle : 0.510 7.605 27888 Z= 0.293 Chirality : 0.036 0.139 3098 Planarity : 0.003 0.043 2804 Dihedral : 24.677 86.309 4358 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.55 % Allowed : 14.71 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.21), residues: 1780 helix: 2.17 (0.15), residues: 1168 sheet: 0.16 (0.86), residues: 44 loop : 0.13 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 942 TYR 0.039 0.001 TYR D 141 PHE 0.020 0.001 PHE A 128 TRP 0.006 0.001 TRP A 356 HIS 0.003 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00333 (19946) covalent geometry : angle 0.51025 (27888) hydrogen bonds : bond 0.03822 ( 1139) hydrogen bonds : angle 3.51694 ( 3119) *********************** 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 144 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.7585 (mp-120) cc_final: 0.7114 (mp10) REVERT: A 150 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6290 (mm) REVERT: A 359 MET cc_start: 0.8069 (ttp) cc_final: 0.7700 (tmt) REVERT: A 603 GLN cc_start: 0.7777 (tp-100) cc_final: 0.7256 (mp10) REVERT: A 765 LEU cc_start: 0.8321 (pp) cc_final: 0.8079 (tt) REVERT: A 906 GLN cc_start: 0.8826 (mm110) cc_final: 0.8542 (mm110) REVERT: D 150 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6477 (mm) outliers start: 24 outliers final: 8 residues processed: 133 average time/residue: 0.7411 time to fit residues: 109.1397 Evaluate side-chains 127 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 655 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 35 optimal weight: 0.0370 chunk 113 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 164 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN D 368 GLN ** D 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.217384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.177720 restraints weight = 22898.595| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 2.17 r_work: 0.3571 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19946 Z= 0.200 Angle : 0.549 7.932 27888 Z= 0.311 Chirality : 0.038 0.152 3098 Planarity : 0.004 0.043 2804 Dihedral : 24.811 85.476 4358 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.81 % Allowed : 15.68 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.21), residues: 1780 helix: 2.07 (0.15), residues: 1164 sheet: 0.35 (0.88), residues: 44 loop : 0.08 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 942 TYR 0.017 0.001 TYR A 634 PHE 0.015 0.002 PHE D 965 TRP 0.007 0.001 TRP D 923 HIS 0.004 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00457 (19946) covalent geometry : angle 0.54880 (27888) hydrogen bonds : bond 0.04286 ( 1139) hydrogen bonds : angle 3.65168 ( 3119) *********************** 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 147 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6302 (mm) REVERT: A 359 MET cc_start: 0.8069 (ttp) cc_final: 0.7623 (tmt) REVERT: A 603 GLN cc_start: 0.7819 (tp-100) cc_final: 0.7273 (mp10) REVERT: A 894 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7377 (mt0) REVERT: A 906 GLN cc_start: 0.8844 (mm110) cc_final: 0.8535 (mm110) REVERT: D 45 ARG cc_start: 0.6342 (OUTLIER) cc_final: 0.4440 (ttm-80) REVERT: D 150 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6504 (mm) REVERT: D 844 LEU cc_start: 0.6488 (tp) cc_final: 0.6085 (mm) REVERT: D 894 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7381 (mt0) outliers start: 28 outliers final: 13 residues processed: 139 average time/residue: 0.7127 time to fit residues: 110.0393 Evaluate side-chains 137 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 874 GLN Chi-restraints excluded: chain A residue 894 GLN Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 367 LYS Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 894 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 162 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 148 optimal weight: 0.6980 chunk 165 optimal weight: 0.4980 chunk 104 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 110 optimal weight: 0.0370 chunk 52 optimal weight: 4.9990 chunk 87 optimal weight: 0.2980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN A 661 GLN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN D 368 GLN ** D 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.216106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.175093 restraints weight = 22749.991| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.34 r_work: 0.3585 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19946 Z= 0.132 Angle : 0.511 8.206 27888 Z= 0.291 Chirality : 0.035 0.137 3098 Planarity : 0.003 0.043 2804 Dihedral : 24.633 87.357 4358 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.48 % Allowed : 16.77 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.21), residues: 1780 helix: 2.25 (0.15), residues: 1166 sheet: 0.54 (0.87), residues: 44 loop : 0.17 (0.28), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 470 TYR 0.015 0.001 TYR D 141 PHE 0.036 0.002 PHE A 128 TRP 0.008 0.001 TRP A 643 HIS 0.002 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00283 (19946) covalent geometry : angle 0.51117 (27888) hydrogen bonds : bond 0.03683 ( 1139) hydrogen bonds : angle 3.49706 ( 3119) *********************** 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 150 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6296 (mm) REVERT: A 359 MET cc_start: 0.7946 (ttp) cc_final: 0.7628 (tmt) REVERT: A 603 GLN cc_start: 0.7711 (tp-100) cc_final: 0.7270 (mp10) REVERT: A 765 LEU cc_start: 0.8311 (pp) cc_final: 0.8032 (tt) REVERT: A 906 GLN cc_start: 0.8779 (mm110) cc_final: 0.8466 (mm110) REVERT: D 45 ARG cc_start: 0.6107 (OUTLIER) cc_final: 0.4378 (ttm-80) REVERT: D 60 ARG cc_start: 0.6403 (mtm-85) cc_final: 0.5372 (mtm180) REVERT: D 117 PHE cc_start: 0.7645 (t80) cc_final: 0.6892 (m-80) REVERT: D 150 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6515 (mm) outliers start: 23 outliers final: 9 residues processed: 143 average time/residue: 0.7170 time to fit residues: 113.6695 Evaluate side-chains 128 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 655 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 125 optimal weight: 0.7980 chunk 6 optimal weight: 0.0470 chunk 156 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN D 368 GLN ** D 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.219253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.179255 restraints weight = 22768.507| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 2.24 r_work: 0.3598 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19946 Z= 0.155 Angle : 0.536 8.282 27888 Z= 0.304 Chirality : 0.036 0.159 3098 Planarity : 0.003 0.043 2804 Dihedral : 24.668 85.396 4358 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.61 % Allowed : 16.77 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.21), residues: 1780 helix: 2.21 (0.15), residues: 1166 sheet: 0.61 (0.88), residues: 44 loop : 0.18 (0.29), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 470 TYR 0.051 0.001 TYR D 141 PHE 0.013 0.001 PHE A 892 TRP 0.006 0.001 TRP D 923 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00345 (19946) covalent geometry : angle 0.53598 (27888) hydrogen bonds : bond 0.03916 ( 1139) hydrogen bonds : angle 3.57275 ( 3119) *********************** 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 148 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6331 (mm) REVERT: A 603 GLN cc_start: 0.7810 (tp-100) cc_final: 0.7270 (mp10) REVERT: A 894 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7363 (mt0) REVERT: A 906 GLN cc_start: 0.8815 (mm110) cc_final: 0.8512 (mm110) REVERT: D 45 ARG cc_start: 0.6334 (OUTLIER) cc_final: 0.4902 (ttm-80) REVERT: D 60 ARG cc_start: 0.6482 (mtm-85) cc_final: 0.5485 (mtm180) REVERT: D 117 PHE cc_start: 0.7616 (t80) cc_final: 0.6942 (m-80) REVERT: D 150 LEU cc_start: 0.6760 (OUTLIER) cc_final: 0.6479 (mm) REVERT: D 894 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7347 (mt0) REVERT: D 942 ARG cc_start: 0.7276 (mtp85) cc_final: 0.7059 (ttp80) outliers start: 25 outliers final: 11 residues processed: 142 average time/residue: 0.7341 time to fit residues: 115.5107 Evaluate side-chains 131 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 894 GLN Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 894 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 2 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 6 optimal weight: 0.0470 chunk 127 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 136 optimal weight: 0.4980 chunk 4 optimal weight: 7.9990 chunk 194 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 overall best weight: 0.6482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN A 368 GLN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN D 368 GLN ** D 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.215321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.176752 restraints weight = 22731.129| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.13 r_work: 0.3581 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19946 Z= 0.148 Angle : 0.534 8.446 27888 Z= 0.303 Chirality : 0.036 0.156 3098 Planarity : 0.004 0.042 2804 Dihedral : 24.626 85.949 4358 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.29 % Allowed : 17.35 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.21), residues: 1780 helix: 2.22 (0.15), residues: 1166 sheet: 0.69 (0.88), residues: 44 loop : 0.19 (0.29), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 466 TYR 0.049 0.001 TYR A 141 PHE 0.042 0.002 PHE A 128 TRP 0.006 0.001 TRP A 643 HIS 0.003 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00327 (19946) covalent geometry : angle 0.53446 (27888) hydrogen bonds : bond 0.03833 ( 1139) hydrogen bonds : angle 3.55905 ( 3119) ********************** 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 138 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6307 (mm) REVERT: A 603 GLN cc_start: 0.7781 (tp-100) cc_final: 0.7302 (mp10) REVERT: A 894 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7383 (mt0) REVERT: A 906 GLN cc_start: 0.8816 (mm110) cc_final: 0.8511 (mm110) REVERT: D 45 ARG cc_start: 0.6143 (OUTLIER) cc_final: 0.4487 (ttm-80) REVERT: D 60 ARG cc_start: 0.6505 (mtm-85) cc_final: 0.5511 (mtm180) REVERT: D 117 PHE cc_start: 0.7653 (t80) cc_final: 0.7015 (m-80) REVERT: D 150 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6518 (mm) REVERT: D 894 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7350 (mt0) outliers start: 20 outliers final: 12 residues processed: 133 average time/residue: 0.6949 time to fit residues: 102.3579 Evaluate side-chains 131 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 894 GLN Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 367 LYS Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 894 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 199 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 120 optimal weight: 8.9990 chunk 152 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 177 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 163 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 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 368 GLN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN ** D 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.218741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.176910 restraints weight = 22854.416| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 2.48 r_work: 0.3560 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19946 Z= 0.168 Angle : 0.546 8.450 27888 Z= 0.310 Chirality : 0.037 0.161 3098 Planarity : 0.004 0.042 2804 Dihedral : 24.660 86.331 4358 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.23 % Allowed : 17.68 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.21), residues: 1780 helix: 2.16 (0.15), residues: 1166 sheet: 0.72 (0.89), residues: 44 loop : 0.17 (0.29), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 466 TYR 0.052 0.001 TYR D 141 PHE 0.013 0.002 PHE A 892 TRP 0.007 0.001 TRP D 356 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00380 (19946) covalent geometry : angle 0.54592 (27888) hydrogen bonds : bond 0.04041 ( 1139) hydrogen bonds : angle 3.61347 ( 3119) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5719.69 seconds wall clock time: 99 minutes 4.33 seconds (5944.33 seconds total)