Starting phenix.real_space_refine on Mon Jun 16 16:59:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qd4_13906/06_2025/7qd4_13906.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qd4_13906/06_2025/7qd4_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_13906/06_2025/7qd4_13906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qd4_13906/06_2025/7qd4_13906.map" model { file = "/net/cci-nas-00/data/ceres_data/7qd4_13906/06_2025/7qd4_13906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qd4_13906/06_2025/7qd4_13906.cif" } resolution = 2.9 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= 1.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'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: 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: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 12.97, per 1000 atoms: 0.68 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: 5.64 Conformation dependent library (CDL) restraints added in 2.3 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 8 sheets defined 69.7% alpha, 2.2% beta 102 base pairs and 175 stacking pairs defined. Time for finding SS restraints: 9.77 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: 12.63 Time building geometry restraints manager: 6.11 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: 0.01 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: 12.760 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: 0.040 Extract box with map and model: 1.040 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 59.140 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.110 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:16.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.740 ------------------------------------------------------------------------------- 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 (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: -0.77 (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 TRP 0.012 0.001 TRP D 670 HIS 0.005 0.001 HIS D 567 PHE 0.036 0.003 PHE A 128 TYR 0.031 0.002 TYR A 707 ARG 0.006 0.001 ARG D 872 Details of bonding type rmsd hydrogen bonds : bond 0.09968 ( 1139) hydrogen bonds : angle 5.26449 ( 3119) covalent geometry : bond 0.00446 (19946) covalent geometry : angle 0.82270 (27888) *********************** 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 : 1.634 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 1.6659 time to fit residues: 336.9525 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 : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 2.9990 chunk 151 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 95 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 318 ASN A 368 GLN A 661 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 975 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.215983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.174896 restraints weight = 22857.385| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 2.36 r_work: 0.3573 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19946 Z= 0.167 Angle : 0.543 8.196 27888 Z= 0.310 Chirality : 0.037 0.150 3098 Planarity : 0.004 0.050 2804 Dihedral : 24.840 88.578 4358 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.29 % Allowed : 8.06 % Favored : 90.65 % 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: 0.96 (0.20), residues: 1780 helix: 1.18 (0.15), residues: 1170 sheet: -0.21 (0.87), residues: 44 loop : -0.29 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 670 HIS 0.003 0.001 HIS D 183 PHE 0.016 0.002 PHE D 892 TYR 0.018 0.001 TYR D 488 ARG 0.006 0.001 ARG A 942 Details of bonding type rmsd hydrogen bonds : bond 0.04124 ( 1139) hydrogen bonds : angle 3.92651 ( 3119) covalent geometry : bond 0.00371 (19946) covalent geometry : angle 0.54321 (27888) *********************** 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: 20 poor density : 146 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.7461 (mp-120) cc_final: 0.7070 (mp10) REVERT: D 681 MET cc_start: 0.3881 (OUTLIER) cc_final: 0.3593 (ptp) REVERT: D 933 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7526 (pp20) outliers start: 20 outliers final: 6 residues processed: 152 average time/residue: 1.5910 time to fit residues: 268.4838 Evaluate side-chains 130 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 1.815 ------------------------------------------------------------------------------- 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 D residue 144 GLU 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 139 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 177 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN A 318 ASN 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 252 GLN D 368 GLN ** D 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 878 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.214658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.175820 restraints weight = 22612.440| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 2.10 r_work: 0.3562 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19946 Z= 0.177 Angle : 0.534 7.841 27888 Z= 0.305 Chirality : 0.037 0.144 3098 Planarity : 0.004 0.046 2804 Dihedral : 24.840 86.581 4358 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.55 % Allowed : 10.71 % Favored : 87.74 % 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: 1.54 (0.20), residues: 1780 helix: 1.67 (0.15), residues: 1168 sheet: -0.15 (0.88), residues: 44 loop : -0.13 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 670 HIS 0.004 0.001 HIS A 418 PHE 0.015 0.002 PHE D 965 TYR 0.016 0.001 TYR A 634 ARG 0.004 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 1139) hydrogen bonds : angle 3.73607 ( 3119) covalent geometry : bond 0.00396 (19946) covalent geometry : angle 0.53350 (27888) *********************** 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 159 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.7598 (mp-120) cc_final: 0.7141 (mp10) REVERT: D 121 TYR cc_start: 0.7160 (m-80) cc_final: 0.6892 (m-80) REVERT: D 150 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6408 (mm) REVERT: D 844 LEU cc_start: 0.6595 (tp) cc_final: 0.6189 (mm) outliers start: 24 outliers final: 8 residues processed: 145 average time/residue: 1.4942 time to fit residues: 241.7066 Evaluate side-chains 128 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 1.620 ------------------------------------------------------------------------------- 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 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 655 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 60 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 165 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 20 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.4618 r_free = 0.4618 target = 0.216021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.169673 restraints weight = 22738.707| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 2.35 r_work: 0.3589 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19946 Z= 0.143 Angle : 0.503 7.840 27888 Z= 0.289 Chirality : 0.035 0.156 3098 Planarity : 0.003 0.042 2804 Dihedral : 24.688 86.597 4358 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.55 % Allowed : 12.52 % Favored : 85.94 % 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: 1.95 (0.20), residues: 1780 helix: 1.99 (0.15), residues: 1172 sheet: -0.11 (0.88), residues: 44 loop : 0.00 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 643 HIS 0.004 0.001 HIS D 525 PHE 0.018 0.001 PHE A 128 TYR 0.020 0.001 TYR A 141 ARG 0.004 0.000 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 1139) hydrogen bonds : angle 3.52869 ( 3119) covalent geometry : bond 0.00311 (19946) covalent geometry : angle 0.50252 (27888) *********************** 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 151 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.7532 (mp-120) cc_final: 0.7119 (mp10) REVERT: D 150 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6413 (mm) outliers start: 24 outliers final: 6 residues processed: 137 average time/residue: 1.4925 time to fit residues: 228.0144 Evaluate side-chains 124 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 150 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 199 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 171 optimal weight: 0.6980 chunk 180 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 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 311 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 = 0.4591 r_free = 0.4591 target = 0.212998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.172477 restraints weight = 22763.974| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 2.24 r_work: 0.3535 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 19946 Z= 0.209 Angle : 0.549 6.991 27888 Z= 0.312 Chirality : 0.038 0.159 3098 Planarity : 0.004 0.043 2804 Dihedral : 24.855 85.291 4358 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.74 % Allowed : 14.13 % Favored : 84.13 % 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: 1.86 (0.20), residues: 1780 helix: 1.91 (0.15), residues: 1166 sheet: 0.03 (0.89), residues: 44 loop : -0.02 (0.28), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 356 HIS 0.005 0.001 HIS A 418 PHE 0.015 0.002 PHE A 965 TYR 0.033 0.002 TYR D 141 ARG 0.003 0.000 ARG A 909 Details of bonding type rmsd hydrogen bonds : bond 0.04337 ( 1139) hydrogen bonds : angle 3.69503 ( 3119) covalent geometry : bond 0.00477 (19946) covalent geometry : angle 0.54861 (27888) *********************** 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 158 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.7683 (mp-120) cc_final: 0.7269 (mp10) REVERT: A 150 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6317 (mm) REVERT: A 603 GLN cc_start: 0.7734 (tp-100) cc_final: 0.7300 (mp10) REVERT: A 765 LEU cc_start: 0.8382 (pp) cc_final: 0.8139 (tt) REVERT: A 906 GLN cc_start: 0.8828 (mm110) cc_final: 0.8569 (mm110) REVERT: D 150 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6486 (mm) REVERT: D 844 LEU cc_start: 0.6543 (tp) cc_final: 0.6152 (mm) outliers start: 27 outliers final: 7 residues processed: 145 average time/residue: 1.6039 time to fit residues: 260.3156 Evaluate side-chains 127 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 430 HIS 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 121 optimal weight: 5.9990 chunk 89 optimal weight: 0.0970 chunk 67 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 160 optimal weight: 10.0000 chunk 197 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 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 311 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.213806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.173853 restraints weight = 22767.271| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 2.22 r_work: 0.3549 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19946 Z= 0.176 Angle : 0.529 7.817 27888 Z= 0.302 Chirality : 0.037 0.143 3098 Planarity : 0.004 0.042 2804 Dihedral : 24.779 85.588 4358 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.19 % Allowed : 14.26 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.01 (0.20), residues: 1780 helix: 2.02 (0.15), residues: 1168 sheet: 0.14 (0.89), residues: 44 loop : 0.05 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 356 HIS 0.003 0.001 HIS D 183 PHE 0.019 0.002 PHE A 128 TYR 0.030 0.001 TYR D 141 ARG 0.003 0.000 ARG D 942 Details of bonding type rmsd hydrogen bonds : bond 0.04070 ( 1139) hydrogen bonds : angle 3.59155 ( 3119) covalent geometry : bond 0.00397 (19946) covalent geometry : angle 0.52885 (27888) *********************** 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 162 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6294 (mm) REVERT: A 603 GLN cc_start: 0.7754 (tp-100) cc_final: 0.7315 (mp10) REVERT: A 894 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7268 (mt0) REVERT: A 906 GLN cc_start: 0.8811 (mm110) cc_final: 0.8531 (mm110) REVERT: D 45 ARG cc_start: 0.6335 (OUTLIER) cc_final: 0.4556 (ttm-80) REVERT: D 150 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6464 (mm) REVERT: D 844 LEU cc_start: 0.6506 (tp) cc_final: 0.6110 (mm) REVERT: D 894 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7358 (mt0) outliers start: 34 outliers final: 12 residues processed: 150 average time/residue: 1.5576 time to fit residues: 259.6534 Evaluate side-chains 140 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 140 LEU 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 606 GLN 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 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 Chi-restraints excluded: chain D residue 894 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 135 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 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 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 = 0.4646 r_free = 0.4646 target = 0.218883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.169532 restraints weight = 22980.605| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 2.54 r_work: 0.3598 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19946 Z= 0.156 Angle : 0.526 7.999 27888 Z= 0.300 Chirality : 0.036 0.138 3098 Planarity : 0.003 0.042 2804 Dihedral : 24.718 85.866 4358 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.61 % Allowed : 15.61 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.20), residues: 1780 helix: 2.13 (0.15), residues: 1168 sheet: 0.23 (0.88), residues: 44 loop : 0.06 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 643 HIS 0.003 0.001 HIS D 183 PHE 0.013 0.001 PHE D 892 TYR 0.013 0.001 TYR A 927 ARG 0.004 0.000 ARG A 942 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 1139) hydrogen bonds : angle 3.54964 ( 3119) covalent geometry : bond 0.00346 (19946) covalent geometry : angle 0.52605 (27888) *********************** 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 159 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.6199 (mm) REVERT: A 603 GLN cc_start: 0.7676 (tp-100) cc_final: 0.7192 (mp10) REVERT: A 894 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7193 (mt0) REVERT: A 906 GLN cc_start: 0.8724 (mm110) cc_final: 0.8410 (mm110) REVERT: D 150 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.6354 (mm) REVERT: D 844 LEU cc_start: 0.6169 (tp) cc_final: 0.5744 (mm) outliers start: 25 outliers final: 13 residues processed: 151 average time/residue: 1.4947 time to fit residues: 251.5961 Evaluate side-chains 142 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 139 THR 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 894 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 162 VAL Chi-restraints excluded: chain D residue 367 LYS Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 762 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 164 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 169 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4638 r_free = 0.4638 target = 0.218142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.177267 restraints weight = 23023.454| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 2.20 r_work: 0.3573 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19946 Z= 0.176 Angle : 0.546 8.434 27888 Z= 0.309 Chirality : 0.037 0.154 3098 Planarity : 0.004 0.043 2804 Dihedral : 24.757 89.340 4358 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.94 % Allowed : 16.39 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.21), residues: 1780 helix: 2.09 (0.15), residues: 1164 sheet: 0.32 (0.89), residues: 44 loop : 0.16 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 495 HIS 0.003 0.001 HIS A 183 PHE 0.029 0.002 PHE A 128 TYR 0.014 0.001 TYR A 927 ARG 0.007 0.000 ARG A 470 Details of bonding type rmsd hydrogen bonds : bond 0.04098 ( 1139) hydrogen bonds : angle 3.63692 ( 3119) covalent geometry : bond 0.00398 (19946) covalent geometry : angle 0.54561 (27888) *********************** 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 157 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.6611 (OUTLIER) cc_final: 0.6218 (mm) REVERT: A 603 GLN cc_start: 0.7762 (tp-100) cc_final: 0.7264 (mp10) REVERT: A 894 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7327 (mt0) REVERT: A 906 GLN cc_start: 0.8809 (mm110) cc_final: 0.8507 (mm110) REVERT: D 45 ARG cc_start: 0.6277 (OUTLIER) cc_final: 0.4391 (ttm-80) REVERT: D 150 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6439 (mm) REVERT: D 844 LEU cc_start: 0.6399 (tp) cc_final: 0.6000 (mm) REVERT: D 894 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7362 (mt0) outliers start: 30 outliers final: 13 residues processed: 149 average time/residue: 1.6756 time to fit residues: 279.1922 Evaluate side-chains 142 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 140 LEU 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 195 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 196 optimal weight: 0.9980 chunk 188 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 chunk 49 optimal weight: 0.0000 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 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 = 0.4639 r_free = 0.4639 target = 0.218029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.177909 restraints weight = 22947.467| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 2.20 r_work: 0.3594 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19946 Z= 0.177 Angle : 0.559 8.417 27888 Z= 0.316 Chirality : 0.037 0.170 3098 Planarity : 0.004 0.043 2804 Dihedral : 24.739 86.292 4358 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.81 % Allowed : 16.65 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.11 (0.21), residues: 1780 helix: 2.07 (0.15), residues: 1164 sheet: 0.41 (0.90), residues: 44 loop : 0.16 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 356 HIS 0.003 0.001 HIS A 183 PHE 0.013 0.002 PHE A 965 TYR 0.014 0.001 TYR D 634 ARG 0.007 0.000 ARG A 470 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 1139) hydrogen bonds : angle 3.68676 ( 3119) covalent geometry : bond 0.00399 (19946) covalent geometry : angle 0.55881 (27888) *********************** 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 154 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6214 (mm) REVERT: A 603 GLN cc_start: 0.7771 (tp-100) cc_final: 0.7288 (mp10) REVERT: A 894 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7297 (mt0) REVERT: A 906 GLN cc_start: 0.8813 (mm110) cc_final: 0.8517 (mm110) REVERT: D 45 ARG cc_start: 0.6346 (OUTLIER) cc_final: 0.4495 (ttm-80) REVERT: D 117 PHE cc_start: 0.7675 (t80) cc_final: 0.6970 (m-80) REVERT: D 150 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6536 (mm) REVERT: D 358 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7344 (pp20) REVERT: D 844 LEU cc_start: 0.6504 (tp) cc_final: 0.6125 (mm) REVERT: D 894 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7322 (mt0) outliers start: 28 outliers final: 13 residues processed: 147 average time/residue: 2.0757 time to fit residues: 341.4143 Evaluate side-chains 140 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 140 LEU 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 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 358 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 149 optimal weight: 1.9990 chunk 116 optimal weight: 0.0870 chunk 95 optimal weight: 8.9990 chunk 176 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 164 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- 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 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 = 0.4641 r_free = 0.4641 target = 0.218305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.177721 restraints weight = 22897.023| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 2.22 r_work: 0.3582 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19946 Z= 0.166 Angle : 0.554 8.547 27888 Z= 0.313 Chirality : 0.037 0.186 3098 Planarity : 0.004 0.058 2804 Dihedral : 24.720 86.249 4358 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.48 % Allowed : 17.35 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.21), residues: 1780 helix: 2.08 (0.15), residues: 1164 sheet: 0.46 (0.90), residues: 44 loop : 0.17 (0.29), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 495 HIS 0.003 0.001 HIS A 183 PHE 0.036 0.002 PHE A 128 TYR 0.014 0.001 TYR A 927 ARG 0.009 0.000 ARG D 466 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 1139) hydrogen bonds : angle 3.66552 ( 3119) covalent geometry : bond 0.00372 (19946) covalent geometry : angle 0.55368 (27888) ********************** 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 146 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6219 (mm) REVERT: A 603 GLN cc_start: 0.7794 (tp-100) cc_final: 0.7290 (mp10) REVERT: A 894 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7298 (mt0) REVERT: A 906 GLN cc_start: 0.8816 (mm110) cc_final: 0.8515 (mm110) REVERT: D 45 ARG cc_start: 0.6290 (OUTLIER) cc_final: 0.4419 (ttm-80) REVERT: D 117 PHE cc_start: 0.7699 (t80) cc_final: 0.6932 (m-80) REVERT: D 150 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6450 (mm) REVERT: D 358 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7349 (pp20) REVERT: D 844 LEU cc_start: 0.6430 (tp) cc_final: 0.6044 (mm) REVERT: D 894 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7326 (mt0) outliers start: 23 outliers final: 13 residues processed: 140 average time/residue: 1.4459 time to fit residues: 226.8732 Evaluate side-chains 139 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 139 THR 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 765 LEU 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 358 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 114 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 137 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 192 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.217752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.176171 restraints weight = 22911.183| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.21 r_work: 0.3576 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19946 Z= 0.181 Angle : 0.565 8.584 27888 Z= 0.319 Chirality : 0.037 0.184 3098 Planarity : 0.004 0.043 2804 Dihedral : 24.731 86.533 4358 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.55 % Allowed : 17.29 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.11 (0.21), residues: 1780 helix: 2.06 (0.15), residues: 1164 sheet: 0.47 (0.91), residues: 44 loop : 0.16 (0.29), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 495 HIS 0.003 0.001 HIS D 183 PHE 0.013 0.002 PHE A 965 TYR 0.015 0.001 TYR D 634 ARG 0.008 0.000 ARG D 466 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 1139) hydrogen bonds : angle 3.70287 ( 3119) covalent geometry : bond 0.00410 (19946) covalent geometry : angle 0.56516 (27888) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13378.71 seconds wall clock time: 232 minutes 23.06 seconds (13943.06 seconds total)