Starting phenix.real_space_refine on Sat Sep 12 22:27:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qd4_13906/09_2026/7qd4_13906.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qd4_13906/09_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_13906/09_2026/7qd4_13906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qd4_13906/09_2026/7qd4_13906.map" model { file = "/net/cci-nas-00/data/ceres_data/7qd4_13906/09_2026/7qd4_13906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qd4_13906/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 4.11, 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: 1.58 Conformation dependent library (CDL) restraints added in 668.2 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: 2.84 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: 5.62 Time building geometry restraints manager: 2.08 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=" C3' DC B 24 " pdb=" C2' DC B 24 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DC E 24 " pdb=" C2' DC E 24 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DA B 59 " pdb=" C2' DA B 59 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DG F1062 " pdb=" C2' DG F1062 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.79e+00 bond pdb=" C3' DG C1062 " pdb=" C2' DG C1062 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.59e+00 ... (remaining 19941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 26912 2.19 - 4.39: 855 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=" O4' DC B 42 " pdb=" C1' DC B 42 " pdb=" N1 DC B 42 " ideal model delta sigma weight residual 108.00 111.38 -3.38 7.00e-01 2.04e+00 2.33e+01 angle pdb=" O4' DC E 42 " pdb=" C1' DC E 42 " pdb=" N1 DC E 42 " ideal model delta sigma weight residual 108.00 111.33 -3.33 7.00e-01 2.04e+00 2.27e+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 ... (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: 2300 0.053 - 0.105: 669 0.105 - 0.158: 109 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: 0.03 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: 8.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 22.010 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:10.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 19946 Z= 0.424 Angle : 0.893 10.974 27888 Z= 0.622 Chirality : 0.050 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/Z covalent geometry : bond 0.00545 / 0.42 (19946) covalent geometry : angle 0.89303 / 0.62 (27888) hydrogen bonds : bond 0.09968 / 6.46 ( 1139) hydrogen bonds : angle 5.26449 / 3.70 ( 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 : 0.708 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.8218 time to fit residues: 166.0736 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 : 0.618 ------------------------------------------------------------------------------- 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: 6.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 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: 10.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 318 ASN A 368 GLN A 661 GLN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN D 318 ASN D 368 GLN D 874 GLN D 904 GLN D 975 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.214125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.175255 restraints weight = 22766.646| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 2.01 r_work: 0.3566 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 19946 Z= 0.215 Angle : 0.640 9.147 27888 Z= 0.363 Chirality : 0.044 0.190 3098 Planarity : 0.005 0.058 2804 Dihedral : 25.317 89.619 4358 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.16 % Allowed : 8.58 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.60 (0.19), residues: 1780 helix: 0.89 (0.14), residues: 1166 sheet: -0.26 (0.89), residues: 44 loop : -0.41 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 267 TYR 0.022 0.002 TYR D 488 PHE 0.017 0.002 PHE D 128 TRP 0.010 0.001 TRP D 102 HIS 0.006 0.001 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.22 (19946) covalent geometry : angle 0.64013 / 0.36 (27888) hydrogen bonds : bond 0.05071 / 3.35 ( 1139) hydrogen bonds : angle 4.16022 / 2.93 ( 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 162 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.7561 (mp-120) cc_final: 0.7146 (mp10) REVERT: A 603 GLN cc_start: 0.7757 (tp40) cc_final: 0.7329 (mp10) REVERT: D 933 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7561 (pp20) outliers start: 18 outliers final: 7 residues processed: 148 average time/residue: 0.7096 time to fit residues: 116.7333 Evaluate side-chains 129 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 430 HIS Chi-restraints excluded: chain D residue 655 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 175 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 193 optimal weight: 0.9980 chunk 188 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 178 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 112 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 252 GLN A 318 ASN A 368 GLN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN D 131 GLN D 252 GLN D 318 ASN D 368 GLN ** D 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.215317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.175909 restraints weight = 22906.798| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 2.18 r_work: 0.3572 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19946 Z= 0.147 Angle : 0.559 7.665 27888 Z= 0.323 Chirality : 0.040 0.186 3098 Planarity : 0.004 0.044 2804 Dihedral : 25.244 88.379 4358 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.16 % Allowed : 10.97 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.32 (0.20), residues: 1780 helix: 1.49 (0.15), residues: 1172 sheet: -0.18 (0.88), residues: 44 loop : -0.23 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 390 TYR 0.013 0.001 TYR A 927 PHE 0.015 0.001 PHE D 891 TRP 0.007 0.001 TRP A 670 HIS 0.003 0.001 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (19946) covalent geometry : angle 0.55851 / 0.32 (27888) hydrogen bonds : bond 0.04379 / 2.91 ( 1139) hydrogen bonds : angle 3.84509 / 2.71 ( 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 149 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.7595 (mp-120) cc_final: 0.7173 (mp10) REVERT: D 150 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6517 (mm) REVERT: D 933 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7542 (pp20) outliers start: 18 outliers final: 7 residues processed: 139 average time/residue: 0.6728 time to fit residues: 104.4595 Evaluate side-chains 122 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU 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 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: 3.9990 chunk 121 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 318 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.215111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.175712 restraints weight = 22766.336| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 2.19 r_work: 0.3582 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19946 Z= 0.148 Angle : 0.542 7.488 27888 Z= 0.315 Chirality : 0.040 0.181 3098 Planarity : 0.004 0.042 2804 Dihedral : 25.182 88.498 4358 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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 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: 1.65 (0.20), residues: 1780 helix: 1.75 (0.15), residues: 1172 sheet: -0.12 (0.89), residues: 44 loop : -0.10 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 390 TYR 0.028 0.001 TYR A 141 PHE 0.013 0.001 PHE D 891 TRP 0.007 0.001 TRP A 670 HIS 0.003 0.001 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (19946) covalent geometry : angle 0.54218 / 0.31 (27888) hydrogen bonds : bond 0.04276 / 2.84 ( 1139) hydrogen bonds : angle 3.72495 / 2.63 ( 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 149 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.7620 (mp-120) cc_final: 0.7224 (mp10) REVERT: D 134 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.6417 (mpp) REVERT: D 150 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6524 (mm) REVERT: D 681 MET cc_start: 0.3994 (OUTLIER) cc_final: 0.3661 (ptp) REVERT: D 844 LEU cc_start: 0.6609 (tp) cc_final: 0.6217 (mm) outliers start: 24 outliers final: 9 residues processed: 136 average time/residue: 0.6491 time to fit residues: 99.2859 Evaluate side-chains 123 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU 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 134 MET Chi-restraints excluded: chain D residue 140 LEU 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 Chi-restraints excluded: chain D residue 681 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 41 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 185 optimal weight: 0.1980 chunk 52 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 88 optimal weight: 0.6980 chunk 109 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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 = 0.4604 r_free = 0.4604 target = 0.214573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.176384 restraints weight = 22767.250| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 2.05 r_work: 0.3585 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19946 Z= 0.153 Angle : 0.544 8.242 27888 Z= 0.314 Chirality : 0.040 0.178 3098 Planarity : 0.004 0.046 2804 Dihedral : 25.110 88.280 4358 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.16 % Allowed : 14.45 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.20), residues: 1780 helix: 1.83 (0.15), residues: 1172 sheet: -0.20 (0.88), residues: 44 loop : -0.08 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 390 TYR 0.031 0.001 TYR A 141 PHE 0.022 0.002 PHE A 128 TRP 0.007 0.001 TRP A 923 HIS 0.003 0.001 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (19946) covalent geometry : angle 0.54412 / 0.31 (27888) hydrogen bonds : bond 0.04280 / 2.85 ( 1139) hydrogen bonds : angle 3.67600 / 2.59 ( 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 144 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.7593 (mp-120) cc_final: 0.7186 (mp10) REVERT: A 134 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.6406 (mpp) REVERT: A 762 LEU cc_start: 0.8631 (mt) cc_final: 0.8414 (tt) REVERT: D 150 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6475 (mm) REVERT: D 844 LEU cc_start: 0.6624 (tp) cc_final: 0.6239 (mm) outliers start: 18 outliers final: 9 residues processed: 135 average time/residue: 0.7073 time to fit residues: 106.2409 Evaluate side-chains 126 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 140 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 430 HIS Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 762 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 158 optimal weight: 0.4980 chunk 57 optimal weight: 0.0770 chunk 117 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 159 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 105 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4600 r_free = 0.4600 target = 0.214056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.174829 restraints weight = 22622.012| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 2.10 r_work: 0.3573 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19946 Z= 0.161 Angle : 0.550 8.205 27888 Z= 0.316 Chirality : 0.040 0.175 3098 Planarity : 0.004 0.042 2804 Dihedral : 25.101 88.028 4358 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.48 % Allowed : 15.48 % Favored : 83.03 % 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: 1.85 (0.20), residues: 1780 helix: 1.90 (0.15), residues: 1168 sheet: -0.12 (0.89), residues: 44 loop : -0.01 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 390 TYR 0.015 0.001 TYR A 141 PHE 0.013 0.002 PHE A 965 TRP 0.009 0.001 TRP A 356 HIS 0.003 0.001 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (19946) covalent geometry : angle 0.54970 / 0.32 (27888) hydrogen bonds : bond 0.04332 / 2.88 ( 1139) hydrogen bonds : angle 3.67428 / 2.59 ( 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 140 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.7589 (mp-120) cc_final: 0.7158 (mp10) REVERT: A 150 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6367 (mm) REVERT: A 762 LEU cc_start: 0.8660 (mt) cc_final: 0.8391 (tt) REVERT: D 134 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.6752 (mpp) REVERT: D 150 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6502 (mm) REVERT: D 298 ARG cc_start: 0.8189 (mpt180) cc_final: 0.7942 (mmt180) REVERT: D 844 LEU cc_start: 0.6644 (tp) cc_final: 0.6243 (mm) outliers start: 23 outliers final: 12 residues processed: 129 average time/residue: 0.6610 time to fit residues: 95.7390 Evaluate side-chains 127 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 313 GLU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 140 LEU 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 313 GLU 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: 5.9990 chunk 113 optimal weight: 0.4980 chunk 107 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 164 optimal weight: 0.3980 chunk 65 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4600 r_free = 0.4600 target = 0.214009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.174003 restraints weight = 22662.161| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 2.18 r_work: 0.3555 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19946 Z= 0.157 Angle : 0.547 7.775 27888 Z= 0.315 Chirality : 0.039 0.177 3098 Planarity : 0.004 0.043 2804 Dihedral : 25.089 87.847 4358 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.55 % Allowed : 15.94 % 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: 1.91 (0.20), residues: 1780 helix: 1.96 (0.15), residues: 1170 sheet: -0.13 (0.88), residues: 44 loop : 0.01 (0.28), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 390 TYR 0.017 0.001 TYR A 141 PHE 0.028 0.002 PHE A 128 TRP 0.008 0.001 TRP A 923 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (19946) covalent geometry : angle 0.54702 / 0.31 (27888) hydrogen bonds : bond 0.04274 / 2.84 ( 1139) hydrogen bonds : angle 3.65963 / 2.58 ( 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 146 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6336 (mm) REVERT: A 894 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7270 (mt0) REVERT: A 906 GLN cc_start: 0.8824 (mm110) cc_final: 0.8525 (mm110) REVERT: D 150 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6490 (mm) REVERT: D 894 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7371 (mt0) outliers start: 24 outliers final: 12 residues processed: 139 average time/residue: 0.6888 time to fit residues: 106.8534 Evaluate side-chains 130 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 A residue 762 LEU 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 162 VAL Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 395 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 162 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 165 optimal weight: 0.5980 chunk 104 optimal weight: 20.0000 chunk 142 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 87 optimal weight: 0.0170 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4608 r_free = 0.4608 target = 0.214824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.175541 restraints weight = 22700.530| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 2.14 r_work: 0.3589 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19946 Z= 0.135 Angle : 0.536 7.773 27888 Z= 0.309 Chirality : 0.038 0.180 3098 Planarity : 0.003 0.042 2804 Dihedral : 25.055 88.007 4358 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.10 % Allowed : 16.84 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.20), residues: 1780 helix: 2.02 (0.15), residues: 1172 sheet: -0.14 (0.88), residues: 44 loop : 0.04 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 390 TYR 0.014 0.001 TYR A 927 PHE 0.033 0.002 PHE D 128 TRP 0.007 0.001 TRP A 643 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (19946) covalent geometry : angle 0.53644 / 0.31 (27888) hydrogen bonds : bond 0.04084 / 2.71 ( 1139) hydrogen bonds : angle 3.63083 / 2.57 ( 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 140 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6338 (mm) REVERT: A 603 GLN cc_start: 0.7712 (tp-100) cc_final: 0.7313 (mp10) REVERT: A 906 GLN cc_start: 0.8806 (mm110) cc_final: 0.8501 (mm110) REVERT: D 150 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6565 (mm) REVERT: D 894 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7315 (mt0) outliers start: 17 outliers final: 10 residues processed: 137 average time/residue: 0.7074 time to fit residues: 108.3119 Evaluate side-chains 131 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 395 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 162 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 430 HIS 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 125 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 156 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 143 optimal weight: 0.9990 chunk 165 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4608 r_free = 0.4608 target = 0.214804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.175388 restraints weight = 22501.798| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 2.16 r_work: 0.3584 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19946 Z= 0.140 Angle : 0.548 8.070 27888 Z= 0.314 Chirality : 0.039 0.179 3098 Planarity : 0.003 0.043 2804 Dihedral : 25.045 88.239 4358 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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: 2.03 (0.20), residues: 1780 helix: 2.05 (0.15), residues: 1172 sheet: -0.02 (0.89), residues: 44 loop : 0.04 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 390 TYR 0.014 0.001 TYR D 121 PHE 0.038 0.002 PHE A 128 TRP 0.007 0.001 TRP A 356 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (19946) covalent geometry : angle 0.54835 / 0.31 (27888) hydrogen bonds : bond 0.04118 / 2.74 ( 1139) hydrogen bonds : angle 3.64012 / 2.58 ( 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 146 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.6869 (mpp) REVERT: A 150 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6275 (mm) REVERT: A 603 GLN cc_start: 0.7717 (tp-100) cc_final: 0.7278 (mp10) REVERT: A 894 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7242 (mt0) REVERT: A 906 GLN cc_start: 0.8815 (mm110) cc_final: 0.8509 (mm110) REVERT: D 45 ARG cc_start: 0.6161 (OUTLIER) cc_final: 0.4519 (ttm-80) REVERT: D 134 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.6863 (mpp) REVERT: D 150 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6526 (mm) REVERT: D 894 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7366 (mt0) outliers start: 23 outliers final: 12 residues processed: 139 average time/residue: 0.6645 time to fit residues: 103.2320 Evaluate side-chains 137 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 395 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 134 MET 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 395 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 762 LEU 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: 5.9990 chunk 17 optimal weight: 0.9990 chunk 183 optimal weight: 9.9990 chunk 6 optimal weight: 0.2980 chunk 127 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 198 optimal weight: 0.6980 chunk 136 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 194 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4611 r_free = 0.4611 target = 0.215143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.175989 restraints weight = 22749.385| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 2.16 r_work: 0.3582 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19946 Z= 0.136 Angle : 0.554 10.213 27888 Z= 0.316 Chirality : 0.039 0.180 3098 Planarity : 0.003 0.042 2804 Dihedral : 25.020 88.340 4358 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.35 % Allowed : 17.55 % 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: 2.07 (0.21), residues: 1780 helix: 2.08 (0.15), residues: 1172 sheet: 0.01 (0.88), residues: 44 loop : 0.04 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 97 TYR 0.015 0.001 TYR D 121 PHE 0.044 0.002 PHE D 128 TRP 0.007 0.001 TRP A 643 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (19946) covalent geometry : angle 0.55426 / 0.32 (27888) hydrogen bonds : bond 0.04069 / 2.71 ( 1139) hydrogen bonds : angle 3.65623 / 2.59 ( 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 143 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.6888 (mpp) REVERT: A 150 LEU cc_start: 0.6623 (OUTLIER) cc_final: 0.6296 (mm) REVERT: A 603 GLN cc_start: 0.7722 (tp-100) cc_final: 0.7272 (mp10) REVERT: A 881 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8156 (mm-30) REVERT: A 894 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7235 (mt0) REVERT: A 906 GLN cc_start: 0.8814 (mm110) cc_final: 0.8501 (mm110) REVERT: D 45 ARG cc_start: 0.6201 (OUTLIER) cc_final: 0.4597 (ttm-80) REVERT: D 134 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.6838 (mpp) REVERT: D 150 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6514 (mm) REVERT: D 894 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7344 (mt0) outliers start: 21 outliers final: 9 residues processed: 135 average time/residue: 0.6496 time to fit residues: 98.0821 Evaluate side-chains 135 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 881 GLU Chi-restraints excluded: chain A residue 894 GLN Chi-restraints excluded: chain D residue 45 ARG 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 162 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 430 HIS 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: 0.9980 chunk 17 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 132 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4584 r_free = 0.4584 target = 0.212162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.172113 restraints weight = 22566.059| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 2.10 r_work: 0.3554 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 19946 Z= 0.219 Angle : 0.616 8.745 27888 Z= 0.346 Chirality : 0.043 0.187 3098 Planarity : 0.004 0.044 2804 Dihedral : 25.171 87.789 4358 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.48 % Allowed : 17.55 % Favored : 80.97 % 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: 1.83 (0.20), residues: 1780 helix: 1.88 (0.15), residues: 1162 sheet: 0.03 (0.88), residues: 44 loop : 0.03 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 816 TYR 0.020 0.002 TYR A 634 PHE 0.043 0.002 PHE A 128 TRP 0.014 0.001 TRP D 495 HIS 0.005 0.001 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.22 (19946) covalent geometry : angle 0.61569 / 0.35 (27888) hydrogen bonds : bond 0.04926 / 3.26 ( 1139) hydrogen bonds : angle 3.85321 / 2.72 ( 3119) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5650.39 seconds wall clock time: 97 minutes 18.24 seconds (5838.24 seconds total)