Starting phenix.real_space_refine on Thu Jul 2 19:38:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qee_53058/07_2026/9qee_53058.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qee_53058/07_2026/9qee_53058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qee_53058/07_2026/9qee_53058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qee_53058/07_2026/9qee_53058.map" model { file = "/net/cci-nas-00/data/ceres_data/9qee_53058/07_2026/9qee_53058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qee_53058/07_2026/9qee_53058.cif" } resolution = 3.4 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= 0.003 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: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 P 40 5.49 5 S 39 5.16 5 C 6135 2.51 5 N 1685 2.21 5 O 1888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9789 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1568 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 11, 'TRANS': 185} Chain: "C" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 976 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "U" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 409 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "V" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 546 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 5, 'TRANS': 64} Chain breaks: 1 Chain: "A" Number of atoms: 5877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5877 Classifications: {'peptide': 732} Link IDs: {'PTRANS': 36, 'TRANS': 695} Chain breaks: 4 Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Time building chain proxies: 1.62, per 1000 atoms: 0.17 Number of scatterers: 9789 At special positions: 0 Unit cell: (107.433, 108.575, 126.862, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 39 16.00 P 40 15.00 O 1888 8.00 N 1685 7.00 C 6135 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: 0.64 Conformation dependent library (CDL) restraints added in 200.4 milliseconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 8 sheets defined 55.5% alpha, 12.9% beta 19 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'B' and resid 105 through 108 removed outlier: 4.055A pdb=" N ARG B 108 " --> pdb=" O PRO B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 105 through 108' Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.793A pdb=" N VAL B 116 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 149 Processing helix chain 'B' and resid 151 through 161 removed outlier: 4.285A pdb=" N GLY B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 219 through 223 removed outlier: 4.317A pdb=" N LEU B 222 " --> pdb=" O PRO B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 239 Processing helix chain 'B' and resid 246 through 258 Processing helix chain 'B' and resid 259 through 266 removed outlier: 3.765A pdb=" N LEU B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 274 removed outlier: 4.183A pdb=" N CYS B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 290 Processing helix chain 'C' and resid 34 through 37 Processing helix chain 'C' and resid 38 through 45 removed outlier: 3.970A pdb=" N CYS C 42 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 61 removed outlier: 3.691A pdb=" N ILE C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU C 57 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 474 removed outlier: 3.689A pdb=" N VAL D 473 " --> pdb=" O PRO D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 491 Processing helix chain 'D' and resid 506 through 511 removed outlier: 3.606A pdb=" N LYS D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'A' and resid 18 through 29 removed outlier: 3.995A pdb=" N LEU A 22 " --> pdb=" O TYR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 52 removed outlier: 3.879A pdb=" N LEU A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 80 Processing helix chain 'A' and resid 93 through 104 removed outlier: 4.000A pdb=" N TYR A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N GLU A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY A 104 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 120 removed outlier: 3.673A pdb=" N LEU A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.642A pdb=" N PHE A 171 " --> pdb=" O ALA A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 185 Processing helix chain 'A' and resid 197 through 205 Processing helix chain 'A' and resid 219 through 244 removed outlier: 3.543A pdb=" N ASN A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 261 through 271 removed outlier: 3.681A pdb=" N THR A 265 " --> pdb=" O PRO A 261 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A 271 " --> pdb=" O ARG A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 removed outlier: 4.255A pdb=" N HIS A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN A 276 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 276' Processing helix chain 'A' and resid 279 through 282 Processing helix chain 'A' and resid 283 through 301 Processing helix chain 'A' and resid 302 through 320 removed outlier: 3.666A pdb=" N PHE A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 343 Processing helix chain 'A' and resid 378 through 398 removed outlier: 4.200A pdb=" N GLU A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 Processing helix chain 'A' and resid 427 through 440 removed outlier: 3.511A pdb=" N PHE A 431 " --> pdb=" O GLY A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 565 through 573 Processing helix chain 'A' and resid 584 through 597 Processing helix chain 'A' and resid 613 through 642 removed outlier: 3.585A pdb=" N GLN A 617 " --> pdb=" O SER A 613 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 691 No H-bonds generated for 'chain 'A' and resid 689 through 691' Processing helix chain 'A' and resid 694 through 703 removed outlier: 3.751A pdb=" N ARG A 702 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY A 703 " --> pdb=" O ILE A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 739 Processing helix chain 'A' and resid 739 through 752 removed outlier: 3.981A pdb=" N SER A 743 " --> pdb=" O GLY A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 795 Processing helix chain 'A' and resid 805 through 816 removed outlier: 3.669A pdb=" N GLU A 811 " --> pdb=" O HIS A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 855 removed outlier: 3.733A pdb=" N LYS A 854 " --> pdb=" O ASP A 850 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET A 855 " --> pdb=" O PHE A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 870 removed outlier: 3.548A pdb=" N LEU A 866 " --> pdb=" O ASN A 862 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 879 removed outlier: 3.527A pdb=" N LEU A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 889 Processing helix chain 'A' and resid 890 through 903 Processing sheet with id=AA1, first strand: chain 'B' and resid 121 through 123 removed outlier: 5.587A pdb=" N ILE B 101 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 102 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 131 " --> pdb=" O ILE B 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 136 through 137 Processing sheet with id=AA3, first strand: chain 'B' and resid 140 through 142 removed outlier: 6.797A pdb=" N LEU B 141 " --> pdb=" O GLN B 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.638A pdb=" N ALA C 87 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER C 119 " --> pdb=" O GLN C 84 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASP C 112 " --> pdb=" O ALA C 14 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU C 16 " --> pdb=" O ASP C 112 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE C 114 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N CYS C 98 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 407 " --> pdb=" O ILE A 553 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N HIS A 555 " --> pdb=" O VAL A 407 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE A 409 " --> pdb=" O HIS A 555 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLN A 406 " --> pdb=" O TYR A 577 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL A 579 " --> pdb=" O GLN A 406 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU A 408 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 90 through 91 removed outlier: 7.548A pdb=" N ASP C 112 " --> pdb=" O ALA C 14 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU C 16 " --> pdb=" O ASP C 112 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE C 114 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY A 545 " --> pdb=" O LYS C 9 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 88 removed outlier: 6.929A pdb=" N ARG A 86 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 59 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA A 109 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL A 61 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU A 58 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N LEU A 132 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU A 60 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY A 31 " --> pdb=" O ILE A 161 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU A 32 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N TRP A 193 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL A 34 " --> pdb=" O TRP A 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 344 through 345 removed outlier: 3.770A pdb=" N GLU A 372 " --> pdb=" O HIS A 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 705 through 709 removed outlier: 6.893A pdb=" N ILE A 684 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL A 709 " --> pdb=" O ILE A 684 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL A 686 " --> pdb=" O VAL A 709 " (cutoff:3.500A) removed outlier: 9.972A pdb=" N SER A 683 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N THR A 719 " --> pdb=" O SER A 683 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 685 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 718 " --> pdb=" O MET A 722 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N MET A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N CYS A 723 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU A 758 " --> pdb=" O CYS A 723 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A 725 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N GLU A 760 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS A 727 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 799 " --> pdb=" O PRO A 755 " (cutoff:3.500A) 427 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 1.76 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2200 1.33 - 1.45: 2163 1.45 - 1.57: 5570 1.57 - 1.69: 79 1.69 - 1.81: 53 Bond restraints: 10065 Sorted by residual: bond pdb=" C3' DC V 21 " pdb=" C2' DC V 21 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DC V 6 " pdb=" C2' DC V 6 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.41e+00 bond pdb=" C3' DT V 14 " pdb=" O3' DT V 14 " ideal model delta sigma weight residual 1.435 1.396 0.039 1.30e-02 5.92e+03 9.13e+00 bond pdb=" C3' DA U 23 " pdb=" C2' DA U 23 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.02e+00 bond pdb=" C3' DT U 22 " pdb=" C2' DT U 22 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.77e+00 ... (remaining 10060 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 13186 1.57 - 3.14: 541 3.14 - 4.71: 56 4.71 - 6.28: 12 6.28 - 7.85: 6 Bond angle restraints: 13801 Sorted by residual: angle pdb=" N3 DT V 5 " pdb=" C4 DT V 5 " pdb=" O4 DT V 5 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT V 12 " pdb=" C4 DT V 12 " pdb=" O4 DT V 12 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT V 2 " pdb=" C4 DT V 2 " pdb=" O4 DT V 2 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" O4' DA V 15 " pdb=" C4' DA V 15 " pdb=" C3' DA V 15 " ideal model delta sigma weight residual 106.00 103.46 2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT U 22 " pdb=" C4 DT U 22 " pdb=" O4 DT U 22 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 ... (remaining 13796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.74: 5380 28.74 - 57.48: 600 57.48 - 86.21: 46 86.21 - 114.95: 6 114.95 - 143.69: 1 Dihedral angle restraints: 6033 sinusoidal: 2738 harmonic: 3295 Sorted by residual: dihedral pdb=" CA THR A 165 " pdb=" C THR A 165 " pdb=" N ASP A 166 " pdb=" CA ASP A 166 " ideal model delta harmonic sigma weight residual 180.00 157.94 22.06 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ASP A 166 " pdb=" C ASP A 166 " pdb=" N ASN A 167 " pdb=" CA ASN A 167 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" C4' DT U 22 " pdb=" C3' DT U 22 " pdb=" O3' DT U 22 " pdb=" P DA U 23 " ideal model delta sinusoidal sigma weight residual 220.00 76.31 143.69 1 3.50e+01 8.16e-04 1.42e+01 ... (remaining 6030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 910 0.033 - 0.065: 466 0.065 - 0.098: 130 0.098 - 0.130: 74 0.130 - 0.163: 7 Chirality restraints: 1587 Sorted by residual: chirality pdb=" C3' DT U 22 " pdb=" C4' DT U 22 " pdb=" O3' DT U 22 " pdb=" C2' DT U 22 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.63e-01 chirality pdb=" CA ASN C 104 " pdb=" N ASN C 104 " pdb=" C ASN C 104 " pdb=" CB ASN C 104 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA ILE C 85 " pdb=" N ILE C 85 " pdb=" C ILE C 85 " pdb=" CB ILE C 85 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 1584 not shown) Planarity restraints: 1619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 129 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.52e+00 pdb=" CG ASP B 129 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASP B 129 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP B 129 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 110 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO C 111 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 111 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 111 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 719 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO A 720 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 720 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 720 " 0.025 5.00e-02 4.00e+02 ... (remaining 1616 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 85 2.58 - 3.16: 7976 3.16 - 3.74: 14780 3.74 - 4.32: 19945 4.32 - 4.90: 33065 Nonbonded interactions: 75851 Sorted by model distance: nonbonded pdb=" OP1 DA U 27 " pdb="MN MN U 101 " model vdw 2.000 3.060 nonbonded pdb=" OG1 THR A 165 " pdb=" O ASP A 166 " model vdw 2.180 3.040 nonbonded pdb=" O ARG C 100 " pdb=" N ASN C 104 " model vdw 2.225 3.120 nonbonded pdb=" O PRO D 504 " pdb=" NH2 ARG A 604 " model vdw 2.237 3.120 nonbonded pdb=" OD1 ASP A 413 " pdb=" N ASP A 414 " model vdw 2.243 3.120 ... (remaining 75846 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.590 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.930 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 0.006 0.072 10065 Z= 0.344 Angle : 0.712 7.847 13801 Z= 0.448 Chirality : 0.045 0.163 1587 Planarity : 0.005 0.053 1619 Dihedral : 20.907 143.690 3885 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.50 % Allowed : 28.49 % Favored : 71.01 % 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: -0.86 (0.25), residues: 1102 helix: 0.42 (0.22), residues: 564 sheet: -1.27 (0.41), residues: 155 loop : -1.64 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 234 TYR 0.021 0.002 TYR C 88 PHE 0.021 0.002 PHE A 186 TRP 0.012 0.002 TRP A 274 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.34 (10065) covalent geometry : angle 0.71245 / 0.45 (13801) hydrogen bonds : bond 0.15408 / 10.35 ( 469) hydrogen bonds : angle 5.94738 / 4.22 ( 1301) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.223 Fit side-chains REVERT: B 224 MET cc_start: 0.8166 (mmm) cc_final: 0.7795 (mmm) REVERT: C 84 GLN cc_start: 0.7901 (tp40) cc_final: 0.7547 (tp40) outliers start: 5 outliers final: 2 residues processed: 114 average time/residue: 0.0860 time to fit residues: 13.5101 Evaluate side-chains 104 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 246 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 172 GLN C 67 ASN D 474 GLN A 197 HIS A 201 ASN A 286 GLN A 700 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.145409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.108887 restraints weight = 15289.780| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.32 r_work: 0.3207 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10065 Z= 0.146 Angle : 0.594 7.351 13801 Z= 0.319 Chirality : 0.041 0.172 1587 Planarity : 0.004 0.046 1619 Dihedral : 18.291 146.790 1663 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.91 % Allowed : 25.58 % Favored : 71.51 % 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: -0.21 (0.26), residues: 1102 helix: 0.98 (0.23), residues: 565 sheet: -1.01 (0.43), residues: 152 loop : -1.38 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 234 TYR 0.010 0.001 TYR B 152 PHE 0.012 0.001 PHE A 186 TRP 0.006 0.001 TRP A 274 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (10065) covalent geometry : angle 0.59367 / 0.32 (13801) hydrogen bonds : bond 0.05213 / 3.46 ( 469) hydrogen bonds : angle 4.42062 / 3.18 ( 1301) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.269 Fit side-chains REVERT: B 224 MET cc_start: 0.8208 (mmm) cc_final: 0.7962 (mmm) REVERT: C 84 GLN cc_start: 0.8207 (tp40) cc_final: 0.7783 (tp40) REVERT: D 542 MET cc_start: 0.7527 (tpt) cc_final: 0.7303 (tpt) REVERT: A 392 GLU cc_start: 0.8192 (tp30) cc_final: 0.7955 (tm-30) REVERT: A 897 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6421 (tt) outliers start: 29 outliers final: 17 residues processed: 136 average time/residue: 0.0885 time to fit residues: 16.7927 Evaluate side-chains 117 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 93 optimal weight: 0.4980 chunk 4 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 179 GLN D 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.144541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.108157 restraints weight = 15411.339| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.31 r_work: 0.3162 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10065 Z= 0.182 Angle : 0.616 8.609 13801 Z= 0.325 Chirality : 0.042 0.166 1587 Planarity : 0.004 0.045 1619 Dihedral : 18.288 146.061 1659 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.31 % Allowed : 25.78 % Favored : 69.91 % 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: -0.16 (0.26), residues: 1102 helix: 1.07 (0.23), residues: 566 sheet: -0.99 (0.42), residues: 152 loop : -1.46 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 52 TYR 0.017 0.002 TYR B 152 PHE 0.016 0.001 PHE A 160 TRP 0.008 0.001 TRP A 274 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (10065) covalent geometry : angle 0.61588 / 0.32 (13801) hydrogen bonds : bond 0.05208 / 3.45 ( 469) hydrogen bonds : angle 4.24725 / 3.07 ( 1301) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 107 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: C 5 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8135 (mttt) REVERT: C 84 GLN cc_start: 0.8210 (tp40) cc_final: 0.7804 (tp40) REVERT: A 392 GLU cc_start: 0.8320 (tp30) cc_final: 0.8111 (tm-30) REVERT: A 722 MET cc_start: 0.8812 (tpp) cc_final: 0.8526 (ttm) REVERT: A 897 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6468 (tt) outliers start: 43 outliers final: 34 residues processed: 142 average time/residue: 0.0777 time to fit residues: 15.5673 Evaluate side-chains 137 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 474 GLN Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 689 ARG Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 17 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 474 GLN A 890 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.146905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.110550 restraints weight = 15374.826| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.33 r_work: 0.3228 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 10065 Z= 0.118 Angle : 0.557 8.417 13801 Z= 0.296 Chirality : 0.040 0.148 1587 Planarity : 0.004 0.042 1619 Dihedral : 18.068 146.700 1659 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.71 % Allowed : 26.28 % Favored : 70.01 % 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: 0.07 (0.26), residues: 1102 helix: 1.24 (0.23), residues: 566 sheet: -0.87 (0.43), residues: 152 loop : -1.34 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 234 TYR 0.019 0.001 TYR B 152 PHE 0.013 0.001 PHE A 607 TRP 0.006 0.001 TRP A 326 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (10065) covalent geometry : angle 0.55666 / 0.30 (13801) hydrogen bonds : bond 0.04241 / 2.81 ( 469) hydrogen bonds : angle 4.03042 / 2.91 ( 1301) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 0.263 Fit side-chains REVERT: C 5 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8007 (mttt) REVERT: C 50 ASP cc_start: 0.7392 (m-30) cc_final: 0.7078 (m-30) REVERT: C 84 GLN cc_start: 0.8141 (tp40) cc_final: 0.7717 (tp40) REVERT: D 532 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7256 (mt-10) REVERT: A 392 GLU cc_start: 0.8273 (tp30) cc_final: 0.8053 (tt0) REVERT: A 722 MET cc_start: 0.8725 (tpp) cc_final: 0.8335 (ttm) REVERT: A 850 ASP cc_start: 0.8547 (t0) cc_final: 0.8258 (t70) REVERT: A 875 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7172 (mm-30) outliers start: 37 outliers final: 26 residues processed: 133 average time/residue: 0.0821 time to fit residues: 15.4802 Evaluate side-chains 130 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 904 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 73 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 58 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.144998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.109043 restraints weight = 15407.033| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.26 r_work: 0.3172 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10065 Z= 0.163 Angle : 0.580 7.874 13801 Z= 0.308 Chirality : 0.041 0.160 1587 Planarity : 0.004 0.060 1619 Dihedral : 18.024 147.653 1659 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 5.12 % Allowed : 25.08 % Favored : 69.81 % 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: 0.07 (0.26), residues: 1102 helix: 1.25 (0.23), residues: 566 sheet: -0.84 (0.43), residues: 152 loop : -1.36 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 52 TYR 0.021 0.002 TYR B 152 PHE 0.014 0.001 PHE A 186 TRP 0.007 0.001 TRP A 326 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (10065) covalent geometry : angle 0.58045 / 0.31 (13801) hydrogen bonds : bond 0.04640 / 3.07 ( 469) hydrogen bonds : angle 3.99986 / 2.91 ( 1301) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 103 time to evaluate : 0.359 Fit side-chains REVERT: C 5 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8149 (mttt) REVERT: C 50 ASP cc_start: 0.7439 (m-30) cc_final: 0.7110 (m-30) REVERT: C 84 GLN cc_start: 0.8152 (tp40) cc_final: 0.7719 (tp40) REVERT: A 121 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8434 (t0) REVERT: A 392 GLU cc_start: 0.8332 (tp30) cc_final: 0.8102 (tt0) REVERT: A 722 MET cc_start: 0.8721 (tpp) cc_final: 0.8366 (ttm) REVERT: A 850 ASP cc_start: 0.8726 (t0) cc_final: 0.8463 (t70) REVERT: A 875 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7153 (mm-30) REVERT: A 897 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6402 (tt) outliers start: 51 outliers final: 38 residues processed: 147 average time/residue: 0.0860 time to fit residues: 17.9268 Evaluate side-chains 141 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 99 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 90 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 32 optimal weight: 30.0000 chunk 103 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 79 optimal weight: 0.0020 chunk 19 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.145626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.109244 restraints weight = 15419.739| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.24 r_work: 0.3186 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10065 Z= 0.146 Angle : 0.569 7.870 13801 Z= 0.302 Chirality : 0.040 0.154 1587 Planarity : 0.004 0.055 1619 Dihedral : 17.971 148.048 1659 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.51 % Allowed : 26.08 % Favored : 69.41 % 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: 0.15 (0.26), residues: 1102 helix: 1.30 (0.23), residues: 566 sheet: -0.81 (0.42), residues: 154 loop : -1.30 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 52 TYR 0.025 0.001 TYR B 130 PHE 0.012 0.001 PHE A 186 TRP 0.006 0.001 TRP A 326 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (10065) covalent geometry : angle 0.56918 / 0.30 (13801) hydrogen bonds : bond 0.04369 / 2.89 ( 469) hydrogen bonds : angle 3.94997 / 2.87 ( 1301) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 104 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: C 5 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8126 (mttt) REVERT: C 50 ASP cc_start: 0.7413 (m-30) cc_final: 0.7078 (m-30) REVERT: C 84 GLN cc_start: 0.8172 (tp40) cc_final: 0.7687 (tp40) REVERT: D 532 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7234 (mt-10) REVERT: A 121 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8415 (t0) REVERT: A 392 GLU cc_start: 0.8328 (tp30) cc_final: 0.8105 (tt0) REVERT: A 441 GLU cc_start: 0.5975 (OUTLIER) cc_final: 0.5719 (tm-30) REVERT: A 722 MET cc_start: 0.8738 (tpp) cc_final: 0.8379 (ttm) REVERT: A 850 ASP cc_start: 0.8718 (t0) cc_final: 0.8442 (t70) REVERT: A 875 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7148 (mm-30) REVERT: A 897 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6487 (tt) outliers start: 45 outliers final: 36 residues processed: 141 average time/residue: 0.0869 time to fit residues: 17.1199 Evaluate side-chains 142 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 100 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 689 ARG Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 48 optimal weight: 0.0970 chunk 67 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.147189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.110580 restraints weight = 15293.384| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.27 r_work: 0.3217 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10065 Z= 0.121 Angle : 0.553 7.876 13801 Z= 0.294 Chirality : 0.039 0.150 1587 Planarity : 0.004 0.049 1619 Dihedral : 17.844 148.358 1659 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.41 % Allowed : 26.38 % Favored : 69.21 % 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: 0.30 (0.26), residues: 1102 helix: 1.43 (0.23), residues: 566 sheet: -0.75 (0.43), residues: 154 loop : -1.23 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 92 TYR 0.020 0.001 TYR B 130 PHE 0.012 0.001 PHE A 607 TRP 0.014 0.001 TRP C 32 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (10065) covalent geometry : angle 0.55349 / 0.29 (13801) hydrogen bonds : bond 0.03951 / 2.61 ( 469) hydrogen bonds : angle 3.87595 / 2.81 ( 1301) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 107 time to evaluate : 0.246 Fit side-chains REVERT: C 5 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8065 (mttt) REVERT: C 50 ASP cc_start: 0.7440 (m-30) cc_final: 0.7090 (m-30) REVERT: C 70 PHE cc_start: 0.5849 (OUTLIER) cc_final: 0.5388 (t80) REVERT: C 84 GLN cc_start: 0.8148 (tp40) cc_final: 0.7662 (tp40) REVERT: D 532 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7225 (mt-10) REVERT: A 121 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8367 (t0) REVERT: A 392 GLU cc_start: 0.8352 (tp30) cc_final: 0.8094 (tt0) REVERT: A 441 GLU cc_start: 0.5950 (OUTLIER) cc_final: 0.5665 (tm-30) REVERT: A 722 MET cc_start: 0.8708 (tpp) cc_final: 0.8302 (ttm) REVERT: A 850 ASP cc_start: 0.8718 (t0) cc_final: 0.8448 (t70) REVERT: A 897 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6378 (tt) outliers start: 44 outliers final: 33 residues processed: 141 average time/residue: 0.0805 time to fit residues: 16.0690 Evaluate side-chains 143 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 21 optimal weight: 0.0000 chunk 48 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 53 optimal weight: 0.0270 chunk 15 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 overall best weight: 1.3646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 ASN C 36 GLN ** D 474 GLN ** 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 = 0.3881 r_free = 0.3881 target = 0.147407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.110727 restraints weight = 15218.128| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.27 r_work: 0.3213 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10065 Z= 0.126 Angle : 0.553 7.986 13801 Z= 0.293 Chirality : 0.040 0.158 1587 Planarity : 0.004 0.062 1619 Dihedral : 17.822 148.526 1659 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.31 % Allowed : 26.68 % Favored : 69.01 % 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: 0.34 (0.26), residues: 1102 helix: 1.46 (0.23), residues: 566 sheet: -0.70 (0.43), residues: 154 loop : -1.22 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 234 TYR 0.020 0.001 TYR B 152 PHE 0.011 0.001 PHE A 160 TRP 0.012 0.001 TRP C 32 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (10065) covalent geometry : angle 0.55299 / 0.29 (13801) hydrogen bonds : bond 0.03943 / 2.60 ( 469) hydrogen bonds : angle 3.84191 / 2.79 ( 1301) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 106 time to evaluate : 0.285 Fit side-chains REVERT: B 213 LYS cc_start: 0.7420 (tptt) cc_final: 0.7154 (tppt) REVERT: C 5 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8063 (mttt) REVERT: C 50 ASP cc_start: 0.7447 (m-30) cc_final: 0.7091 (m-30) REVERT: C 55 GLU cc_start: 0.7132 (pt0) cc_final: 0.6201 (tm-30) REVERT: C 70 PHE cc_start: 0.6109 (OUTLIER) cc_final: 0.5605 (t80) REVERT: C 84 GLN cc_start: 0.8145 (tp40) cc_final: 0.7660 (tp40) REVERT: D 532 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7329 (mt-10) REVERT: A 121 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8387 (t0) REVERT: A 392 GLU cc_start: 0.8381 (tp30) cc_final: 0.8128 (tt0) REVERT: A 441 GLU cc_start: 0.5977 (OUTLIER) cc_final: 0.5704 (tm-30) REVERT: A 722 MET cc_start: 0.8751 (tpp) cc_final: 0.8347 (ttm) REVERT: A 850 ASP cc_start: 0.8735 (t0) cc_final: 0.8464 (t70) REVERT: A 867 MET cc_start: 0.8051 (mtm) cc_final: 0.7746 (mtm) REVERT: A 897 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6397 (tt) outliers start: 43 outliers final: 36 residues processed: 141 average time/residue: 0.0802 time to fit residues: 16.1597 Evaluate side-chains 145 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 103 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 49 optimal weight: 0.0770 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 32 optimal weight: 30.0000 chunk 50 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.146054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109799 restraints weight = 15308.515| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.23 r_work: 0.3211 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10065 Z= 0.141 Angle : 0.565 7.978 13801 Z= 0.299 Chirality : 0.040 0.166 1587 Planarity : 0.004 0.062 1619 Dihedral : 17.873 148.965 1659 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.61 % Allowed : 26.58 % Favored : 68.81 % 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: 0.32 (0.26), residues: 1102 helix: 1.44 (0.23), residues: 566 sheet: -0.70 (0.43), residues: 154 loop : -1.23 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 156 TYR 0.046 0.002 TYR B 152 PHE 0.012 0.001 PHE A 160 TRP 0.013 0.001 TRP C 32 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (10065) covalent geometry : angle 0.56464 / 0.30 (13801) hydrogen bonds : bond 0.04073 / 2.69 ( 469) hydrogen bonds : angle 3.82416 / 2.78 ( 1301) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 108 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: B 213 LYS cc_start: 0.7426 (tptt) cc_final: 0.7158 (tppt) REVERT: C 5 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8108 (mttt) REVERT: C 50 ASP cc_start: 0.7442 (m-30) cc_final: 0.7081 (m-30) REVERT: C 70 PHE cc_start: 0.6154 (OUTLIER) cc_final: 0.5670 (t80) REVERT: C 84 GLN cc_start: 0.8149 (tp40) cc_final: 0.7662 (tp40) REVERT: D 532 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7325 (mt-10) REVERT: A 121 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8379 (t0) REVERT: A 392 GLU cc_start: 0.8384 (tp30) cc_final: 0.8120 (tt0) REVERT: A 441 GLU cc_start: 0.5975 (OUTLIER) cc_final: 0.5700 (tm-30) REVERT: A 722 MET cc_start: 0.8710 (tpp) cc_final: 0.8321 (ttm) REVERT: A 850 ASP cc_start: 0.8742 (t0) cc_final: 0.8468 (t70) REVERT: A 867 MET cc_start: 0.8036 (mtm) cc_final: 0.7729 (mtm) REVERT: A 897 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6390 (tt) outliers start: 46 outliers final: 37 residues processed: 146 average time/residue: 0.0798 time to fit residues: 16.4693 Evaluate side-chains 148 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 105 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 689 ARG Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 114 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 36 GLN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.147183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111863 restraints weight = 15132.026| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.25 r_work: 0.3210 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10065 Z= 0.119 Angle : 0.552 7.977 13801 Z= 0.291 Chirality : 0.039 0.156 1587 Planarity : 0.004 0.059 1619 Dihedral : 17.835 148.886 1659 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.01 % Allowed : 27.28 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.41 (0.27), residues: 1102 helix: 1.49 (0.23), residues: 566 sheet: -0.66 (0.43), residues: 154 loop : -1.15 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 234 TYR 0.014 0.001 TYR B 145 PHE 0.012 0.001 PHE A 607 TRP 0.041 0.001 TRP C 32 HIS 0.002 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (10065) covalent geometry : angle 0.55157 / 0.29 (13801) hydrogen bonds : bond 0.03733 / 2.46 ( 469) hydrogen bonds : angle 3.78433 / 2.75 ( 1301) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 0.219 Fit side-chains REVERT: B 213 LYS cc_start: 0.7400 (tptt) cc_final: 0.7149 (tppt) REVERT: C 5 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8042 (mttt) REVERT: C 50 ASP cc_start: 0.7447 (m-30) cc_final: 0.7081 (m-30) REVERT: C 55 GLU cc_start: 0.7086 (pt0) cc_final: 0.6148 (tm-30) REVERT: C 70 PHE cc_start: 0.6105 (OUTLIER) cc_final: 0.5619 (t80) REVERT: C 84 GLN cc_start: 0.8172 (tp40) cc_final: 0.7681 (tp40) REVERT: D 532 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: A 121 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8404 (t0) REVERT: A 250 GLU cc_start: 0.7330 (tp30) cc_final: 0.6910 (tm-30) REVERT: A 392 GLU cc_start: 0.8407 (tp30) cc_final: 0.8112 (tt0) REVERT: A 441 GLU cc_start: 0.5989 (OUTLIER) cc_final: 0.5720 (tm-30) REVERT: A 722 MET cc_start: 0.8721 (tpp) cc_final: 0.8305 (ttm) REVERT: A 850 ASP cc_start: 0.8746 (t0) cc_final: 0.8464 (t70) REVERT: A 867 MET cc_start: 0.8111 (mtm) cc_final: 0.7826 (mtm) REVERT: A 897 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6324 (tt) outliers start: 40 outliers final: 32 residues processed: 140 average time/residue: 0.0814 time to fit residues: 16.1363 Evaluate side-chains 145 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 22 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 0.0770 chunk 31 optimal weight: 40.0000 chunk 68 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.147289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111603 restraints weight = 15284.614| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.25 r_work: 0.3207 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10065 Z= 0.119 Angle : 0.546 7.966 13801 Z= 0.288 Chirality : 0.039 0.159 1587 Planarity : 0.004 0.064 1619 Dihedral : 17.807 148.710 1659 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.91 % Allowed : 27.28 % Favored : 68.81 % 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: 0.42 (0.26), residues: 1102 helix: 1.51 (0.23), residues: 566 sheet: -0.65 (0.43), residues: 154 loop : -1.16 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 234 TYR 0.020 0.001 TYR B 152 PHE 0.011 0.001 PHE A 607 TRP 0.036 0.001 TRP C 32 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (10065) covalent geometry : angle 0.54589 / 0.29 (13801) hydrogen bonds : bond 0.03697 / 2.43 ( 469) hydrogen bonds : angle 3.76775 / 2.74 ( 1301) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1713.93 seconds wall clock time: 30 minutes 4.69 seconds (1804.69 seconds total)