Starting phenix.real_space_refine on Wed Aug 5 12:57:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qee_53058/08_2026/9qee_53058.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qee_53058/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9qee_53058/08_2026/9qee_53058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qee_53058/08_2026/9qee_53058.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qee_53058/08_2026/9qee_53058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qee_53058/08_2026/9qee_53058.map" } 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-2.2rc3-6140/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, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.91, per 1000 atoms: 0.20 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: 0.91 Conformation dependent library (CDL) restraints added in 196.6 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: 0.75 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: 1.43 Time building geometry restraints manager: 1.06 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: 13184 1.57 - 3.14: 543 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 2.320 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: 0.460 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.520 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.220 ------------------------------------------------------------------------------- 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 : 0.714 7.847 13801 Z= 0.449 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 0.71368 / 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 : 0.257 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: 0.1102 time to fit residues: 17.1878 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 : 0.376 ------------------------------------------------------------------------------- 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: 30.0000 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 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 = 0.3854 r_free = 0.3854 target = 0.145009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.108693 restraints weight = 15292.749| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.24 r_work: 0.3192 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.0762 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= 0.144 Angle : 0.592 7.313 13801 Z= 0.317 Chirality : 0.041 0.183 1587 Planarity : 0.004 0.047 1619 Dihedral : 18.254 146.764 1663 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.91 % Allowed : 25.38 % Favored : 71.72 % 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: -0.17 (0.26), residues: 1102 helix: 1.00 (0.23), residues: 565 sheet: -1.01 (0.43), residues: 152 loop : -1.33 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 234 TYR 0.012 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 0.00316 / 0.14 (10065) covalent geometry : angle 0.59194 / 0.32 (13801) hydrogen bonds : bond 0.05172 / 3.43 ( 469) hydrogen bonds : angle 4.39714 / 3.16 ( 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 142 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.414 Fit side-chains REVERT: B 224 MET cc_start: 0.8154 (mmm) cc_final: 0.7892 (mmm) REVERT: C 84 GLN cc_start: 0.8217 (tp40) cc_final: 0.7815 (tp40) REVERT: D 542 MET cc_start: 0.7588 (tpt) cc_final: 0.7368 (tpt) REVERT: A 392 GLU cc_start: 0.8219 (tp30) cc_final: 0.7984 (tm-30) REVERT: A 897 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6483 (tt) outliers start: 29 outliers final: 17 residues processed: 135 average time/residue: 0.0977 time to fit residues: 18.3610 Evaluate side-chains 116 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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: 1.9990 chunk 4 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 113 optimal weight: 20.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 179 GLN D 474 GLN A 893 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.145273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.109020 restraints weight = 15359.921| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.36 r_work: 0.3147 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.0958 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= 0.157 Angle : 0.594 8.430 13801 Z= 0.315 Chirality : 0.041 0.171 1587 Planarity : 0.004 0.044 1619 Dihedral : 18.173 145.241 1659 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.01 % Allowed : 25.78 % Favored : 70.21 % 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: -0.08 (0.26), residues: 1102 helix: 1.13 (0.23), residues: 566 sheet: -0.95 (0.43), residues: 152 loop : -1.41 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 52 TYR 0.016 0.001 TYR B 152 PHE 0.013 0.001 PHE A 160 TRP 0.007 0.001 TRP A 274 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (10065) covalent geometry : angle 0.59419 / 0.31 (13801) hydrogen bonds : bond 0.04957 / 3.29 ( 469) hydrogen bonds : angle 4.21230 / 3.04 ( 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 148 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: C 5 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8120 (mttt) REVERT: C 84 GLN cc_start: 0.8223 (tp40) cc_final: 0.7809 (tp40) REVERT: A 392 GLU cc_start: 0.8363 (tp30) cc_final: 0.8153 (tt0) REVERT: A 722 MET cc_start: 0.8794 (tpp) cc_final: 0.8522 (ttm) REVERT: A 875 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7229 (mm-30) REVERT: A 897 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6465 (tt) outliers start: 40 outliers final: 30 residues processed: 137 average time/residue: 0.0854 time to fit residues: 16.3735 Evaluate side-chains 135 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 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 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 A residue 58 LEU 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 875 GLU 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: 0.0030 chunk 95 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 474 GLN A 890 ASN A 893 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.146707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.110515 restraints weight = 15359.958| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.30 r_work: 0.3220 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1157 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= 0.124 Angle : 0.563 8.491 13801 Z= 0.299 Chirality : 0.040 0.158 1587 Planarity : 0.004 0.043 1619 Dihedral : 18.019 146.190 1659 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.61 % Allowed : 26.38 % 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: 0.09 (0.26), residues: 1102 helix: 1.26 (0.23), residues: 566 sheet: -0.85 (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 0.015 0.001 TYR B 130 PHE 0.012 0.001 PHE A 607 TRP 0.006 0.001 TRP A 326 HIS 0.002 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (10065) covalent geometry : angle 0.56251 / 0.30 (13801) hydrogen bonds : bond 0.04344 / 2.88 ( 469) hydrogen bonds : angle 4.04447 / 2.92 ( 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 143 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.279 Fit side-chains REVERT: C 5 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8001 (mttt) REVERT: C 50 ASP cc_start: 0.7394 (m-30) cc_final: 0.7087 (m-30) REVERT: C 84 GLN cc_start: 0.8147 (tp40) cc_final: 0.7724 (tp40) REVERT: A 392 GLU cc_start: 0.8284 (tp30) cc_final: 0.8078 (tt0) REVERT: A 722 MET cc_start: 0.8726 (tpp) cc_final: 0.8335 (ttm) REVERT: A 850 ASP cc_start: 0.8539 (t0) cc_final: 0.8257 (t70) REVERT: A 875 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7191 (mm-30) REVERT: A 897 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6448 (tt) outliers start: 36 outliers final: 28 residues processed: 134 average time/residue: 0.0805 time to fit residues: 15.5535 Evaluate side-chains 130 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 88 TYR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 530 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 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 603 LEU Chi-restraints excluded: chain A residue 633 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 73 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.142353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.105165 restraints weight = 15480.043| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.28 r_work: 0.3105 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 10065 Z= 0.300 Angle : 0.711 8.252 13801 Z= 0.372 Chirality : 0.046 0.191 1587 Planarity : 0.005 0.068 1619 Dihedral : 18.314 147.294 1659 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 5.92 % Allowed : 24.87 % 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: -0.31 (0.26), residues: 1102 helix: 0.93 (0.22), residues: 565 sheet: -1.09 (0.44), residues: 143 loop : -1.48 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 52 TYR 0.020 0.003 TYR C 88 PHE 0.024 0.002 PHE A 160 TRP 0.012 0.002 TRP D 540 HIS 0.008 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.30 (10065) covalent geometry : angle 0.71102 / 0.37 (13801) hydrogen bonds : bond 0.06017 / 4.00 ( 469) hydrogen bonds : angle 4.26928 / 3.12 ( 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 168 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 109 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: C 5 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8173 (mttt) REVERT: C 50 ASP cc_start: 0.7540 (m-30) cc_final: 0.7245 (m-30) REVERT: C 84 GLN cc_start: 0.8197 (tp40) cc_final: 0.7782 (tp40) REVERT: A 121 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8505 (t0) REVERT: A 850 ASP cc_start: 0.8756 (t0) cc_final: 0.8515 (t70) REVERT: A 897 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6486 (tt) outliers start: 59 outliers final: 43 residues processed: 158 average time/residue: 0.0946 time to fit residues: 21.3131 Evaluate side-chains 147 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 101 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 198 LEU 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 288 VAL 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 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 529 PHE 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 74 ASN 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 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 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 689 ARG Chi-restraints excluded: chain A residue 738 ASN 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 870 VAL 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: 0.8980 chunk 4 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 32 optimal weight: 30.0000 chunk 103 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.145073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.109189 restraints weight = 15355.289| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.27 r_work: 0.3180 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10065 Z= 0.139 Angle : 0.580 8.194 13801 Z= 0.307 Chirality : 0.041 0.158 1587 Planarity : 0.004 0.056 1619 Dihedral : 18.132 147.391 1659 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.51 % Allowed : 26.68 % 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: -0.01 (0.26), residues: 1102 helix: 1.17 (0.23), residues: 566 sheet: -0.84 (0.43), residues: 152 loop : -1.39 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 92 TYR 0.029 0.001 TYR B 130 PHE 0.014 0.001 PHE A 607 TRP 0.007 0.001 TRP A 326 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (10065) covalent geometry : angle 0.57985 / 0.31 (13801) hydrogen bonds : bond 0.04484 / 2.96 ( 469) hydrogen bonds : angle 4.03928 / 2.93 ( 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 148 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 103 time to evaluate : 0.368 Fit side-chains REVERT: C 5 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8094 (mttt) REVERT: C 50 ASP cc_start: 0.7443 (m-30) cc_final: 0.7124 (m-30) REVERT: C 84 GLN cc_start: 0.8173 (tp40) cc_final: 0.7718 (tp40) REVERT: D 532 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7326 (mt-10) REVERT: A 121 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8418 (t0) REVERT: A 250 GLU cc_start: 0.7329 (tp30) cc_final: 0.6988 (tm-30) REVERT: A 441 GLU cc_start: 0.6004 (OUTLIER) cc_final: 0.5753 (tm-30) REVERT: A 850 ASP cc_start: 0.8733 (t0) cc_final: 0.8468 (t70) REVERT: A 897 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6511 (tt) outliers start: 45 outliers final: 35 residues processed: 139 average time/residue: 0.0988 time to fit residues: 19.5569 Evaluate side-chains 142 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 15 VAL Chi-restraints excluded: chain C residue 38 LYS 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 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 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 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: 2.9990 chunk 67 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 108 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.144847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108923 restraints weight = 15336.050| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.24 r_work: 0.3174 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10065 Z= 0.156 Angle : 0.591 7.961 13801 Z= 0.311 Chirality : 0.041 0.154 1587 Planarity : 0.004 0.054 1619 Dihedral : 18.069 147.590 1659 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.81 % Allowed : 26.48 % 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: 0.08 (0.26), residues: 1102 helix: 1.26 (0.23), residues: 565 sheet: -0.82 (0.43), residues: 154 loop : -1.35 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 234 TYR 0.024 0.002 TYR B 130 PHE 0.013 0.001 PHE A 186 TRP 0.006 0.001 TRP A 326 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (10065) covalent geometry : angle 0.59056 / 0.31 (13801) hydrogen bonds : bond 0.04511 / 2.98 ( 469) hydrogen bonds : angle 3.97333 / 2.89 ( 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: 48 poor density : 103 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: C 5 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8128 (mttt) REVERT: C 39 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.8026 (pm20) REVERT: C 50 ASP cc_start: 0.7430 (m-30) cc_final: 0.7097 (m-30) REVERT: C 84 GLN cc_start: 0.8165 (tp40) cc_final: 0.7700 (tp40) REVERT: D 532 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7363 (mt-10) REVERT: A 121 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8431 (t0) REVERT: A 250 GLU cc_start: 0.7322 (tp30) cc_final: 0.6831 (tm-30) REVERT: A 441 GLU cc_start: 0.6015 (OUTLIER) cc_final: 0.5752 (tm-30) REVERT: A 850 ASP cc_start: 0.8707 (t0) cc_final: 0.8444 (t70) REVERT: A 897 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6486 (tt) outliers start: 48 outliers final: 41 residues processed: 142 average time/residue: 0.1035 time to fit residues: 20.7220 Evaluate side-chains 149 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 102 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 15 VAL Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 39 GLU 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 131 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 200 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 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 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: 0.0670 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.147956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111592 restraints weight = 15148.410| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.25 r_work: 0.3229 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10065 Z= 0.112 Angle : 0.554 7.959 13801 Z= 0.292 Chirality : 0.039 0.146 1587 Planarity : 0.004 0.049 1619 Dihedral : 17.855 147.668 1659 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.31 % Allowed : 27.98 % 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: 0.31 (0.26), residues: 1102 helix: 1.45 (0.23), residues: 566 sheet: -0.74 (0.43), residues: 154 loop : -1.24 (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 130 PHE 0.014 0.001 PHE A 607 TRP 0.015 0.001 TRP C 32 HIS 0.002 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (10065) covalent geometry : angle 0.55358 / 0.29 (13801) hydrogen bonds : bond 0.03738 / 2.47 ( 469) hydrogen bonds : angle 3.84586 / 2.78 ( 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 146 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.364 Fit side-chains REVERT: B 213 LYS cc_start: 0.7494 (tptt) cc_final: 0.7222 (tppt) REVERT: C 50 ASP cc_start: 0.7432 (m-30) cc_final: 0.7130 (m-30) REVERT: C 55 GLU cc_start: 0.7076 (pt0) cc_final: 0.6105 (tm-30) REVERT: C 70 PHE cc_start: 0.6071 (OUTLIER) cc_final: 0.5590 (t80) REVERT: C 84 GLN cc_start: 0.8154 (tp40) cc_final: 0.7665 (tp40) REVERT: D 532 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: A 250 GLU cc_start: 0.7270 (tp30) cc_final: 0.6826 (tm-30) REVERT: A 441 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5674 (tm-30) REVERT: A 722 MET cc_start: 0.8742 (tpp) cc_final: 0.8380 (ttm) REVERT: A 850 ASP cc_start: 0.8717 (t0) cc_final: 0.8452 (t70) REVERT: A 875 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7168 (mm-30) outliers start: 33 outliers final: 26 residues processed: 138 average time/residue: 0.0939 time to fit residues: 18.6136 Evaluate side-chains 137 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 70 PHE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 88 TYR 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 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 249 VAL Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 441 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 49 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 32 optimal weight: 30.0000 chunk 50 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3868 r_free = 0.3868 target = 0.146067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.110273 restraints weight = 15325.036| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.23 r_work: 0.3190 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1514 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= 0.151 Angle : 0.580 8.091 13801 Z= 0.305 Chirality : 0.041 0.171 1587 Planarity : 0.004 0.065 1619 Dihedral : 17.901 147.940 1659 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % 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: 0.26 (0.26), residues: 1102 helix: 1.41 (0.23), residues: 566 sheet: -0.77 (0.43), residues: 154 loop : -1.27 (0.31), residues: 382 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 0.012 0.001 PHE A 186 TRP 0.011 0.001 TRP C 32 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (10065) covalent geometry : angle 0.58013 / 0.31 (13801) hydrogen bonds : bond 0.04142 / 2.73 ( 469) hydrogen bonds : angle 3.89070 / 2.83 ( 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 147 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 0.283 Fit side-chains REVERT: C 5 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8064 (mttt) REVERT: C 50 ASP cc_start: 0.7465 (m-30) cc_final: 0.7118 (m-30) REVERT: C 84 GLN cc_start: 0.8169 (tp40) cc_final: 0.7670 (tp40) REVERT: D 532 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7244 (mt-10) REVERT: A 250 GLU cc_start: 0.7322 (tp30) cc_final: 0.6860 (tm-30) REVERT: A 441 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5790 (tm-30) REVERT: A 722 MET cc_start: 0.8745 (tpp) cc_final: 0.8411 (ttm) REVERT: A 850 ASP cc_start: 0.8741 (t0) cc_final: 0.8471 (t70) REVERT: A 875 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7231 (mm-30) outliers start: 40 outliers final: 33 residues processed: 139 average time/residue: 0.0846 time to fit residues: 16.8624 Evaluate side-chains 142 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 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 92 ILE Chi-restraints excluded: chain A residue 100 VAL 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 332 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 875 GLU 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: 6.9990 chunk 21 optimal weight: 0.0370 chunk 108 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3895 r_free = 0.3895 target = 0.148502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111829 restraints weight = 15179.079| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.27 r_work: 0.3249 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1697 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= 0.115 Angle : 0.562 8.061 13801 Z= 0.297 Chirality : 0.039 0.161 1587 Planarity : 0.004 0.063 1619 Dihedral : 17.823 148.015 1659 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.21 % Allowed : 28.49 % Favored : 68.30 % 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: 0.39 (0.26), residues: 1102 helix: 1.52 (0.23), residues: 561 sheet: -0.69 (0.43), residues: 154 loop : -1.19 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 234 TYR 0.045 0.001 TYR B 152 PHE 0.013 0.001 PHE A 607 TRP 0.014 0.001 TRP C 32 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (10065) covalent geometry : angle 0.56167 / 0.30 (13801) hydrogen bonds : bond 0.03643 / 2.41 ( 469) hydrogen bonds : angle 3.82212 / 2.78 ( 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 137 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.269 Fit side-chains REVERT: B 213 LYS cc_start: 0.7324 (tptt) cc_final: 0.7055 (tppt) REVERT: C 5 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8005 (mttt) REVERT: C 50 ASP cc_start: 0.7415 (m-30) cc_final: 0.7063 (m-30) REVERT: C 55 GLU cc_start: 0.7020 (pt0) cc_final: 0.6101 (tm-30) REVERT: C 84 GLN cc_start: 0.8124 (tp40) cc_final: 0.7680 (tp40) REVERT: D 532 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: A 250 GLU cc_start: 0.7221 (tp30) cc_final: 0.6817 (tm-30) REVERT: A 441 GLU cc_start: 0.5939 (OUTLIER) cc_final: 0.5685 (tm-30) REVERT: A 722 MET cc_start: 0.8712 (tpp) cc_final: 0.8334 (ttm) REVERT: A 850 ASP cc_start: 0.8692 (t0) cc_final: 0.8419 (t70) REVERT: A 875 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7207 (mm-30) outliers start: 32 outliers final: 27 residues processed: 129 average time/residue: 0.0960 time to fit residues: 17.4148 Evaluate side-chains 136 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 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 92 ILE Chi-restraints excluded: chain A residue 100 VAL 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 373 LEU Chi-restraints excluded: chain A residue 441 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 22 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 12 optimal weight: 0.0040 chunk 31 optimal weight: 30.0000 chunk 68 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 overall best weight: 0.7392 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.148100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.112077 restraints weight = 15242.739| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.17 r_work: 0.3281 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1775 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= 0.113 Angle : 0.555 8.045 13801 Z= 0.292 Chirality : 0.039 0.159 1587 Planarity : 0.004 0.059 1619 Dihedral : 17.776 147.660 1659 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.41 % Allowed : 28.08 % Favored : 68.51 % 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: 0.48 (0.26), residues: 1102 helix: 1.58 (0.23), residues: 561 sheet: -0.63 (0.43), residues: 154 loop : -1.14 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 234 TYR 0.018 0.001 TYR B 145 PHE 0.011 0.001 PHE A 607 TRP 0.041 0.001 TRP C 32 HIS 0.003 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (10065) covalent geometry : angle 0.55529 / 0.29 (13801) hydrogen bonds : bond 0.03526 / 2.32 ( 469) hydrogen bonds : angle 3.77646 / 2.75 ( 1301) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1920.67 seconds wall clock time: 33 minutes 37.83 seconds (2017.83 seconds total)