Starting phenix.real_space_refine on Thu Mar 5 02:01:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r1u_4705/03_2026/6r1u_4705.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r1u_4705/03_2026/6r1u_4705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6r1u_4705/03_2026/6r1u_4705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r1u_4705/03_2026/6r1u_4705.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6r1u_4705/03_2026/6r1u_4705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r1u_4705/03_2026/6r1u_4705.map" } resolution = 4.36 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 Zn 3 6.06 5 P 296 5.49 5 S 54 5.16 5 C 10684 2.51 5 N 3372 2.21 5 O 3985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18394 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 689 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 811 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 820 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 870 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "H" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 775 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 5837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5837 Classifications: {'peptide': 737} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 36, 'TRANS': 698} Chain breaks: 2 Chain: "L" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "M" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 193 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "K" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {' ZN': 3, 'FAD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12239 SG CYS K 53 75.441 111.267 70.128 1.00 48.02 S ATOM 12272 SG CYS K 58 73.966 113.629 73.201 1.00 47.27 S ATOM 12317 SG CYS K 65 85.145 104.914 75.500 1.00 37.13 S ATOM 12376 SG CYS K 73 88.895 105.346 75.202 1.00 40.55 S ATOM 12534 SG CYS K 92 86.794 104.861 71.584 1.00 37.37 S ATOM 12557 SG CYS K 95 87.344 102.062 74.063 1.00 36.80 S ATOM 12964 SG CYS K 142 77.571 111.293 100.726 1.00 35.45 S ATOM 13002 SG CYS K 147 77.414 114.859 99.519 1.00 37.39 S ATOM 13195 SG CYS K 169 80.000 112.370 98.082 1.00 34.97 S ATOM 13246 SG CYS K 185 80.326 113.849 101.839 1.00 38.56 S Time building chain proxies: 3.75, per 1000 atoms: 0.20 Number of scatterers: 18394 At special positions: 0 Unit cell: (134.62, 132.5, 137.8, 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) Zn 3 29.99 S 54 16.00 P 296 15.00 O 3985 8.00 N 3372 7.00 C 10684 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 Atom "ATOM 9765 O5' DC J -46 .*. O " rejected from bonding due to valence issues. Atom "ATOM 9765 O5' DC J -46 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 469.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 902 " pdb="ZN ZN K 902 " - pdb=" NE2 HIS K 90 " pdb="ZN ZN K 902 " - pdb=" SG CYS K 58 " pdb="ZN ZN K 902 " - pdb=" ND1 HIS K 84 " pdb="ZN ZN K 902 " - pdb=" SG CYS K 53 " pdb=" ZN K 903 " pdb="ZN ZN K 903 " - pdb=" SG CYS K 95 " pdb="ZN ZN K 903 " - pdb=" SG CYS K 65 " pdb="ZN ZN K 903 " - pdb=" SG CYS K 73 " pdb="ZN ZN K 903 " - pdb=" SG CYS K 92 " pdb=" ZN K 904 " pdb="ZN ZN K 904 " - pdb=" SG CYS K 147 " pdb="ZN ZN K 904 " - pdb=" SG CYS K 142 " pdb="ZN ZN K 904 " - pdb=" SG CYS K 185 " pdb="ZN ZN K 904 " - pdb=" SG CYS K 169 " Number of angles added : 13 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 16 sheets defined 55.0% alpha, 5.9% beta 142 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.087A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.547A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.607A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.681A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.545A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 79 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.747A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 113 removed outlier: 3.599A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.549A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 75 removed outlier: 3.698A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.863A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 88 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.518A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 4.309A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.603A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 101 Processing helix chain 'K' and resid 106 through 117 Processing helix chain 'K' and resid 126 through 135 Processing helix chain 'K' and resid 160 through 167 Processing helix chain 'K' and resid 183 through 187 Processing helix chain 'K' and resid 191 through 196 removed outlier: 3.947A pdb=" N GLU K 195 " --> pdb=" O LEU K 191 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL K 196 " --> pdb=" O ARG K 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 191 through 196' Processing helix chain 'K' and resid 198 through 204 removed outlier: 4.047A pdb=" N TYR K 202 " --> pdb=" O ASN K 198 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER K 203 " --> pdb=" O HIS K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 216 through 220 Processing helix chain 'K' and resid 224 through 228 Processing helix chain 'K' and resid 290 through 297 Processing helix chain 'K' and resid 298 through 301 Processing helix chain 'K' and resid 304 through 321 Processing helix chain 'K' and resid 327 through 332 Processing helix chain 'K' and resid 333 through 335 No H-bonds generated for 'chain 'K' and resid 333 through 335' Processing helix chain 'K' and resid 340 through 359 removed outlier: 3.592A pdb=" N ARG K 344 " --> pdb=" O LEU K 340 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU K 350 " --> pdb=" O VAL K 346 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG K 351 " --> pdb=" O GLN K 347 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 381 Processing helix chain 'K' and resid 391 through 405 Processing helix chain 'K' and resid 445 through 455 Processing helix chain 'K' and resid 476 through 498 Processing helix chain 'K' and resid 499 through 501 No H-bonds generated for 'chain 'K' and resid 499 through 501' Processing helix chain 'K' and resid 502 through 506 Processing helix chain 'K' and resid 508 through 524 Processing helix chain 'K' and resid 529 through 548 Processing helix chain 'K' and resid 560 through 565 Processing helix chain 'K' and resid 579 through 588 Processing helix chain 'K' and resid 628 through 635 Processing helix chain 'K' and resid 644 through 653 Processing helix chain 'K' and resid 671 through 676 Processing helix chain 'K' and resid 715 through 721 removed outlier: 4.197A pdb=" N ALA K 719 " --> pdb=" O GLY K 715 " (cutoff:3.500A) Processing helix chain 'K' and resid 725 through 741 Processing helix chain 'K' and resid 756 through 760 Processing helix chain 'K' and resid 776 through 784 removed outlier: 4.028A pdb=" N ASP K 780 " --> pdb=" O GLY K 776 " (cutoff:3.500A) Processing helix chain 'K' and resid 794 through 798 Processing helix chain 'K' and resid 804 through 822 removed outlier: 3.731A pdb=" N PHE K 822 " --> pdb=" O LYS K 818 " (cutoff:3.500A) Processing helix chain 'L' and resid 219 through 223 removed outlier: 3.846A pdb=" N SER L 223 " --> pdb=" O PHE L 220 " (cutoff:3.500A) Processing helix chain 'M' and resid 1 through 5 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.061A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.677A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.781A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.765A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'K' and resid 82 through 86 removed outlier: 6.486A pdb=" N GLU K 89 " --> pdb=" O LEU K 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 139 through 141 Processing sheet with id=AB2, first strand: chain 'K' and resid 592 through 593 removed outlier: 8.207A pdb=" N GLN K 593 " --> pdb=" O VAL K 408 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL K 410 " --> pdb=" O GLN K 593 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL K 385 " --> pdb=" O THR K 409 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU K 411 " --> pdb=" O VAL K 385 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE K 387 " --> pdb=" O LEU K 411 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 423 through 424 Processing sheet with id=AB4, first strand: chain 'K' and resid 438 through 440 Processing sheet with id=AB5, first strand: chain 'K' and resid 467 through 468 removed outlier: 5.345A pdb=" N ALA K 695 " --> pdb=" O HIS K 683 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL K 696 " --> pdb=" O VAL K 712 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL K 712 " --> pdb=" O VAL K 696 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS K 751 " --> pdb=" O GLN K 665 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 617 through 620 removed outlier: 6.794A pdb=" N GLN K 599 " --> pdb=" O GLN K 638 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ASN K 640 " --> pdb=" O GLN K 599 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE K 601 " --> pdb=" O ASN K 640 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 654 through 657 612 hydrogen bonds defined for protein. 1749 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 363 hydrogen bonds 722 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 4.66 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2389 1.31 - 1.44: 6635 1.44 - 1.57: 9668 1.57 - 1.70: 586 1.70 - 1.82: 81 Bond restraints: 19359 Sorted by residual: bond pdb=" O5B FAD K 901 " pdb=" PA FAD K 901 " ideal model delta sigma weight residual 1.634 1.386 0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" O3P FAD K 901 " pdb=" P FAD K 901 " ideal model delta sigma weight residual 1.660 1.470 0.190 2.00e-02 2.50e+03 9.07e+01 bond pdb=" O3P FAD K 901 " pdb=" PA FAD K 901 " ideal model delta sigma weight residual 1.633 1.454 0.179 2.00e-02 2.50e+03 8.05e+01 bond pdb=" O5' FAD K 901 " pdb=" P FAD K 901 " ideal model delta sigma weight residual 1.637 1.464 0.173 2.00e-02 2.50e+03 7.48e+01 bond pdb=" O1A FAD K 901 " pdb=" PA FAD K 901 " ideal model delta sigma weight residual 1.509 1.365 0.144 2.00e-02 2.50e+03 5.22e+01 ... (remaining 19354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 27127 3.43 - 6.86: 273 6.86 - 10.29: 18 10.29 - 13.72: 3 13.72 - 17.15: 2 Bond angle restraints: 27423 Sorted by residual: angle pdb=" C LYS K 75 " pdb=" CA LYS K 75 " pdb=" CB LYS K 75 " ideal model delta sigma weight residual 117.23 108.32 8.91 1.36e+00 5.41e-01 4.29e+01 angle pdb=" O1P FAD K 901 " pdb=" P FAD K 901 " pdb=" O2P FAD K 901 " ideal model delta sigma weight residual 122.50 105.35 17.15 3.00e+00 1.11e-01 3.27e+01 angle pdb=" C ASP L 214 " pdb=" N PRO L 215 " pdb=" CA PRO L 215 " ideal model delta sigma weight residual 119.47 125.97 -6.50 1.16e+00 7.43e-01 3.14e+01 angle pdb=" CA LYS K 75 " pdb=" C LYS K 75 " pdb=" N ASN K 76 " ideal model delta sigma weight residual 119.98 115.33 4.65 8.50e-01 1.38e+00 3.00e+01 angle pdb=" C ASP K 760 " pdb=" N PRO K 761 " pdb=" CA PRO K 761 " ideal model delta sigma weight residual 119.05 125.04 -5.99 1.11e+00 8.12e-01 2.92e+01 ... (remaining 27418 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 9220 35.91 - 71.82: 1648 71.82 - 107.73: 32 107.73 - 143.64: 1 143.64 - 179.56: 1 Dihedral angle restraints: 10902 sinusoidal: 6408 harmonic: 4494 Sorted by residual: dihedral pdb=" CD ARG A 40 " pdb=" NE ARG A 40 " pdb=" CZ ARG A 40 " pdb=" NH1 ARG A 40 " ideal model delta sinusoidal sigma weight residual 0.00 -85.61 85.61 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CD ARG G 11 " pdb=" NE ARG G 11 " pdb=" CZ ARG G 11 " pdb=" NH1 ARG G 11 " ideal model delta sinusoidal sigma weight residual 0.00 -66.88 66.88 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CD ARG H 30 " pdb=" NE ARG H 30 " pdb=" CZ ARG H 30 " pdb=" NH1 ARG H 30 " ideal model delta sinusoidal sigma weight residual 0.00 -57.45 57.45 1 1.00e+01 1.00e-02 4.43e+01 ... (remaining 10899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2312 0.062 - 0.124: 630 0.124 - 0.186: 107 0.186 - 0.247: 16 0.247 - 0.309: 3 Chirality restraints: 3068 Sorted by residual: chirality pdb=" C3' FAD K 901 " pdb=" C2' FAD K 901 " pdb=" C4' FAD K 901 " pdb=" O3' FAD K 901 " both_signs ideal model delta sigma weight residual False -2.55 -2.24 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA THR K 143 " pdb=" N THR K 143 " pdb=" C THR K 143 " pdb=" CB THR K 143 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CG LEU G 34 " pdb=" CB LEU G 34 " pdb=" CD1 LEU G 34 " pdb=" CD2 LEU G 34 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 3065 not shown) Planarity restraints: 2456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FAD K 901 " -0.396 2.00e-02 2.50e+03 2.24e-01 2.38e+03 pdb=" C10 FAD K 901 " -0.140 2.00e-02 2.50e+03 pdb=" C2 FAD K 901 " 0.214 2.00e-02 2.50e+03 pdb=" C4 FAD K 901 " 0.037 2.00e-02 2.50e+03 pdb=" C4X FAD K 901 " -0.149 2.00e-02 2.50e+03 pdb=" C5X FAD K 901 " -0.219 2.00e-02 2.50e+03 pdb=" C6 FAD K 901 " -0.124 2.00e-02 2.50e+03 pdb=" C7 FAD K 901 " 0.076 2.00e-02 2.50e+03 pdb=" C7M FAD K 901 " 0.199 2.00e-02 2.50e+03 pdb=" C8 FAD K 901 " 0.173 2.00e-02 2.50e+03 pdb=" C8M FAD K 901 " 0.382 2.00e-02 2.50e+03 pdb=" C9 FAD K 901 " 0.055 2.00e-02 2.50e+03 pdb=" C9A FAD K 901 " -0.148 2.00e-02 2.50e+03 pdb=" N1 FAD K 901 " 0.045 2.00e-02 2.50e+03 pdb=" N10 FAD K 901 " -0.262 2.00e-02 2.50e+03 pdb=" N3 FAD K 901 " 0.222 2.00e-02 2.50e+03 pdb=" N5 FAD K 901 " -0.369 2.00e-02 2.50e+03 pdb=" O2 FAD K 901 " 0.371 2.00e-02 2.50e+03 pdb=" O4 FAD K 901 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 40 " 1.099 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG A 40 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 40 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 40 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 40 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 11 " 1.007 9.50e-02 1.11e+02 4.51e-01 1.23e+02 pdb=" NE ARG G 11 " -0.061 2.00e-02 2.50e+03 pdb=" CZ ARG G 11 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG G 11 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG G 11 " 0.023 2.00e-02 2.50e+03 ... (remaining 2453 not shown) Histogram of nonbonded interaction distances: 0.54 - 1.42: 11 1.42 - 2.29: 63 2.29 - 3.16: 14531 3.16 - 4.03: 54780 4.03 - 4.90: 89241 Warning: very small nonbonded interaction distances. Nonbonded interactions: 158626 Sorted by model distance: nonbonded pdb=" NH1 ARG H 30 " pdb=" O5' DC J -46 " model vdw 0.544 3.120 nonbonded pdb=" NH2 ARG H 30 " pdb=" O3' DT J -47 " model vdw 0.796 3.120 nonbonded pdb=" CB ARG A 128 " pdb=" OE1 GLU A 133 " model vdw 0.821 3.440 nonbonded pdb=" NE ARG A 128 " pdb=" OE2 GLU A 133 " model vdw 0.827 3.120 nonbonded pdb=" NZ LYS D 28 " pdb=" O3' DA J 50 " model vdw 0.922 3.120 ... (remaining 158621 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 37 through 134) selection = (chain 'E' and resid 37 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 101) selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 120) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 26 through 121) } 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 group one per residue 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: 1.730 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: 0.030 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.520 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4616 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 : 0.009 0.346 19371 Z= 0.453 Angle : 1.048 17.149 27436 Z= 0.634 Chirality : 0.058 0.309 3068 Planarity : 0.023 0.492 2456 Dihedral : 25.719 179.556 8006 Min Nonbonded Distance : 0.544 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 1.25 % Allowed : 4.66 % Favored : 94.09 % Rotamer: Outliers : 6.26 % Allowed : 4.58 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.18), residues: 1524 helix: -2.27 (0.14), residues: 787 sheet: 0.51 (0.69), residues: 61 loop : -1.71 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 72 TYR 0.019 0.003 TYR K 767 PHE 0.033 0.003 PHE C 25 TRP 0.014 0.002 TRP K 117 HIS 0.014 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00864 (19359) covalent geometry : angle 1.04313 (27423) hydrogen bonds : bond 0.12953 ( 975) hydrogen bonds : angle 7.15454 ( 2471) metal coordination : bond 0.14820 ( 12) metal coordination : angle 4.91720 ( 13) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 276 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8726 (mp) cc_final: 0.8345 (tp) REVERT: E 74 ILE cc_start: 0.9194 (mt) cc_final: 0.8614 (mm) REVERT: E 107 THR cc_start: 0.8394 (m) cc_final: 0.8033 (p) REVERT: F 88 TYR cc_start: 0.8176 (m-10) cc_final: 0.7941 (m-80) REVERT: K 85 LEU cc_start: 0.1544 (OUTLIER) cc_final: 0.1162 (tp) REVERT: K 204 MET cc_start: 0.2224 (mtm) cc_final: 0.1943 (ttm) REVERT: K 294 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6212 (mt) REVERT: K 458 MET cc_start: -0.1180 (mtm) cc_final: -0.3741 (mtt) REVERT: K 700 MET cc_start: -0.2175 (mmm) cc_final: -0.2801 (mmm) REVERT: M 22 THR cc_start: -0.0210 (OUTLIER) cc_final: -0.0427 (t) outliers start: 82 outliers final: 26 residues processed: 347 average time/residue: 0.1887 time to fit residues: 90.0264 Evaluate side-chains 150 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 40.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 46 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 ASN K 98 HIS K 400 GLN ** K 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 218 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.074687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.038929 restraints weight = 137255.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.039487 restraints weight = 78572.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.040229 restraints weight = 55694.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.040588 restraints weight = 43979.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.040732 restraints weight = 38057.868| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19371 Z= 0.228 Angle : 0.727 10.212 27436 Z= 0.406 Chirality : 0.042 0.184 3068 Planarity : 0.008 0.163 2456 Dihedral : 29.456 177.383 4968 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.35 % Favored : 96.46 % Rotamer: Outliers : 0.23 % Allowed : 2.98 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % 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 (0.20), residues: 1524 helix: 0.28 (0.17), residues: 794 sheet: 1.33 (0.66), residues: 61 loop : -0.87 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG E 131 TYR 0.028 0.002 TYR B 88 PHE 0.021 0.002 PHE C 25 TRP 0.008 0.001 TRP K 762 HIS 0.009 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00484 (19359) covalent geometry : angle 0.72288 (27423) hydrogen bonds : bond 0.06520 ( 975) hydrogen bonds : angle 4.04008 ( 2471) metal coordination : bond 0.00888 ( 12) metal coordination : angle 3.45816 ( 13) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 174 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.9564 (tpt-90) cc_final: 0.9192 (tpm170) REVERT: B 84 MET cc_start: 0.9241 (mmm) cc_final: 0.9019 (tpp) REVERT: D 77 LEU cc_start: 0.9668 (tp) cc_final: 0.9423 (tt) REVERT: E 50 GLU cc_start: 0.9174 (tp30) cc_final: 0.8872 (tp30) REVERT: E 51 ILE cc_start: 0.8987 (mt) cc_final: 0.8769 (mm) REVERT: E 79 LYS cc_start: 0.9301 (tmmt) cc_final: 0.9073 (tmtt) REVERT: E 97 GLU cc_start: 0.8589 (pp20) cc_final: 0.8168 (pp20) REVERT: E 119 ILE cc_start: 0.8534 (mp) cc_final: 0.8304 (mm) REVERT: E 120 MET cc_start: 0.8327 (ptp) cc_final: 0.7417 (mpp) REVERT: F 24 ASP cc_start: 0.9102 (t0) cc_final: 0.8735 (p0) REVERT: H 73 GLU cc_start: 0.9034 (tp30) cc_final: 0.8830 (tp30) REVERT: H 103 LEU cc_start: 0.9195 (mm) cc_final: 0.8607 (pt) REVERT: K 265 MET cc_start: 0.8239 (ttt) cc_final: 0.7919 (tpt) REVERT: K 458 MET cc_start: 0.8576 (mtm) cc_final: 0.8183 (mtt) outliers start: 3 outliers final: 0 residues processed: 175 average time/residue: 0.1635 time to fit residues: 41.0284 Evaluate side-chains 118 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 82 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 110 optimal weight: 40.0000 chunk 87 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 172 optimal weight: 30.0000 chunk 129 optimal weight: 40.0000 chunk 143 optimal weight: 40.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN D 81 ASN E 85 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS K 469 GLN ** K 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.068239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.033188 restraints weight = 141418.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.033855 restraints weight = 79263.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.034080 restraints weight = 55663.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.034434 restraints weight = 45215.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.034564 restraints weight = 39543.886| |-----------------------------------------------------------------------------| r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.128 19371 Z= 0.313 Angle : 0.698 8.248 27436 Z= 0.397 Chirality : 0.041 0.210 3068 Planarity : 0.006 0.084 2456 Dihedral : 29.695 177.546 4968 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.35 % Favored : 96.46 % Rotamer: Outliers : 0.15 % Allowed : 3.66 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % 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: 0.47 (0.21), residues: 1524 helix: 0.96 (0.18), residues: 809 sheet: 1.47 (0.60), residues: 71 loop : -0.59 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 30 TYR 0.025 0.002 TYR A 54 PHE 0.017 0.002 PHE K 91 TRP 0.011 0.001 TRP K 200 HIS 0.022 0.002 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00680 (19359) covalent geometry : angle 0.69535 (27423) hydrogen bonds : bond 0.09393 ( 975) hydrogen bonds : angle 4.02024 ( 2471) metal coordination : bond 0.00397 ( 12) metal coordination : angle 2.75792 ( 13) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.9138 (pt0) cc_final: 0.8897 (pt0) REVERT: B 84 MET cc_start: 0.9338 (mmm) cc_final: 0.8636 (tpp) REVERT: E 50 GLU cc_start: 0.9289 (tp30) cc_final: 0.8972 (tp30) REVERT: E 65 LEU cc_start: 0.9807 (mt) cc_final: 0.9228 (mt) REVERT: E 97 GLU cc_start: 0.8527 (pp20) cc_final: 0.8183 (pp20) REVERT: E 103 LEU cc_start: 0.9793 (tt) cc_final: 0.9583 (tt) REVERT: E 120 MET cc_start: 0.9004 (ptp) cc_final: 0.8301 (mmm) REVERT: F 59 LYS cc_start: 0.9654 (tptp) cc_final: 0.9358 (tppt) REVERT: H 73 GLU cc_start: 0.9127 (tp30) cc_final: 0.8753 (tp30) REVERT: H 76 ARG cc_start: 0.9265 (ptp90) cc_final: 0.8815 (ptp90) REVERT: K 458 MET cc_start: 0.8569 (mtm) cc_final: 0.8132 (mtt) outliers start: 2 outliers final: 0 residues processed: 140 average time/residue: 0.1586 time to fit residues: 32.4906 Evaluate side-chains 96 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 39 optimal weight: 0.9980 chunk 149 optimal weight: 40.0000 chunk 99 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 129 optimal weight: 50.0000 chunk 29 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 112 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 184 HIS ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.069017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.033417 restraints weight = 141059.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.033869 restraints weight = 81464.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.034123 restraints weight = 54184.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.034395 restraints weight = 43117.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.034522 restraints weight = 36904.940| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19371 Z= 0.180 Angle : 0.613 8.040 27436 Z= 0.346 Chirality : 0.039 0.184 3068 Planarity : 0.005 0.067 2456 Dihedral : 29.631 177.731 4968 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.15 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % 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: 0.81 (0.21), residues: 1524 helix: 1.29 (0.18), residues: 809 sheet: 1.47 (0.62), residues: 73 loop : -0.51 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 134 TYR 0.023 0.001 TYR K 273 PHE 0.015 0.001 PHE C 25 TRP 0.007 0.001 TRP K 762 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00394 (19359) covalent geometry : angle 0.61070 (27423) hydrogen bonds : bond 0.05255 ( 975) hydrogen bonds : angle 3.67199 ( 2471) metal coordination : bond 0.00236 ( 12) metal coordination : angle 2.24065 ( 13) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9332 (mmm) cc_final: 0.9114 (mmm) REVERT: C 56 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8661 (mm-30) REVERT: D 73 GLU cc_start: 0.9332 (tp30) cc_final: 0.9029 (tp30) REVERT: D 77 LEU cc_start: 0.9730 (tp) cc_final: 0.9525 (tt) REVERT: E 36 LYS cc_start: 0.6256 (mppt) cc_final: 0.5519 (pttm) REVERT: E 50 GLU cc_start: 0.9254 (tp30) cc_final: 0.8950 (tp30) REVERT: E 51 ILE cc_start: 0.8915 (mt) cc_final: 0.8612 (mm) REVERT: E 106 ASP cc_start: 0.8846 (m-30) cc_final: 0.8433 (m-30) REVERT: E 120 MET cc_start: 0.8852 (ptp) cc_final: 0.8100 (mmm) REVERT: E 124 ILE cc_start: 0.9778 (mm) cc_final: 0.9475 (mp) REVERT: H 73 GLU cc_start: 0.9152 (tp30) cc_final: 0.8803 (tp30) REVERT: H 76 ARG cc_start: 0.9175 (ptp90) cc_final: 0.8826 (ptp90) REVERT: K 306 MET cc_start: 0.4708 (tmm) cc_final: 0.4166 (tpp) REVERT: K 458 MET cc_start: 0.8574 (mtm) cc_final: 0.8108 (mtt) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1564 time to fit residues: 32.9230 Evaluate side-chains 99 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 125 optimal weight: 20.0000 chunk 166 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 151 optimal weight: 30.0000 chunk 62 optimal weight: 0.0570 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 139 optimal weight: 30.0000 chunk 75 optimal weight: 6.9990 overall best weight: 1.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN C 31 HIS F 25 ASN G 104 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.068850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.033331 restraints weight = 140692.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.033809 restraints weight = 77424.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.034369 restraints weight = 54658.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.034388 restraints weight = 42533.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.034592 restraints weight = 38497.846| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19371 Z= 0.162 Angle : 0.599 9.370 27436 Z= 0.338 Chirality : 0.038 0.203 3068 Planarity : 0.004 0.055 2456 Dihedral : 29.404 177.737 4968 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.15 % Favored : 96.72 % Rotamer: Outliers : 0.08 % Allowed : 1.98 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % 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: 0.97 (0.22), residues: 1524 helix: 1.42 (0.18), residues: 810 sheet: 1.35 (0.62), residues: 75 loop : -0.41 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 129 TYR 0.016 0.001 TYR K 273 PHE 0.015 0.001 PHE C 25 TRP 0.008 0.001 TRP K 762 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00354 (19359) covalent geometry : angle 0.59698 (27423) hydrogen bonds : bond 0.04914 ( 975) hydrogen bonds : angle 3.57417 ( 2471) metal coordination : bond 0.01298 ( 12) metal coordination : angle 2.33575 ( 13) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8610 (t0) cc_final: 0.8251 (m-30) REVERT: B 44 LYS cc_start: 0.9001 (tmmt) cc_final: 0.8753 (tmmt) REVERT: B 63 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8626 (tm-30) REVERT: B 84 MET cc_start: 0.9335 (mmm) cc_final: 0.9120 (mmm) REVERT: C 56 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8720 (mm-30) REVERT: D 77 LEU cc_start: 0.9706 (tp) cc_final: 0.9500 (tt) REVERT: E 50 GLU cc_start: 0.9226 (tp30) cc_final: 0.8966 (tp30) REVERT: E 64 LYS cc_start: 0.9591 (mppt) cc_final: 0.9352 (mmtm) REVERT: E 81 ASP cc_start: 0.8593 (m-30) cc_final: 0.8391 (m-30) REVERT: E 106 ASP cc_start: 0.8543 (m-30) cc_final: 0.8134 (m-30) REVERT: E 120 MET cc_start: 0.8955 (ptp) cc_final: 0.8234 (mmm) REVERT: E 124 ILE cc_start: 0.9794 (mm) cc_final: 0.9575 (mp) REVERT: F 59 LYS cc_start: 0.9666 (mmmt) cc_final: 0.9395 (mmmm) REVERT: G 104 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8082 (tp-100) REVERT: H 76 ARG cc_start: 0.9121 (ptp90) cc_final: 0.8887 (ptp90) REVERT: K 306 MET cc_start: 0.4761 (tmm) cc_final: 0.4191 (tpp) REVERT: K 458 MET cc_start: 0.8598 (mtm) cc_final: 0.8108 (mtt) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.1597 time to fit residues: 33.4978 Evaluate side-chains 101 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 85 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 134 optimal weight: 50.0000 chunk 13 optimal weight: 0.7980 chunk 163 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 132 optimal weight: 50.0000 chunk 137 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 104 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.063457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.029229 restraints weight = 148584.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.029612 restraints weight = 81736.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.030053 restraints weight = 57507.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.030184 restraints weight = 46259.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.030311 restraints weight = 42663.361| |-----------------------------------------------------------------------------| r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.6530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 19371 Z= 0.346 Angle : 0.690 7.834 27436 Z= 0.392 Chirality : 0.042 0.189 3068 Planarity : 0.005 0.049 2456 Dihedral : 29.752 176.505 4968 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.67 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % 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: 0.99 (0.22), residues: 1524 helix: 1.42 (0.18), residues: 799 sheet: 0.85 (0.60), residues: 85 loop : -0.27 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 49 TYR 0.018 0.002 TYR A 54 PHE 0.032 0.001 PHE E 104 TRP 0.009 0.001 TRP K 762 HIS 0.010 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00763 (19359) covalent geometry : angle 0.68890 (27423) hydrogen bonds : bond 0.11222 ( 975) hydrogen bonds : angle 4.03682 ( 2471) metal coordination : bond 0.00740 ( 12) metal coordination : angle 1.94996 ( 13) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8818 (t0) cc_final: 0.8614 (m-30) REVERT: B 91 LYS cc_start: 0.9732 (tptp) cc_final: 0.9502 (tptp) REVERT: C 56 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8786 (mm-30) REVERT: D 64 ASN cc_start: 0.9366 (m-40) cc_final: 0.9001 (m-40) REVERT: E 50 GLU cc_start: 0.9387 (tp30) cc_final: 0.9122 (tp30) REVERT: E 68 GLN cc_start: 0.9324 (pp30) cc_final: 0.9118 (pp30) REVERT: E 81 ASP cc_start: 0.8833 (m-30) cc_final: 0.8610 (m-30) REVERT: E 94 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8322 (mm-30) REVERT: E 97 GLU cc_start: 0.8678 (pp20) cc_final: 0.8434 (pp20) REVERT: F 59 LYS cc_start: 0.9690 (mmmt) cc_final: 0.9461 (mmmm) REVERT: G 92 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8739 (mt-10) REVERT: H 73 GLU cc_start: 0.9211 (tp30) cc_final: 0.8729 (tp30) REVERT: H 76 ARG cc_start: 0.9148 (ptp90) cc_final: 0.8775 (ptp90) REVERT: H 97 LEU cc_start: 0.9569 (mt) cc_final: 0.9268 (mt) REVERT: K 306 MET cc_start: 0.4992 (tmm) cc_final: 0.4379 (tpp) REVERT: K 458 MET cc_start: 0.8713 (mtm) cc_final: 0.8245 (mtt) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1553 time to fit residues: 27.9287 Evaluate side-chains 88 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 173 optimal weight: 50.0000 chunk 103 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 166 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 162 optimal weight: 50.0000 chunk 26 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 170 optimal weight: 50.0000 chunk 15 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN E 125 GLN F 25 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 135 GLN ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.097222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.040949 restraints weight = 202201.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.040621 restraints weight = 115814.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.040318 restraints weight = 88465.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.040261 restraints weight = 84663.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.039954 restraints weight = 79556.403| |-----------------------------------------------------------------------------| r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.6730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19371 Z= 0.229 Angle : 0.624 8.670 27436 Z= 0.355 Chirality : 0.039 0.155 3068 Planarity : 0.004 0.050 2456 Dihedral : 29.826 178.273 4968 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.02 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.22), residues: 1524 helix: 1.50 (0.18), residues: 802 sheet: 0.84 (0.61), residues: 85 loop : -0.27 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 72 TYR 0.021 0.001 TYR E 54 PHE 0.014 0.001 PHE K 753 TRP 0.006 0.001 TRP K 762 HIS 0.008 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00499 (19359) covalent geometry : angle 0.62207 (27423) hydrogen bonds : bond 0.06701 ( 975) hydrogen bonds : angle 3.83955 ( 2471) metal coordination : bond 0.00286 ( 12) metal coordination : angle 2.04416 ( 13) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.9303 (pt0) cc_final: 0.9078 (pt0) REVERT: A 105 GLU cc_start: 0.9280 (pm20) cc_final: 0.8903 (pm20) REVERT: A 106 ASP cc_start: 0.9077 (t0) cc_final: 0.8651 (m-30) REVERT: A 110 CYS cc_start: 0.9107 (t) cc_final: 0.8867 (t) REVERT: A 120 MET cc_start: 0.8882 (mmm) cc_final: 0.8665 (mmm) REVERT: B 84 MET cc_start: 0.9538 (mmm) cc_final: 0.9303 (mmm) REVERT: B 91 LYS cc_start: 0.9754 (tptp) cc_final: 0.9520 (tptp) REVERT: D 64 ASN cc_start: 0.9402 (m-40) cc_final: 0.8968 (m110) REVERT: E 50 GLU cc_start: 0.9474 (tp30) cc_final: 0.9093 (tp30) REVERT: E 59 GLU cc_start: 0.9221 (pm20) cc_final: 0.9004 (pm20) REVERT: E 81 ASP cc_start: 0.8946 (m-30) cc_final: 0.8709 (m-30) REVERT: E 120 MET cc_start: 0.9058 (mmp) cc_final: 0.8422 (mmm) REVERT: F 59 LYS cc_start: 0.9701 (mmmt) cc_final: 0.9277 (mmmm) REVERT: G 92 GLU cc_start: 0.9277 (mt-10) cc_final: 0.8908 (mt-10) REVERT: H 73 GLU cc_start: 0.9260 (tp30) cc_final: 0.8851 (tp30) REVERT: H 76 ARG cc_start: 0.9104 (ptp90) cc_final: 0.8759 (ptp90) REVERT: K 306 MET cc_start: 0.5372 (tmm) cc_final: 0.4755 (tpp) REVERT: K 458 MET cc_start: 0.8965 (mtm) cc_final: 0.8604 (ttt) REVERT: M 4 MET cc_start: 0.3812 (tmm) cc_final: 0.2358 (ptm) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1570 time to fit residues: 29.5122 Evaluate side-chains 88 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 127 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 171 optimal weight: 20.0000 chunk 56 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 134 optimal weight: 30.0000 chunk 113 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 GLN E 125 GLN F 25 ASN G 112 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.066487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.030723 restraints weight = 140660.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.031043 restraints weight = 74671.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.031681 restraints weight = 52351.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.031741 restraints weight = 40024.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.031860 restraints weight = 35012.554| |-----------------------------------------------------------------------------| r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.6865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 19371 Z= 0.161 Angle : 0.607 9.922 27436 Z= 0.340 Chirality : 0.038 0.191 3068 Planarity : 0.004 0.055 2456 Dihedral : 29.623 178.372 4968 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.82 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.22), residues: 1524 helix: 1.53 (0.18), residues: 805 sheet: 0.55 (0.60), residues: 88 loop : -0.17 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 76 TYR 0.017 0.001 TYR E 54 PHE 0.019 0.001 PHE K 753 TRP 0.007 0.001 TRP K 200 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00359 (19359) covalent geometry : angle 0.60556 (27423) hydrogen bonds : bond 0.04822 ( 975) hydrogen bonds : angle 3.65880 ( 2471) metal coordination : bond 0.00437 ( 12) metal coordination : angle 1.93798 ( 13) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.9118 (pm20) cc_final: 0.8547 (pm20) REVERT: A 115 LYS cc_start: 0.9363 (mppt) cc_final: 0.9145 (mmtt) REVERT: B 91 LYS cc_start: 0.9742 (tptp) cc_final: 0.9519 (tptp) REVERT: D 64 ASN cc_start: 0.9294 (m-40) cc_final: 0.8914 (m110) REVERT: E 50 GLU cc_start: 0.9359 (tp30) cc_final: 0.9069 (tp30) REVERT: E 81 ASP cc_start: 0.8732 (m-30) cc_final: 0.8522 (m-30) REVERT: E 120 MET cc_start: 0.8862 (mmp) cc_final: 0.8160 (mmp) REVERT: F 49 LEU cc_start: 0.9257 (mp) cc_final: 0.8992 (mp) REVERT: F 59 LYS cc_start: 0.9667 (mmmt) cc_final: 0.9247 (mmmm) REVERT: H 24 LYS cc_start: 0.6903 (mmtt) cc_final: 0.6464 (ttpp) REVERT: H 73 GLU cc_start: 0.9267 (tp30) cc_final: 0.8963 (tp30) REVERT: H 76 ARG cc_start: 0.9127 (ptp90) cc_final: 0.8868 (ptp90) REVERT: K 171 MET cc_start: 0.7181 (ptt) cc_final: 0.5800 (ptt) REVERT: K 204 MET cc_start: 0.2613 (ttt) cc_final: 0.2166 (mtt) REVERT: K 306 MET cc_start: 0.4798 (tmm) cc_final: 0.4220 (tpp) REVERT: K 458 MET cc_start: 0.8635 (mtm) cc_final: 0.8144 (mtt) REVERT: M 4 MET cc_start: 0.3289 (tmm) cc_final: 0.1933 (ptm) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1562 time to fit residues: 29.5133 Evaluate side-chains 90 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 31 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 130 optimal weight: 30.0000 chunk 52 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 GLN E 125 GLN F 25 ASN G 110 ASN G 112 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.068304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.031958 restraints weight = 145203.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.032427 restraints weight = 70679.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.032655 restraints weight = 47430.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.032776 restraints weight = 38513.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.032890 restraints weight = 33328.340| |-----------------------------------------------------------------------------| r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.7160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19371 Z= 0.199 Angle : 0.607 9.951 27436 Z= 0.340 Chirality : 0.038 0.164 3068 Planarity : 0.004 0.051 2456 Dihedral : 29.505 178.086 4968 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.02 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.22), residues: 1524 helix: 1.66 (0.18), residues: 810 sheet: 0.53 (0.59), residues: 88 loop : -0.19 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 131 TYR 0.019 0.001 TYR E 54 PHE 0.031 0.001 PHE A 104 TRP 0.007 0.001 TRP K 200 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00438 (19359) covalent geometry : angle 0.60639 (27423) hydrogen bonds : bond 0.06199 ( 975) hydrogen bonds : angle 3.72647 ( 2471) metal coordination : bond 0.00147 ( 12) metal coordination : angle 1.71047 ( 13) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8879 (mt-10) REVERT: A 105 GLU cc_start: 0.9019 (pm20) cc_final: 0.8773 (pm20) REVERT: A 106 ASP cc_start: 0.8764 (m-30) cc_final: 0.8152 (m-30) REVERT: A 115 LYS cc_start: 0.9370 (mppt) cc_final: 0.9153 (mmtt) REVERT: B 37 LEU cc_start: 0.9766 (mm) cc_final: 0.9309 (tt) REVERT: B 91 LYS cc_start: 0.9667 (tptp) cc_final: 0.9339 (tppt) REVERT: D 64 ASN cc_start: 0.9280 (m-40) cc_final: 0.8896 (m110) REVERT: E 120 MET cc_start: 0.8849 (mmp) cc_final: 0.8136 (mmp) REVERT: F 59 LYS cc_start: 0.9622 (mmmt) cc_final: 0.9251 (mmmm) REVERT: K 171 MET cc_start: 0.6401 (ptt) cc_final: 0.5661 (ppp) REVERT: K 204 MET cc_start: 0.2421 (ttt) cc_final: 0.2007 (mtt) REVERT: K 306 MET cc_start: 0.4907 (tmm) cc_final: 0.3723 (tpt) REVERT: K 458 MET cc_start: 0.8685 (mtm) cc_final: 0.8255 (mtt) REVERT: M 4 MET cc_start: 0.3801 (tmm) cc_final: 0.2473 (ptm) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1515 time to fit residues: 27.2046 Evaluate side-chains 86 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 38 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 112 optimal weight: 50.0000 chunk 45 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 16 optimal weight: 0.0470 chunk 57 optimal weight: 0.7980 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 GLN E 125 GLN F 25 ASN G 110 ASN G 112 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.067326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.031343 restraints weight = 141160.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.031605 restraints weight = 76252.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.031921 restraints weight = 49353.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.032167 restraints weight = 39330.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.032368 restraints weight = 33972.567| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.7209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19371 Z= 0.137 Angle : 0.589 10.924 27436 Z= 0.328 Chirality : 0.038 0.168 3068 Planarity : 0.004 0.051 2456 Dihedral : 29.311 179.004 4968 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.56 % Favored : 97.31 % Rotamer: Outliers : 0.08 % Allowed : 0.46 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.22), residues: 1524 helix: 1.69 (0.18), residues: 805 sheet: 0.58 (0.59), residues: 87 loop : -0.18 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 39 TYR 0.014 0.001 TYR A 54 PHE 0.015 0.001 PHE K 753 TRP 0.007 0.001 TRP K 200 HIS 0.008 0.001 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00299 (19359) covalent geometry : angle 0.58822 (27423) hydrogen bonds : bond 0.03995 ( 975) hydrogen bonds : angle 3.57793 ( 2471) metal coordination : bond 0.00137 ( 12) metal coordination : angle 1.48063 ( 13) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8874 (mt-10) REVERT: A 105 GLU cc_start: 0.9001 (pm20) cc_final: 0.8635 (pm20) REVERT: A 106 ASP cc_start: 0.8705 (m-30) cc_final: 0.8091 (m-30) REVERT: B 37 LEU cc_start: 0.9775 (mm) cc_final: 0.9388 (tt) REVERT: B 91 LYS cc_start: 0.9745 (tptp) cc_final: 0.9386 (tppt) REVERT: D 64 ASN cc_start: 0.9327 (m-40) cc_final: 0.8919 (m110) REVERT: E 81 ASP cc_start: 0.8810 (m-30) cc_final: 0.8543 (m-30) REVERT: E 120 MET cc_start: 0.8971 (mmp) cc_final: 0.8210 (mmp) REVERT: F 59 LYS cc_start: 0.9639 (mmmt) cc_final: 0.9198 (mmmm) REVERT: H 24 LYS cc_start: 0.7273 (mmtm) cc_final: 0.6548 (ttpp) REVERT: H 65 ASP cc_start: 0.9054 (t0) cc_final: 0.8736 (t0) REVERT: H 99 LEU cc_start: 0.9259 (tp) cc_final: 0.9048 (tp) REVERT: K 171 MET cc_start: 0.5869 (ptt) cc_final: 0.5027 (ppp) REVERT: K 204 MET cc_start: 0.2502 (ttt) cc_final: 0.2081 (mtt) REVERT: K 306 MET cc_start: 0.4779 (tmm) cc_final: 0.3560 (tpt) REVERT: K 458 MET cc_start: 0.8664 (mtm) cc_final: 0.8214 (mtt) REVERT: M 4 MET cc_start: 0.3474 (tmm) cc_final: 0.2256 (ptm) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.1397 time to fit residues: 26.3722 Evaluate side-chains 90 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 34 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 176 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 16 optimal weight: 0.4980 chunk 108 optimal weight: 9.9990 chunk 143 optimal weight: 20.0000 chunk 79 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 151 optimal weight: 50.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 GLN E 125 GLN F 25 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 539 HIS ** K 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.066122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.031186 restraints weight = 141766.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.031311 restraints weight = 76710.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.031752 restraints weight = 55528.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.031775 restraints weight = 39431.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.031903 restraints weight = 33913.811| |-----------------------------------------------------------------------------| r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.7387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19371 Z= 0.165 Angle : 0.582 10.521 27436 Z= 0.326 Chirality : 0.037 0.161 3068 Planarity : 0.004 0.052 2456 Dihedral : 29.207 178.648 4968 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.76 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.22), residues: 1524 helix: 1.71 (0.18), residues: 808 sheet: 0.99 (0.61), residues: 77 loop : -0.21 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 69 TYR 0.022 0.001 TYR E 54 PHE 0.015 0.001 PHE K 753 TRP 0.007 0.001 TRP K 200 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00362 (19359) covalent geometry : angle 0.58125 (27423) hydrogen bonds : bond 0.05108 ( 975) hydrogen bonds : angle 3.57139 ( 2471) metal coordination : bond 0.00123 ( 12) metal coordination : angle 1.40293 ( 13) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4941.80 seconds wall clock time: 85 minutes 35.74 seconds (5135.74 seconds total)