Starting phenix.real_space_refine on Sat Sep 12 20:35:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6r1u_4705/09_2026/6r1u_4705.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r1u_4705/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6r1u_4705/09_2026/6r1u_4705.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6r1u_4705/09_2026/6r1u_4705.cif" model { file = "/net/cci-nas-00/data/ceres_data/6r1u_4705/09_2026/6r1u_4705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r1u_4705/09_2026/6r1u_4705.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6r1u_4705/09_2026/6r1u_4705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r1u_4705/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.77, 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: 1.75 Conformation dependent library (CDL) restraints added in 564.8 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: 2.60 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: 5.40 Time building geometry restraints manager: 2.27 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=" C1' DG J 71 " pdb=" N9 DG J 71 " ideal model delta sigma weight residual 1.468 1.352 0.116 1.40e-02 5.10e+03 6.86e+01 ... (remaining 19354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 27079 3.43 - 6.86: 321 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: 9177 35.91 - 71.82: 1648 71.82 - 107.73: 32 107.73 - 143.64: 1 143.64 - 179.56: 1 Dihedral angle restraints: 10859 sinusoidal: 6365 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 10856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2221 0.062 - 0.124: 702 0.124 - 0.186: 123 0.186 - 0.247: 19 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: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 23.170 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4498 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 : 0.010 0.346 19371 Z= 0.695 Angle : 1.131 17.149 27436 Z= 0.849 Chirality : 0.061 0.309 3068 Planarity : 0.023 0.492 2456 Dihedral : 25.763 179.556 7963 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/Z covalent geometry : bond 0.00921 / 0.69 (19359) covalent geometry : angle 1.12632 / 0.85 (27423) hydrogen bonds : bond 0.12953 / 8.65 ( 975) hydrogen bonds : angle 7.15454 / 5.04 ( 2471) metal coordination : bond 0.14820 / 10.02 ( 12) metal coordination : angle 4.91720 / 2.69 ( 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 : 0.624 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: A 48 LEU cc_start: 0.8726 (mp) cc_final: 0.8349 (tp) REVERT: E 74 ILE cc_start: 0.9194 (mt) cc_final: 0.8615 (mm) REVERT: E 107 THR cc_start: 0.8394 (m) cc_final: 0.8035 (p) REVERT: F 88 TYR cc_start: 0.8176 (m-10) cc_final: 0.7937 (m-80) REVERT: K 85 LEU cc_start: 0.1544 (OUTLIER) cc_final: 0.1159 (tp) REVERT: K 204 MET cc_start: 0.2224 (mtm) cc_final: 0.1942 (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: -0.2804 (mmm) REVERT: M 22 THR cc_start: -0.0210 (OUTLIER) cc_final: -0.0433 (t) outliers start: 82 outliers final: 25 residues processed: 347 average time/residue: 0.1977 time to fit residues: 95.2709 Evaluate side-chains 150 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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: 20.0000 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: 20.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 40.0000 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN E 68 GLN ** 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 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 218 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.075810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.040048 restraints weight = 132775.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.040631 restraints weight = 76842.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.041367 restraints weight = 54763.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.041710 restraints weight = 44238.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.041914 restraints weight = 38318.938| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 19371 Z= 0.217 Angle : 0.840 9.443 27436 Z= 0.458 Chirality : 0.052 0.298 3068 Planarity : 0.009 0.200 2456 Dihedral : 29.926 177.291 4925 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.41 % Favored : 96.19 % Rotamer: Outliers : 0.31 % Allowed : 2.90 % 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: -0.81 (0.20), residues: 1524 helix: -0.18 (0.17), residues: 797 sheet: 1.11 (0.66), residues: 61 loop : -1.03 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 134 TYR 0.024 0.002 TYR B 88 PHE 0.027 0.002 PHE C 25 TRP 0.007 0.001 TRP K 117 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.22 (19359) covalent geometry : angle 0.83686 / 0.46 (27423) hydrogen bonds : bond 0.07353 / 4.84 ( 975) hydrogen bonds : angle 4.49321 / 3.20 ( 2471) metal coordination : bond 0.01606 / 0.99 ( 12) metal coordination : angle 3.52730 / 2.14 ( 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 172 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 168 time to evaluate : 0.615 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: 0.9043 (mmm) cc_final: 0.7456 (tpp) REVERT: E 50 GLU cc_start: 0.9175 (tp30) cc_final: 0.8803 (tp30) REVERT: E 51 ILE cc_start: 0.9043 (mt) cc_final: 0.8826 (mm) REVERT: E 74 ILE cc_start: 0.9468 (mt) cc_final: 0.9160 (tt) REVERT: E 119 ILE cc_start: 0.8651 (mp) cc_final: 0.8333 (mp) REVERT: E 120 MET cc_start: 0.8444 (ptp) cc_final: 0.7548 (mmm) REVERT: F 59 LYS cc_start: 0.9521 (tptp) cc_final: 0.9139 (tppt) REVERT: K 265 MET cc_start: 0.8369 (ttt) cc_final: 0.7959 (tpp) REVERT: K 458 MET cc_start: 0.8605 (mtm) cc_final: 0.8205 (mtt) outliers start: 4 outliers final: 0 residues processed: 171 average time/residue: 0.1724 time to fit residues: 43.0278 Evaluate side-chains 116 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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: 30.0000 chunk 85 optimal weight: 20.0000 chunk 108 optimal weight: 50.0000 chunk 95 optimal weight: 30.0000 chunk 91 optimal weight: 30.0000 chunk 110 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 172 optimal weight: 50.0000 chunk 129 optimal weight: 40.0000 chunk 143 optimal weight: 10.0000 overall best weight: 13.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 104 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS ** 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 = 0.3544 r_free = 0.3544 target = 0.062533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.029741 restraints weight = 152334.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.030319 restraints weight = 83463.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.030602 restraints weight = 58106.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.030720 restraints weight = 46849.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.030810 restraints weight = 41008.278| |-----------------------------------------------------------------------------| r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.097 19371 Z= 0.548 Angle : 1.166 14.499 27436 Z= 0.621 Chirality : 0.063 0.340 3068 Planarity : 0.009 0.088 2456 Dihedral : 30.572 176.342 4925 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 35.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.46 % Favored : 95.34 % Rotamer: Outliers : 0.31 % Allowed : 5.65 % Favored : 94.05 % 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 (0.20), residues: 1524 helix: -0.52 (0.17), residues: 804 sheet: 1.27 (0.59), residues: 71 loop : -0.86 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG E 131 TYR 0.036 0.003 TYR H 80 PHE 0.021 0.002 PHE K 91 TRP 0.009 0.001 TRP K 762 HIS 0.015 0.003 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.01018 / 0.55 (19359) covalent geometry : angle 1.16347 / 0.62 (27423) hydrogen bonds : bond 0.23345 / 15.61 ( 975) hydrogen bonds : angle 5.64216 / 4.05 ( 2471) metal coordination : bond 0.00842 / 0.48 ( 12) metal coordination : angle 3.91868 / 2.07 ( 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 118 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 114 time to evaluate : 0.600 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: A 105 GLU cc_start: 0.9481 (mp0) cc_final: 0.9170 (mp0) REVERT: A 120 MET cc_start: 0.8960 (mmm) cc_final: 0.8750 (mmm) REVERT: D 64 ASN cc_start: 0.9512 (m-40) cc_final: 0.9130 (m-40) REVERT: D 73 GLU cc_start: 0.9583 (tp30) cc_final: 0.9265 (tp30) REVERT: E 50 GLU cc_start: 0.9485 (tp30) cc_final: 0.8983 (tp30) REVERT: E 60 LEU cc_start: 0.8817 (mm) cc_final: 0.7833 (mt) REVERT: E 65 LEU cc_start: 0.9792 (mt) cc_final: 0.9315 (mt) REVERT: E 81 ASP cc_start: 0.9076 (m-30) cc_final: 0.8862 (m-30) REVERT: E 97 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8721 (pt0) REVERT: E 105 GLU cc_start: 0.9226 (tm-30) cc_final: 0.8985 (tm-30) REVERT: E 120 MET cc_start: 0.9105 (ptp) cc_final: 0.8461 (mmm) REVERT: F 59 LYS cc_start: 0.9741 (tptp) cc_final: 0.9086 (tptp) REVERT: F 84 MET cc_start: 0.8771 (mmm) cc_final: 0.8518 (mmm) REVERT: H 76 ARG cc_start: 0.9400 (ptp90) cc_final: 0.9124 (ptp90) REVERT: H 99 LEU cc_start: 0.9473 (mm) cc_final: 0.9217 (mm) REVERT: K 265 MET cc_start: 0.8465 (ttt) cc_final: 0.8208 (tpt) REVERT: K 458 MET cc_start: 0.8658 (mtm) cc_final: 0.8227 (mtt) outliers start: 4 outliers final: 3 residues processed: 118 average time/residue: 0.1664 time to fit residues: 29.0407 Evaluate side-chains 86 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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: 0.6980 chunk 149 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 116 optimal weight: 0.1980 chunk 97 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 135 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.063202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.027832 restraints weight = 154173.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.028616 restraints weight = 80459.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.029050 restraints weight = 55119.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.029365 restraints weight = 43997.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.029533 restraints weight = 38454.955| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19371 Z= 0.167 Angle : 0.739 8.699 27436 Z= 0.404 Chirality : 0.050 0.269 3068 Planarity : 0.006 0.088 2456 Dihedral : 30.812 176.005 4925 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.48 % Favored : 96.39 % Rotamer: Outliers : 0.08 % Allowed : 2.37 % Favored : 97.56 % 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: 0.18 (0.21), residues: 1524 helix: 0.61 (0.18), residues: 808 sheet: 1.36 (0.61), residues: 72 loop : -0.56 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 131 TYR 0.021 0.002 TYR C 57 PHE 0.018 0.001 PHE K 753 TRP 0.007 0.001 TRP K 762 HIS 0.009 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.17 (19359) covalent geometry : angle 0.73667 / 0.40 (27423) hydrogen bonds : bond 0.06546 / 4.42 ( 975) hydrogen bonds : angle 4.14356 / 2.95 ( 2471) metal coordination : bond 0.00371 / 0.20 ( 12) metal coordination : angle 2.73761 / 1.54 ( 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 135 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.579 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 90 MET cc_start: 0.9307 (mmp) cc_final: 0.9067 (mmm) REVERT: A 97 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8896 (mt-10) REVERT: A 108 ASN cc_start: 0.9724 (t0) cc_final: 0.9494 (t0) REVERT: B 88 TYR cc_start: 0.9383 (m-80) cc_final: 0.9069 (m-10) REVERT: D 64 ASN cc_start: 0.9259 (m-40) cc_final: 0.8965 (m110) REVERT: E 50 GLU cc_start: 0.9307 (tp30) cc_final: 0.8848 (tp30) REVERT: E 120 MET cc_start: 0.8955 (ptp) cc_final: 0.8169 (mmm) REVERT: F 24 ASP cc_start: 0.9160 (t0) cc_final: 0.8861 (p0) REVERT: H 73 GLU cc_start: 0.9035 (tp30) cc_final: 0.8782 (tp30) REVERT: H 76 ARG cc_start: 0.9270 (ptp90) cc_final: 0.9031 (ptp90) REVERT: K 265 MET cc_start: 0.8458 (ttt) cc_final: 0.8226 (tpt) REVERT: K 458 MET cc_start: 0.8677 (mtm) cc_final: 0.8219 (mtt) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.1511 time to fit residues: 30.9045 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 : 0.545 ------------------------------------------------------------------------------- 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: 6.9990 chunk 166 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 127 optimal weight: 30.0000 chunk 151 optimal weight: 40.0000 chunk 62 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 chunk 75 optimal weight: 30.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN G 104 GLN G 110 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.068336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.032747 restraints weight = 136489.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.033309 restraints weight = 74485.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.033559 restraints weight = 51605.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.033816 restraints weight = 42081.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.033895 restraints weight = 36989.699| |-----------------------------------------------------------------------------| r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 19371 Z= 0.157 Angle : 0.683 9.011 27436 Z= 0.378 Chirality : 0.046 0.227 3068 Planarity : 0.005 0.097 2456 Dihedral : 30.436 174.300 4925 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 0.15 % Allowed : 1.83 % 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: 0.50 (0.21), residues: 1524 helix: 0.95 (0.18), residues: 807 sheet: 1.43 (0.62), residues: 72 loop : -0.52 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 131 TYR 0.032 0.002 TYR K 167 PHE 0.016 0.001 PHE K 753 TRP 0.008 0.001 TRP K 200 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 (19359) covalent geometry : angle 0.68141 / 0.38 (27423) hydrogen bonds : bond 0.06784 / 4.53 ( 975) hydrogen bonds : angle 3.95006 / 2.80 ( 2471) metal coordination : bond 0.00437 / 0.30 ( 12) metal coordination : angle 2.48411 / 1.13 ( 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 133 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.681 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 90 MET cc_start: 0.9433 (mmp) cc_final: 0.9185 (mmm) REVERT: A 97 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8923 (mt-10) REVERT: A 108 ASN cc_start: 0.9744 (t0) cc_final: 0.9515 (t0) REVERT: D 64 ASN cc_start: 0.9351 (m-40) cc_final: 0.9019 (m110) REVERT: E 50 GLU cc_start: 0.9287 (tp30) cc_final: 0.8850 (tp30) REVERT: E 81 ASP cc_start: 0.8735 (m-30) cc_final: 0.8522 (m-30) REVERT: E 105 GLU cc_start: 0.9160 (tm-30) cc_final: 0.8952 (tm-30) REVERT: E 120 MET cc_start: 0.8867 (ptp) cc_final: 0.8245 (mmm) REVERT: G 104 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8053 (tp-100) REVERT: G 112 GLN cc_start: 0.9144 (mm-40) cc_final: 0.8904 (mm-40) REVERT: H 73 GLU cc_start: 0.9177 (tp30) cc_final: 0.8960 (tp30) REVERT: H 76 ARG cc_start: 0.9207 (ptp90) cc_final: 0.8944 (ptp90) REVERT: K 171 MET cc_start: 0.7853 (ptt) cc_final: 0.7101 (ppp) REVERT: K 204 MET cc_start: -0.3671 (ptp) cc_final: -0.4046 (ttt) REVERT: K 265 MET cc_start: 0.8429 (ttt) cc_final: 0.8144 (tpt) REVERT: K 458 MET cc_start: 0.8632 (mtm) cc_final: 0.8140 (mtt) REVERT: M 4 MET cc_start: 0.3464 (tmm) cc_final: 0.2496 (ptm) outliers start: 2 outliers final: 0 residues processed: 132 average time/residue: 0.1454 time to fit residues: 29.3812 Evaluate side-chains 95 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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: 30.0000 chunk 74 optimal weight: 20.0000 chunk 134 optimal weight: 50.0000 chunk 13 optimal weight: 0.7980 chunk 163 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 132 optimal weight: 50.0000 chunk 137 optimal weight: 50.0000 chunk 81 optimal weight: 20.0000 chunk 71 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 overall best weight: 7.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.063640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.029869 restraints weight = 144343.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.030365 restraints weight = 81350.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.030563 restraints weight = 57984.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.030750 restraints weight = 47493.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.030793 restraints weight = 42039.463| |-----------------------------------------------------------------------------| r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.6239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 19371 Z= 0.319 Angle : 0.796 9.461 27436 Z= 0.436 Chirality : 0.049 0.263 3068 Planarity : 0.006 0.079 2456 Dihedral : 30.520 174.509 4925 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.67 % Favored : 96.19 % Rotamer: Outliers : 0.08 % Allowed : 1.91 % 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: 0.37 (0.21), residues: 1524 helix: 0.75 (0.18), residues: 812 sheet: 1.36 (0.62), residues: 74 loop : -0.45 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG B 92 TYR 0.020 0.002 TYR A 54 PHE 0.016 0.002 PHE K 91 TRP 0.008 0.001 TRP K 762 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.32 (19359) covalent geometry : angle 0.79511 / 0.44 (27423) hydrogen bonds : bond 0.12984 / 8.59 ( 975) hydrogen bonds : angle 4.43245 / 3.18 ( 2471) metal coordination : bond 0.00545 / 0.35 ( 12) metal coordination : angle 2.19057 / 1.30 ( 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 113 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.576 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: A 90 MET cc_start: 0.9402 (mmp) cc_final: 0.9145 (mmm) REVERT: A 110 CYS cc_start: 0.8773 (t) cc_final: 0.8506 (t) REVERT: B 84 MET cc_start: 0.9383 (mmm) cc_final: 0.9034 (mmm) REVERT: D 64 ASN cc_start: 0.9403 (m-40) cc_final: 0.9093 (m110) REVERT: E 50 GLU cc_start: 0.9326 (tp30) cc_final: 0.8989 (tp30) REVERT: E 105 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8770 (tm-30) REVERT: E 106 ASP cc_start: 0.9143 (m-30) cc_final: 0.8505 (m-30) REVERT: E 120 MET cc_start: 0.9047 (ptp) cc_final: 0.8478 (mmp) REVERT: G 36 LYS cc_start: 0.9420 (mptt) cc_final: 0.9175 (mmtt) REVERT: H 73 GLU cc_start: 0.9274 (tp30) cc_final: 0.9016 (tp30) REVERT: H 76 ARG cc_start: 0.9224 (ptp90) cc_final: 0.8949 (ptp90) REVERT: K 171 MET cc_start: 0.8033 (ptt) cc_final: 0.6128 (ppp) REVERT: K 458 MET cc_start: 0.8646 (mtm) cc_final: 0.8172 (mtt) REVERT: M 4 MET cc_start: 0.3584 (tmm) cc_final: 0.2793 (ptm) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.1537 time to fit residues: 26.3595 Evaluate side-chains 81 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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: 9.9990 chunk 103 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 166 optimal weight: 9.9990 chunk 108 optimal weight: 50.0000 chunk 162 optimal weight: 50.0000 chunk 26 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 overall best weight: 4.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.065455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.030184 restraints weight = 142207.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.030617 restraints weight = 76956.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.031066 restraints weight = 55281.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.031194 restraints weight = 43550.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.031335 restraints weight = 38198.368| |-----------------------------------------------------------------------------| r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.6410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19371 Z= 0.204 Angle : 0.696 9.102 27436 Z= 0.384 Chirality : 0.046 0.226 3068 Planarity : 0.005 0.062 2456 Dihedral : 30.624 174.365 4925 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.28 % Favored : 96.65 % 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: 0.68 (0.22), residues: 1524 helix: 1.09 (0.18), residues: 813 sheet: 1.35 (0.63), residues: 74 loop : -0.41 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 131 TYR 0.034 0.002 TYR B 88 PHE 0.020 0.001 PHE C 25 TRP 0.007 0.001 TRP K 762 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.20 (19359) covalent geometry : angle 0.69468 / 0.38 (27423) hydrogen bonds : bond 0.08004 / 5.32 ( 975) hydrogen bonds : angle 4.13893 / 2.94 ( 2471) metal coordination : bond 0.00433 / 0.31 ( 12) metal coordination : angle 2.36557 / 1.54 ( 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 123 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.612 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: A 90 MET cc_start: 0.9380 (mmp) cc_final: 0.9154 (mmm) REVERT: A 108 ASN cc_start: 0.9771 (t0) cc_final: 0.9566 (t0) REVERT: A 110 CYS cc_start: 0.8639 (t) cc_final: 0.8384 (t) REVERT: A 120 MET cc_start: 0.9043 (mmm) cc_final: 0.8790 (mmm) REVERT: C 110 ASN cc_start: 0.9635 (t0) cc_final: 0.9354 (t0) REVERT: D 64 ASN cc_start: 0.9382 (m-40) cc_final: 0.9065 (m110) REVERT: E 50 GLU cc_start: 0.9307 (tp30) cc_final: 0.8962 (tp30) REVERT: E 81 ASP cc_start: 0.8812 (m-30) cc_final: 0.8577 (m-30) REVERT: E 106 ASP cc_start: 0.9170 (m-30) cc_final: 0.8560 (m-30) REVERT: E 120 MET cc_start: 0.8519 (ptp) cc_final: 0.8259 (mmm) REVERT: H 73 GLU cc_start: 0.9266 (tp30) cc_final: 0.9041 (tp30) REVERT: H 76 ARG cc_start: 0.9232 (ptp90) cc_final: 0.8963 (ptp90) REVERT: K 171 MET cc_start: 0.6532 (ptt) cc_final: 0.5749 (ppp) REVERT: K 204 MET cc_start: -0.3051 (ptp) cc_final: -0.3481 (ttt) REVERT: K 458 MET cc_start: 0.8628 (mtm) cc_final: 0.8155 (mtt) REVERT: M 4 MET cc_start: 0.3572 (tmm) cc_final: 0.2827 (ptm) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1538 time to fit residues: 28.8212 Evaluate side-chains 84 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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: 0.9980 chunk 23 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 127 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 171 optimal weight: 50.0000 chunk 56 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 134 optimal weight: 30.0000 chunk 113 optimal weight: 40.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS E 125 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.065519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.030083 restraints weight = 140990.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.030541 restraints weight = 77077.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.030784 restraints weight = 53291.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.030968 restraints weight = 43105.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.031155 restraints weight = 38071.798| |-----------------------------------------------------------------------------| r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.6612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19371 Z= 0.188 Angle : 0.679 9.386 27436 Z= 0.374 Chirality : 0.045 0.213 3068 Planarity : 0.005 0.079 2456 Dihedral : 30.548 174.704 4925 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.15 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: 0.86 (0.22), residues: 1524 helix: 1.28 (0.18), residues: 812 sheet: 1.32 (0.63), residues: 74 loop : -0.38 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 131 TYR 0.026 0.001 TYR B 88 PHE 0.022 0.001 PHE C 25 TRP 0.008 0.001 TRP K 762 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.19 (19359) covalent geometry : angle 0.67769 / 0.37 (27423) hydrogen bonds : bond 0.07460 / 4.96 ( 975) hydrogen bonds : angle 4.02262 / 2.86 ( 2471) metal coordination : bond 0.00287 / 0.19 ( 12) metal coordination : angle 2.23419 / 1.51 ( 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 117 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.538 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: A 108 ASN cc_start: 0.9774 (t0) cc_final: 0.9571 (t0) REVERT: A 110 CYS cc_start: 0.8649 (t) cc_final: 0.8369 (t) REVERT: A 115 LYS cc_start: 0.9356 (mppt) cc_final: 0.9112 (mmtt) REVERT: A 120 MET cc_start: 0.9071 (mmm) cc_final: 0.8813 (mmm) REVERT: B 37 LEU cc_start: 0.9786 (mm) cc_final: 0.9421 (tt) REVERT: B 91 LYS cc_start: 0.9563 (ttpt) cc_final: 0.9359 (tptp) REVERT: C 110 ASN cc_start: 0.9654 (t0) cc_final: 0.9397 (t0) REVERT: D 64 ASN cc_start: 0.9413 (m-40) cc_final: 0.9068 (m110) REVERT: E 50 GLU cc_start: 0.9310 (tp30) cc_final: 0.8988 (tp30) REVERT: E 81 ASP cc_start: 0.8841 (m-30) cc_final: 0.8591 (m-30) REVERT: E 105 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8773 (tm-30) REVERT: E 106 ASP cc_start: 0.9181 (m-30) cc_final: 0.8533 (m-30) REVERT: H 76 ARG cc_start: 0.9200 (ptp90) cc_final: 0.8853 (ptp90) REVERT: K 171 MET cc_start: 0.6519 (ptt) cc_final: 0.5709 (ppp) REVERT: K 204 MET cc_start: -0.3119 (ptp) cc_final: -0.3515 (ttt) REVERT: K 458 MET cc_start: 0.8613 (mtm) cc_final: 0.8132 (mtt) REVERT: M 4 MET cc_start: 0.3831 (tmm) cc_final: 0.3571 (ttt) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1539 time to fit residues: 27.5184 Evaluate side-chains 83 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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: 3.9990 chunk 71 optimal weight: 2.9990 chunk 147 optimal weight: 40.0000 chunk 98 optimal weight: 20.0000 chunk 166 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 chunk 106 optimal weight: 50.0000 chunk 17 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN G 112 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.060867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.028321 restraints weight = 153292.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.028995 restraints weight = 78312.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.029384 restraints weight = 52379.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.029592 restraints weight = 41295.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.029766 restraints weight = 36098.946| |-----------------------------------------------------------------------------| r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.6747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19371 Z= 0.176 Angle : 0.680 9.225 27436 Z= 0.374 Chirality : 0.045 0.213 3068 Planarity : 0.005 0.058 2456 Dihedral : 30.504 175.290 4925 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.89 % Favored : 97.05 % 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: 0.90 (0.22), residues: 1524 helix: 1.32 (0.18), residues: 812 sheet: 1.26 (0.63), residues: 74 loop : -0.36 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 131 TYR 0.022 0.001 TYR B 88 PHE 0.039 0.002 PHE C 25 TRP 0.007 0.001 TRP K 762 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.18 (19359) covalent geometry : angle 0.67892 / 0.37 (27423) hydrogen bonds : bond 0.06904 / 4.58 ( 975) hydrogen bonds : angle 4.02412 / 2.90 ( 2471) metal coordination : bond 0.00302 / 0.20 ( 12) metal coordination : angle 2.03467 / 1.38 ( 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 116 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.627 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 110 CYS cc_start: 0.8753 (t) cc_final: 0.8448 (t) REVERT: A 115 LYS cc_start: 0.9390 (mppt) cc_final: 0.9090 (mmtm) REVERT: A 120 MET cc_start: 0.9097 (mmm) cc_final: 0.8815 (mmm) REVERT: B 37 LEU cc_start: 0.9794 (mm) cc_final: 0.9393 (tt) REVERT: B 91 LYS cc_start: 0.9574 (ttpt) cc_final: 0.9352 (tptp) REVERT: C 110 ASN cc_start: 0.9669 (t0) cc_final: 0.9418 (t0) REVERT: D 64 ASN cc_start: 0.9477 (m-40) cc_final: 0.9118 (m110) REVERT: E 50 GLU cc_start: 0.9409 (tp30) cc_final: 0.9036 (tp30) REVERT: E 81 ASP cc_start: 0.8869 (m-30) cc_final: 0.8650 (m-30) REVERT: E 105 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8858 (tm-30) REVERT: E 106 ASP cc_start: 0.9260 (m-30) cc_final: 0.8639 (m-30) REVERT: E 120 MET cc_start: 0.8940 (mmp) cc_final: 0.8173 (mmp) REVERT: H 73 GLU cc_start: 0.9402 (tp30) cc_final: 0.9053 (tp30) REVERT: H 76 ARG cc_start: 0.9268 (ptp90) cc_final: 0.8900 (ptp90) REVERT: K 171 MET cc_start: 0.6417 (ptt) cc_final: 0.5600 (ppp) REVERT: K 204 MET cc_start: -0.3005 (ptp) cc_final: -0.3416 (ttt) REVERT: K 458 MET cc_start: 0.8590 (mtm) cc_final: 0.8091 (mtt) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1515 time to fit residues: 26.5889 Evaluate side-chains 83 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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: 4.9990 chunk 63 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 91 optimal weight: 30.0000 chunk 112 optimal weight: 50.0000 chunk 45 optimal weight: 0.7980 chunk 81 optimal weight: 30.0000 chunk 16 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN G 112 GLN ** K 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.066583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.030380 restraints weight = 139135.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.030908 restraints weight = 74406.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.031095 restraints weight = 51386.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.031345 restraints weight = 41688.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.031399 restraints weight = 36783.794| |-----------------------------------------------------------------------------| r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.6817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19371 Z= 0.147 Angle : 0.673 10.874 27436 Z= 0.371 Chirality : 0.045 0.236 3068 Planarity : 0.005 0.078 2456 Dihedral : 30.412 175.774 4925 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.15 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 1.00 (0.22), residues: 1524 helix: 1.41 (0.18), residues: 805 sheet: 1.17 (0.62), residues: 74 loop : -0.29 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 42 TYR 0.029 0.001 TYR B 88 PHE 0.019 0.001 PHE C 25 TRP 0.007 0.001 TRP K 762 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (19359) covalent geometry : angle 0.67176 / 0.37 (27423) hydrogen bonds : bond 0.05715 / 3.80 ( 975) hydrogen bonds : angle 3.97000 / 2.85 ( 2471) metal coordination : bond 0.00222 / 0.15 ( 12) metal coordination : angle 1.91911 / 1.31 ( 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 124 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.572 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 110 CYS cc_start: 0.8464 (t) cc_final: 0.8188 (t) REVERT: A 120 MET cc_start: 0.9069 (mmm) cc_final: 0.8840 (mmm) REVERT: B 37 LEU cc_start: 0.9767 (mm) cc_final: 0.9399 (tt) REVERT: B 63 GLU cc_start: 0.9353 (pm20) cc_final: 0.9073 (pm20) REVERT: B 91 LYS cc_start: 0.9570 (ttpt) cc_final: 0.9344 (tptp) REVERT: C 110 ASN cc_start: 0.9612 (t0) cc_final: 0.9348 (t0) REVERT: D 64 ASN cc_start: 0.9401 (m-40) cc_final: 0.9029 (m110) REVERT: E 50 GLU cc_start: 0.9300 (tp30) cc_final: 0.8987 (tp30) REVERT: E 81 ASP cc_start: 0.8881 (m-30) cc_final: 0.8670 (m-30) REVERT: E 106 ASP cc_start: 0.9174 (m-30) cc_final: 0.8595 (m-30) REVERT: E 120 MET cc_start: 0.8742 (mmp) cc_final: 0.8035 (mmp) REVERT: F 49 LEU cc_start: 0.9748 (mp) cc_final: 0.9483 (mp) REVERT: F 59 LYS cc_start: 0.9635 (mmmm) cc_final: 0.9118 (mmmm) REVERT: H 73 GLU cc_start: 0.9338 (tp30) cc_final: 0.9012 (tp30) REVERT: H 76 ARG cc_start: 0.9169 (ptp90) cc_final: 0.8860 (ptp90) REVERT: K 171 MET cc_start: 0.6419 (ptt) cc_final: 0.5885 (ppp) REVERT: K 204 MET cc_start: -0.2944 (ptp) cc_final: -0.3361 (ttt) REVERT: K 458 MET cc_start: 0.8616 (mtm) cc_final: 0.8138 (mtt) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1565 time to fit residues: 29.2677 Evaluate side-chains 89 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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: 6.9990 chunk 170 optimal weight: 0.7980 chunk 83 optimal weight: 20.0000 chunk 176 optimal weight: 30.0000 chunk 140 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 151 optimal weight: 30.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN ** H 81 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.096545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.038898 restraints weight = 198925.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.038412 restraints weight = 114273.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.038021 restraints weight = 78524.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.037978 restraints weight = 56638.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.037978 restraints weight = 48703.987| |-----------------------------------------------------------------------------| r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.7053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19371 Z= 0.209 Angle : 0.703 9.522 27436 Z= 0.385 Chirality : 0.044 0.215 3068 Planarity : 0.005 0.076 2456 Dihedral : 30.386 176.156 4925 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.15 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 0.93 (0.22), residues: 1524 helix: 1.30 (0.18), residues: 798 sheet: 1.33 (0.63), residues: 73 loop : -0.25 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 131 TYR 0.025 0.002 TYR B 88 PHE 0.015 0.001 PHE C 25 TRP 0.008 0.001 TRP K 762 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.21 (19359) covalent geometry : angle 0.70159 / 0.39 (27423) hydrogen bonds : bond 0.08471 / 5.60 ( 975) hydrogen bonds : angle 4.18104 / 3.00 ( 2471) metal coordination : bond 0.00270 / 0.19 ( 12) metal coordination : angle 1.84297 / 1.28 ( 13) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5265.44 seconds wall clock time: 90 minutes 55.57 seconds (5455.57 seconds total)