Starting phenix.real_space_refine on Thu Mar 5 02:34:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r25_4710/03_2026/6r25_4710.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r25_4710/03_2026/6r25_4710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6r25_4710/03_2026/6r25_4710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r25_4710/03_2026/6r25_4710.map" model { file = "/net/cci-nas-00/data/ceres_data/6r25_4710/03_2026/6r25_4710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r25_4710/03_2026/6r25_4710.cif" } resolution = 4.61 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 10651 2.51 5 N 3358 2.21 5 O 4292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18654 Number of models: 1 Model: "" Number of chains: 16 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: "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: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 804 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} 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: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 356 Unusual residues: {' ZN': 3, 'FAD': 1} Classifications: {'undetermined': 4, 'water': 300} Link IDs: {None: 303} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 36 SG CYS K 53 55.670 53.110 19.749 1.00 48.02 S ATOM 69 SG CYS K 58 52.551 50.397 19.415 1.00 47.27 S ATOM 114 SG CYS K 65 49.904 64.512 19.360 1.00 37.13 S ATOM 173 SG CYS K 73 49.674 67.112 16.618 1.00 40.55 S ATOM 331 SG CYS K 92 53.559 65.891 17.690 1.00 37.37 S ATOM 354 SG CYS K 95 51.378 68.058 19.886 1.00 36.80 S ATOM 761 SG CYS K 142 25.258 54.078 23.619 1.00 35.45 S ATOM 799 SG CYS K 147 26.048 51.692 20.812 1.00 37.39 S ATOM 992 SG CYS K 169 27.431 55.303 20.820 1.00 34.97 S ATOM 1043 SG CYS K 185 23.515 54.522 20.136 1.00 38.56 S Time building chain proxies: 4.13, per 1000 atoms: 0.22 Number of scatterers: 18654 At special positions: 0 Unit cell: (134.62, 155.82, 118.72, 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 4292 8.00 N 3358 7.00 C 10651 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 16378 O5' DC J -20 .*. O " rejected from bonding due to valence issues. Atom "ATOM 16378 O5' DC J -20 .*. O " rejected from bonding due to valence issues. Atom "ATOM 16378 O5' DC J -20 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 588.5 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 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2884 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 16 sheets defined 55.6% alpha, 6.0% beta 142 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... 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: 3.945A pdb=" N GLU K 195 " --> pdb=" O LEU K 191 " (cutoff:3.500A) removed outlier: 3.674A 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: 3.591A pdb=" N ARG K 344 " --> pdb=" O LEU K 340 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU K 350 " --> pdb=" O VAL K 346 " (cutoff:3.500A) removed outlier: 4.558A 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: 4.196A 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: 3.845A pdb=" N SER L 223 " --> pdb=" O PHE L 220 " (cutoff:3.500A) Processing helix chain 'M' and resid 1 through 5 Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.088A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.407A 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: 3.546A 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: 3.682A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.521A 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: 4.333A 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: 3.550A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 75 removed outlier: 3.697A 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 17 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: 3.519A 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: 3.725A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 82 through 86 removed outlier: 6.483A pdb=" N GLU K 89 " --> pdb=" O LEU K 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 139 through 141 Processing sheet with id=AA3, first strand: chain 'K' and resid 592 through 593 removed outlier: 8.208A pdb=" N GLN K 593 " --> pdb=" O VAL K 408 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL K 410 " --> pdb=" O GLN K 593 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL K 385 " --> pdb=" O THR K 409 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU K 411 " --> pdb=" O VAL K 385 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE K 387 " --> pdb=" O LEU K 411 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 423 through 424 Processing sheet with id=AA5, first strand: chain 'K' and resid 438 through 440 Processing sheet with id=AA6, 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: 3.896A pdb=" N LYS K 751 " --> pdb=" O GLN K 665 " (cutoff:3.500A) Processing sheet with id=AA7, 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: 7.979A pdb=" N ASN K 640 " --> pdb=" O GLN K 599 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE K 601 " --> pdb=" O ASN K 640 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 654 through 657 Processing sheet with id=AA9, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AB1, 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=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.678A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AB4, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.780A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB6, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.766A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'G' and resid 77 through 78 614 hydrogen bonds defined for protein. 1755 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: 5.64 Time building geometry restraints manager: 2.06 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: 2381 1.31 - 1.44: 6614 1.44 - 1.57: 9642 1.57 - 1.69: 586 1.69 - 1.82: 81 Bond restraints: 19304 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 1.469 0.191 2.00e-02 2.50e+03 9.08e+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 8.02e+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 7.49e+01 bond pdb=" O1A FAD K 901 " pdb=" PA FAD K 901 " ideal model delta sigma weight residual 1.509 1.365 0.144 2.00e-02 2.50e+03 5.18e+01 ... (remaining 19299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 27059 3.44 - 6.88: 267 6.88 - 10.32: 18 10.32 - 13.76: 3 13.76 - 17.20: 2 Bond angle restraints: 27349 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 117.23 108.24 8.99 1.36e+00 5.41e-01 4.37e+01 angle pdb=" O1P FAD K 901 " pdb=" P FAD K 901 " pdb=" O2P FAD K 901 " ideal model delta sigma weight residual 122.50 105.30 17.20 3.00e+00 1.11e-01 3.29e+01 angle pdb=" C ASP L 214 " pdb=" N PRO L 215 " pdb=" CA PRO L 215 " ideal model delta sigma weight residual 119.47 125.88 -6.41 1.16e+00 7.43e-01 3.05e+01 angle pdb=" CA ILE K 332 " pdb=" C ILE K 332 " pdb=" N PRO K 333 " ideal model delta sigma weight residual 120.83 117.59 3.24 5.90e-01 2.87e+00 3.02e+01 angle pdb=" CA LYS K 75 " pdb=" C LYS K 75 " pdb=" N ASN K 76 " ideal model delta sigma weight residual 119.98 115.34 4.64 8.50e-01 1.38e+00 2.98e+01 ... (remaining 27344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 9204 35.90 - 71.80: 1631 71.80 - 107.71: 31 107.71 - 143.61: 1 143.61 - 179.51: 1 Dihedral angle restraints: 10868 sinusoidal: 6392 harmonic: 4476 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 -66.86 66.86 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 -57.41 57.41 1 1.00e+01 1.00e-02 4.43e+01 ... (remaining 10865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2323 0.063 - 0.125: 615 0.125 - 0.188: 104 0.188 - 0.250: 14 0.250 - 0.313: 3 Chirality restraints: 3059 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 2.44e+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 1.84e+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 1.75e+00 ... (remaining 3056 not shown) Planarity restraints: 2447 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 " 0.139 2.00e-02 2.50e+03 pdb=" C2 FAD K 901 " -0.215 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 " -0.172 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 " 0.149 2.00e-02 2.50e+03 pdb=" N1 FAD K 901 " -0.045 2.00e-02 2.50e+03 pdb=" N10 FAD K 901 " 0.261 2.00e-02 2.50e+03 pdb=" N3 FAD K 901 " -0.223 2.00e-02 2.50e+03 pdb=" N5 FAD K 901 " 0.370 2.00e-02 2.50e+03 pdb=" O2 FAD K 901 " -0.371 2.00e-02 2.50e+03 pdb=" O4 FAD K 901 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 40 " -1.098 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 " 0.012 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 " 1.006 9.50e-02 1.11e+02 4.51e-01 1.23e+02 pdb=" NE ARG G 11 " -0.060 2.00e-02 2.50e+03 pdb=" CZ ARG G 11 " -0.011 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 2444 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 12 1.81 - 2.58: 204 2.58 - 3.35: 23208 3.35 - 4.13: 55301 4.13 - 4.90: 85202 Nonbonded interactions: 163927 Sorted by model distance: nonbonded pdb=" CB GLN M 19 " pdb=" O5' DC J -20 " model vdw 1.036 3.440 nonbonded pdb=" OE1 GLN M 19 " pdb=" OP2 DC J -20 " model vdw 1.301 3.040 nonbonded pdb=" CG GLN M 19 " pdb=" O5' DC J -20 " model vdw 1.349 3.440 nonbonded pdb=" CD GLN M 19 " pdb=" OP2 DC J -20 " model vdw 1.474 3.270 nonbonded pdb=" O HIS E 39 " pdb=" O ARG E 40 " model vdw 1.497 3.040 ... (remaining 163922 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' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 17 through 120) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 25 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: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 24.340 Find NCS groups from input model: 0.150 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4527 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.347 19316 Z= 0.459 Angle : 1.053 17.201 27362 Z= 0.637 Chirality : 0.058 0.313 3059 Planarity : 0.023 0.492 2447 Dihedral : 25.638 179.511 7984 Min Nonbonded Distance : 1.036 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 1.32 % Allowed : 4.87 % Favored : 93.81 % Rotamer: Outliers : 5.67 % Allowed : 4.68 % Favored : 89.65 % 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: -2.97 (0.18), residues: 1518 helix: -2.25 (0.14), residues: 782 sheet: 0.51 (0.69), residues: 61 loop : -1.69 (0.21), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 72 TYR 0.018 0.003 TYR K 767 PHE 0.033 0.003 PHE C 25 TRP 0.014 0.002 TRP K 117 HIS 0.014 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00871 (19304) covalent geometry : angle 1.04732 (27349) hydrogen bonds : bond 0.12828 ( 977) hydrogen bonds : angle 7.23156 ( 2477) metal coordination : bond 0.14838 ( 12) metal coordination : angle 4.91515 ( 13) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 215 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 119 SER cc_start: 0.1979 (OUTLIER) cc_final: 0.1687 (t) REVERT: K 230 MET cc_start: 0.5294 (mtm) cc_final: 0.4216 (ttt) REVERT: K 265 MET cc_start: -0.0069 (ttm) cc_final: -0.0409 (tpp) REVERT: K 267 ARG cc_start: 0.4737 (OUTLIER) cc_final: 0.4251 (mpp-170) REVERT: K 458 MET cc_start: -0.1116 (mtm) cc_final: -0.1580 (mtt) REVERT: M 4 MET cc_start: -0.5283 (tpp) cc_final: -0.5682 (tpt) REVERT: M 18 LYS cc_start: 0.0005 (OUTLIER) cc_final: -0.0272 (pttt) REVERT: D 38 VAL cc_start: 0.9645 (t) cc_final: 0.9413 (m) REVERT: E 65 LEU cc_start: 0.8813 (mt) cc_final: 0.8374 (mt) REVERT: F 25 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8051 (t0) REVERT: F 62 LEU cc_start: 0.9357 (mt) cc_final: 0.8954 (tt) REVERT: G 112 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8154 (mm-40) outliers start: 74 outliers final: 13 residues processed: 282 average time/residue: 0.2254 time to fit residues: 85.2529 Evaluate side-chains 116 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 76 ASN K 93 ASN K 98 HIS K 400 GLN K 440 ASN ** K 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 218 HIS ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN H 46 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.100059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.059404 restraints weight = 225599.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.058910 restraints weight = 165615.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.054385 restraints weight = 139215.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.051721 restraints weight = 96026.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.051205 restraints weight = 77161.665| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 19316 Z= 0.218 Angle : 0.704 9.252 27362 Z= 0.396 Chirality : 0.041 0.184 3059 Planarity : 0.006 0.086 2447 Dihedral : 29.531 179.753 4960 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.82 % Favored : 95.98 % Rotamer: Outliers : 0.08 % Allowed : 2.30 % Favored : 97.62 % 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: -0.39 (0.20), residues: 1518 helix: 0.21 (0.17), residues: 796 sheet: 1.23 (0.66), residues: 61 loop : -0.90 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 83 TYR 0.015 0.002 TYR D 37 PHE 0.021 0.002 PHE C 25 TRP 0.010 0.001 TRP K 201 HIS 0.012 0.002 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00478 (19304) covalent geometry : angle 0.69936 (27349) hydrogen bonds : bond 0.06898 ( 977) hydrogen bonds : angle 4.24705 ( 2477) metal coordination : bond 0.01000 ( 12) metal coordination : angle 3.76621 ( 13) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.598 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: K 230 MET cc_start: 0.4315 (mtm) cc_final: 0.3927 (ttt) REVERT: K 458 MET cc_start: 0.6780 (mtm) cc_final: 0.6363 (mtt) REVERT: M 4 MET cc_start: -0.2895 (tpp) cc_final: -0.4140 (tpt) REVERT: D 34 TYR cc_start: 0.8382 (m-10) cc_final: 0.8177 (m-10) REVERT: D 99 LEU cc_start: 0.9271 (mm) cc_final: 0.8994 (tp) REVERT: H 59 MET cc_start: 0.9562 (tpt) cc_final: 0.9121 (tpp) REVERT: H 65 ASP cc_start: 0.9476 (t70) cc_final: 0.9101 (t70) REVERT: H 69 ARG cc_start: 0.9261 (mmm-85) cc_final: 0.8987 (ttm110) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.2010 time to fit residues: 37.2870 Evaluate side-chains 79 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 18 optimal weight: 30.0000 chunk 147 optimal weight: 9.9990 chunk 23 optimal weight: 50.0000 chunk 37 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 40.0000 chunk 4 optimal weight: 30.0000 chunk 68 optimal weight: 8.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 469 GLN ** K 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN F 93 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.052634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.024788 restraints weight = 196722.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.025345 restraints weight = 134204.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.025666 restraints weight = 103492.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.025948 restraints weight = 87875.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.026145 restraints weight = 78225.388| |-----------------------------------------------------------------------------| r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 19316 Z= 0.292 Angle : 0.705 10.422 27362 Z= 0.398 Chirality : 0.041 0.182 3059 Planarity : 0.006 0.056 2447 Dihedral : 29.792 177.097 4960 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.49 % Favored : 96.38 % Rotamer: Outliers : 0.08 % Allowed : 3.45 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.21), residues: 1518 helix: 0.90 (0.18), residues: 804 sheet: 0.99 (0.58), residues: 81 loop : -0.52 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 8 TYR 0.024 0.002 TYR A 54 PHE 0.019 0.002 PHE K 91 TRP 0.010 0.001 TRP K 762 HIS 0.014 0.002 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00640 (19304) covalent geometry : angle 0.70197 (27349) hydrogen bonds : bond 0.10256 ( 977) hydrogen bonds : angle 4.09306 ( 2477) metal coordination : bond 0.00336 ( 12) metal coordination : angle 3.30625 ( 13) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.614 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: K 230 MET cc_start: 0.4350 (mtm) cc_final: 0.3869 (ttt) REVERT: M 4 MET cc_start: -0.0011 (tpp) cc_final: -0.2353 (tpt) REVERT: H 59 MET cc_start: 0.9584 (tpt) cc_final: 0.9177 (tpp) outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.1832 time to fit residues: 25.6316 Evaluate side-chains 64 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 66 optimal weight: 30.0000 chunk 170 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 440 ASN ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 572 HIS ** K 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.092636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.050854 restraints weight = 238691.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.049876 restraints weight = 192376.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.048036 restraints weight = 173195.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.048487 restraints weight = 146887.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.046099 restraints weight = 156294.004| |-----------------------------------------------------------------------------| r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 19316 Z= 0.283 Angle : 0.701 9.929 27362 Z= 0.392 Chirality : 0.041 0.188 3059 Planarity : 0.006 0.102 2447 Dihedral : 30.085 173.965 4960 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.36 % Favored : 96.57 % Rotamer: Outliers : 0.15 % Allowed : 3.91 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.21), residues: 1518 helix: 0.92 (0.18), residues: 812 sheet: 0.98 (0.58), residues: 81 loop : -0.39 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 2 TYR 0.043 0.002 TYR E 54 PHE 0.014 0.001 PHE K 91 TRP 0.010 0.001 TRP K 559 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00613 (19304) covalent geometry : angle 0.69924 (27349) hydrogen bonds : bond 0.09113 ( 977) hydrogen bonds : angle 4.11745 ( 2477) metal coordination : bond 0.00642 ( 12) metal coordination : angle 2.25872 ( 13) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.560 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: K 230 MET cc_start: 0.4559 (mtm) cc_final: 0.4063 (ttt) REVERT: K 483 MET cc_start: -0.4228 (ttt) cc_final: -0.4444 (ttp) REVERT: A 120 MET cc_start: 0.8971 (mmp) cc_final: 0.8622 (mmm) REVERT: E 120 MET cc_start: 0.8781 (tmm) cc_final: 0.8408 (tmm) REVERT: H 59 MET cc_start: 0.9651 (tpt) cc_final: 0.9245 (tpp) outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.1884 time to fit residues: 23.6498 Evaluate side-chains 58 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 73 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 64 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 184 HIS ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 572 HIS ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN F 25 ASN F 27 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.051849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.023457 restraints weight = 183624.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.023933 restraints weight = 124561.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.024254 restraints weight = 96559.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.024505 restraints weight = 82260.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.024579 restraints weight = 73052.408| |-----------------------------------------------------------------------------| r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6097 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19316 Z= 0.188 Angle : 0.618 9.464 27362 Z= 0.349 Chirality : 0.039 0.219 3059 Planarity : 0.004 0.049 2447 Dihedral : 30.037 175.267 4960 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.17 % Rotamer: Outliers : 0.08 % Allowed : 2.07 % Favored : 97.85 % 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: 0.93 (0.22), residues: 1518 helix: 1.32 (0.18), residues: 802 sheet: 1.00 (0.59), residues: 81 loop : -0.25 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 89 TYR 0.020 0.001 TYR E 54 PHE 0.015 0.001 PHE C 25 TRP 0.009 0.001 TRP K 762 HIS 0.005 0.001 HIS K 561 Details of bonding type rmsd covalent geometry : bond 0.00404 (19304) covalent geometry : angle 0.61735 (27349) hydrogen bonds : bond 0.05957 ( 977) hydrogen bonds : angle 3.84722 ( 2477) metal coordination : bond 0.00344 ( 12) metal coordination : angle 1.82648 ( 13) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.570 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: K 230 MET cc_start: 0.4528 (mtm) cc_final: 0.4178 (ttt) REVERT: K 483 MET cc_start: -0.1929 (ttt) cc_final: -0.2760 (ttp) REVERT: A 120 MET cc_start: 0.7976 (mmp) cc_final: 0.7736 (mmm) REVERT: H 59 MET cc_start: 0.9464 (tpt) cc_final: 0.8916 (tpp) outliers start: 1 outliers final: 1 residues processed: 87 average time/residue: 0.1945 time to fit residues: 24.3783 Evaluate side-chains 60 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 56 optimal weight: 50.0000 chunk 38 optimal weight: 40.0000 chunk 157 optimal weight: 8.9990 chunk 59 optimal weight: 30.0000 chunk 58 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 70 optimal weight: 40.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** 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 = 0.3263 r_free = 0.3263 target = 0.049107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.021932 restraints weight = 197375.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.022419 restraints weight = 136511.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.022728 restraints weight = 106772.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.022912 restraints weight = 90469.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.023089 restraints weight = 81496.579| |-----------------------------------------------------------------------------| r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.6180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 19316 Z= 0.330 Angle : 0.694 8.878 27362 Z= 0.394 Chirality : 0.042 0.250 3059 Planarity : 0.005 0.050 2447 Dihedral : 30.287 174.680 4960 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.29 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % 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 (0.21), residues: 1518 helix: 0.99 (0.18), residues: 808 sheet: 0.92 (0.59), residues: 81 loop : -0.21 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 42 TYR 0.031 0.002 TYR E 54 PHE 0.013 0.001 PHE K 753 TRP 0.008 0.001 TRP K 762 HIS 0.008 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00724 (19304) covalent geometry : angle 0.69377 (27349) hydrogen bonds : bond 0.11965 ( 977) hydrogen bonds : angle 4.24404 ( 2477) metal coordination : bond 0.00501 ( 12) metal coordination : angle 1.59947 ( 13) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.577 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: K 230 MET cc_start: 0.4855 (mtm) cc_final: 0.4322 (ttt) REVERT: K 483 MET cc_start: -0.3232 (ttt) cc_final: -0.3693 (ttp) REVERT: A 120 MET cc_start: 0.8975 (mmp) cc_final: 0.8631 (mmm) REVERT: D 96 ARG cc_start: 0.9537 (mtp180) cc_final: 0.9041 (mtm110) REVERT: H 59 MET cc_start: 0.9621 (tpt) cc_final: 0.8887 (tpt) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1884 time to fit residues: 20.0058 Evaluate side-chains 53 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 50 optimal weight: 20.0000 chunk 147 optimal weight: 4.9990 chunk 56 optimal weight: 50.0000 chunk 30 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 9 optimal weight: 30.0000 chunk 138 optimal weight: 20.0000 chunk 29 optimal weight: 30.0000 chunk 47 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 28 optimal weight: 50.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN H 44 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.090420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.052961 restraints weight = 240908.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.046286 restraints weight = 204227.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.045303 restraints weight = 139913.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.045303 restraints weight = 108660.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.045303 restraints weight = 108658.815| |-----------------------------------------------------------------------------| r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.6774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 19316 Z= 0.286 Angle : 0.681 9.314 27362 Z= 0.383 Chirality : 0.041 0.174 3059 Planarity : 0.005 0.051 2447 Dihedral : 30.667 174.829 4960 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.23 % Favored : 96.71 % Rotamer: Outliers : 0.08 % Allowed : 1.69 % Favored : 98.24 % 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: 0.70 (0.22), residues: 1518 helix: 0.94 (0.18), residues: 794 sheet: 0.73 (0.58), residues: 81 loop : -0.03 (0.26), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 128 TYR 0.031 0.002 TYR E 54 PHE 0.019 0.001 PHE B 61 TRP 0.008 0.001 TRP K 762 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00619 (19304) covalent geometry : angle 0.68008 (27349) hydrogen bonds : bond 0.09163 ( 977) hydrogen bonds : angle 4.26472 ( 2477) metal coordination : bond 0.00394 ( 12) metal coordination : angle 1.40192 ( 13) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.582 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: K 230 MET cc_start: 0.4793 (mtm) cc_final: 0.4012 (tmm) REVERT: K 483 MET cc_start: -0.3249 (ttt) cc_final: -0.3715 (ttp) REVERT: A 120 MET cc_start: 0.9158 (mmp) cc_final: 0.8807 (mmm) REVERT: D 56 MET cc_start: 0.9558 (mmm) cc_final: 0.9354 (mmm) REVERT: D 96 ARG cc_start: 0.9570 (mtp180) cc_final: 0.9178 (mtt180) REVERT: H 59 MET cc_start: 0.9612 (tpt) cc_final: 0.8846 (tpp) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.1910 time to fit residues: 20.8363 Evaluate side-chains 52 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 31 optimal weight: 50.0000 chunk 71 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 141 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 chunk 62 optimal weight: 30.0000 chunk 35 optimal weight: 50.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** 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 = 0.3547 r_free = 0.3547 target = 0.089793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.049958 restraints weight = 238746.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.049733 restraints weight = 200075.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.048919 restraints weight = 189638.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.046034 restraints weight = 184379.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.045280 restraints weight = 136986.236| |-----------------------------------------------------------------------------| r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.7090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 19316 Z= 0.296 Angle : 0.680 9.710 27362 Z= 0.384 Chirality : 0.041 0.273 3059 Planarity : 0.005 0.057 2447 Dihedral : 30.697 173.943 4960 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.56 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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: 0.77 (0.22), residues: 1518 helix: 1.01 (0.18), residues: 799 sheet: 0.65 (0.59), residues: 81 loop : -0.01 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 26 TYR 0.027 0.002 TYR E 54 PHE 0.012 0.001 PHE F 100 TRP 0.008 0.001 TRP K 762 HIS 0.010 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00648 (19304) covalent geometry : angle 0.67935 (27349) hydrogen bonds : bond 0.10570 ( 977) hydrogen bonds : angle 4.28444 ( 2477) metal coordination : bond 0.00457 ( 12) metal coordination : angle 1.28184 ( 13) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 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: K 230 MET cc_start: 0.4770 (mtm) cc_final: 0.4013 (tmm) REVERT: A 134 ARG cc_start: 0.9170 (tpm170) cc_final: 0.8751 (ttp-110) REVERT: D 96 ARG cc_start: 0.9549 (mtp180) cc_final: 0.9081 (mtm110) REVERT: D 99 LEU cc_start: 0.8436 (tp) cc_final: 0.8216 (tt) REVERT: E 120 MET cc_start: 0.9007 (tmm) cc_final: 0.8807 (tmm) REVERT: H 59 MET cc_start: 0.9637 (tpt) cc_final: 0.9010 (tpp) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1874 time to fit residues: 18.9978 Evaluate side-chains 54 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 66 optimal weight: 6.9990 chunk 138 optimal weight: 0.6980 chunk 9 optimal weight: 50.0000 chunk 132 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 46 optimal weight: 30.0000 chunk 103 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 154 optimal weight: 7.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN H 46 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.091764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.055689 restraints weight = 234748.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.054433 restraints weight = 192685.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.052133 restraints weight = 172965.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.050681 restraints weight = 130431.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.049524 restraints weight = 101450.305| |-----------------------------------------------------------------------------| r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.7131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19316 Z= 0.203 Angle : 0.639 10.934 27362 Z= 0.357 Chirality : 0.040 0.269 3059 Planarity : 0.004 0.054 2447 Dihedral : 30.597 174.682 4960 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.29 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.22), residues: 1518 helix: 1.21 (0.18), residues: 807 sheet: 0.65 (0.59), residues: 81 loop : 0.01 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 482 TYR 0.018 0.001 TYR E 54 PHE 0.015 0.001 PHE K 801 TRP 0.008 0.001 TRP K 559 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00441 (19304) covalent geometry : angle 0.63855 (27349) hydrogen bonds : bond 0.06827 ( 977) hydrogen bonds : angle 4.05732 ( 2477) metal coordination : bond 0.00346 ( 12) metal coordination : angle 1.13279 ( 13) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.503 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: K 230 MET cc_start: 0.4742 (mtm) cc_final: 0.3977 (tmm) REVERT: K 483 MET cc_start: -0.3591 (ttt) cc_final: -0.4228 (ptm) REVERT: A 120 MET cc_start: 0.9151 (mmp) cc_final: 0.8730 (mmm) REVERT: D 34 TYR cc_start: 0.9344 (m-10) cc_final: 0.9015 (m-10) REVERT: D 59 MET cc_start: 0.9800 (mmp) cc_final: 0.9570 (mmm) REVERT: D 96 ARG cc_start: 0.9587 (mtp180) cc_final: 0.9095 (mtm110) REVERT: D 99 LEU cc_start: 0.8739 (tp) cc_final: 0.8496 (tt) REVERT: E 120 MET cc_start: 0.9043 (tmm) cc_final: 0.8840 (tmm) REVERT: H 59 MET cc_start: 0.9561 (tpt) cc_final: 0.9057 (tpp) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1883 time to fit residues: 19.0474 Evaluate side-chains 55 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 175 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 4 optimal weight: 30.0000 chunk 161 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 109 optimal weight: 0.0170 chunk 85 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** H 81 ASN ** 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 = 0.3241 r_free = 0.3241 target = 0.049842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.021850 restraints weight = 194041.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.022368 restraints weight = 131484.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.022700 restraints weight = 101627.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.022893 restraints weight = 85624.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.023053 restraints weight = 76652.728| |-----------------------------------------------------------------------------| r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 moved from start: 0.7310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19316 Z= 0.225 Angle : 0.641 10.596 27362 Z= 0.358 Chirality : 0.039 0.250 3059 Planarity : 0.005 0.055 2447 Dihedral : 30.471 176.213 4960 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % 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: 0.97 (0.22), residues: 1518 helix: 1.21 (0.18), residues: 808 sheet: 0.68 (0.59), residues: 81 loop : 0.02 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 26 TYR 0.021 0.001 TYR E 54 PHE 0.011 0.001 PHE K 91 TRP 0.008 0.001 TRP K 559 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00493 (19304) covalent geometry : angle 0.64078 (27349) hydrogen bonds : bond 0.08140 ( 977) hydrogen bonds : angle 4.06685 ( 2477) metal coordination : bond 0.00316 ( 12) metal coordination : angle 1.10527 ( 13) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.578 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: K 230 MET cc_start: 0.4831 (mtm) cc_final: 0.4227 (tmm) REVERT: K 483 MET cc_start: -0.0756 (ttt) cc_final: -0.1675 (ptm) REVERT: A 120 MET cc_start: 0.8427 (mmp) cc_final: 0.8158 (mmm) REVERT: D 96 ARG cc_start: 0.9198 (mtp180) cc_final: 0.8874 (mtm110) REVERT: H 59 MET cc_start: 0.9407 (tpt) cc_final: 0.9035 (tpp) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1782 time to fit residues: 18.0863 Evaluate side-chains 53 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 157 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 51 optimal weight: 40.0000 chunk 132 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 1 optimal weight: 30.0000 chunk 95 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS F 25 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.050240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.022114 restraints weight = 195695.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.022599 restraints weight = 131679.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.022905 restraints weight = 101130.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.023171 restraints weight = 85211.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.023368 restraints weight = 75218.132| |-----------------------------------------------------------------------------| r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6117 moved from start: 0.7434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19316 Z= 0.199 Angle : 0.623 10.825 27362 Z= 0.348 Chirality : 0.039 0.273 3059 Planarity : 0.004 0.054 2447 Dihedral : 30.407 177.610 4960 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % 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: 1.01 (0.22), residues: 1518 helix: 1.27 (0.18), residues: 808 sheet: 0.69 (0.59), residues: 81 loop : -0.00 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.018 0.001 TYR E 54 PHE 0.009 0.001 PHE K 91 TRP 0.008 0.001 TRP K 559 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00435 (19304) covalent geometry : angle 0.62251 (27349) hydrogen bonds : bond 0.06771 ( 977) hydrogen bonds : angle 4.00137 ( 2477) metal coordination : bond 0.00306 ( 12) metal coordination : angle 1.00502 ( 13) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6017.54 seconds wall clock time: 103 minutes 32.94 seconds (6212.94 seconds total)