Starting phenix.real_space_refine on Sat Sep 28 05:01:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r1u_4705/09_2024/6r1u_4705.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r1u_4705/09_2024/6r1u_4705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r1u_4705/09_2024/6r1u_4705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r1u_4705/09_2024/6r1u_4705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r1u_4705/09_2024/6r1u_4705.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r1u_4705/09_2024/6r1u_4705.cif" } resolution = 4.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 296 5.49 5 S 54 5.16 5 C 10684 2.51 5 N 3372 2.21 5 O 3985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 18394 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 689 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 811 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 820 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 870 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "H" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 775 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 5837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5837 Classifications: {'peptide': 737} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 36, 'TRANS': 698} Chain breaks: 2 Chain: "L" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "M" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 193 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "K" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {' ZN': 3, 'FAD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12239 SG CYS K 53 75.441 111.267 70.128 1.00 48.02 S ATOM 12272 SG CYS K 58 73.966 113.629 73.201 1.00 47.27 S ATOM 12317 SG CYS K 65 85.145 104.914 75.500 1.00 37.13 S ATOM 12376 SG CYS K 73 88.895 105.346 75.202 1.00 40.55 S ATOM 12534 SG CYS K 92 86.794 104.861 71.584 1.00 37.37 S ATOM 12557 SG CYS K 95 87.344 102.062 74.063 1.00 36.80 S ATOM 12964 SG CYS K 142 77.571 111.293 100.726 1.00 35.45 S ATOM 13002 SG CYS K 147 77.414 114.859 99.519 1.00 37.39 S ATOM 13195 SG CYS K 169 80.000 112.370 98.082 1.00 34.97 S ATOM 13246 SG CYS K 185 80.326 113.849 101.839 1.00 38.56 S Time building chain proxies: 10.70, per 1000 atoms: 0.58 Number of scatterers: 18394 At special positions: 0 Unit cell: (134.62, 132.5, 137.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 54 16.00 P 296 15.00 O 3985 8.00 N 3372 7.00 C 10684 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 9765 O5' DC J -46 .*. O " rejected from bonding due to valence issues. Atom "ATOM 9765 O5' DC J -46 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.56 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 902 " pdb="ZN ZN K 902 " - pdb=" NE2 HIS K 90 " pdb="ZN ZN K 902 " - pdb=" SG CYS K 58 " pdb="ZN ZN K 902 " - pdb=" ND1 HIS K 84 " pdb="ZN ZN K 902 " - pdb=" SG CYS K 53 " pdb=" ZN K 903 " pdb="ZN ZN K 903 " - pdb=" SG CYS K 95 " pdb="ZN ZN K 903 " - pdb=" SG CYS K 65 " pdb="ZN ZN K 903 " - pdb=" SG CYS K 73 " pdb="ZN ZN K 903 " - pdb=" SG CYS K 92 " pdb=" ZN K 904 " pdb="ZN ZN K 904 " - pdb=" SG CYS K 147 " pdb="ZN ZN K 904 " - pdb=" SG CYS K 142 " pdb="ZN ZN K 904 " - pdb=" SG CYS K 185 " pdb="ZN ZN K 904 " - pdb=" SG CYS K 169 " Number of angles added : 13 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 16 sheets defined 55.0% alpha, 5.9% beta 142 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 7.86 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.087A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.547A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.607A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.681A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.545A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 79 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.747A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 113 removed outlier: 3.599A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.549A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 75 removed outlier: 3.698A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.863A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 88 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.518A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 4.309A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.603A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 101 Processing helix chain 'K' and resid 106 through 117 Processing helix chain 'K' and resid 126 through 135 Processing helix chain 'K' and resid 160 through 167 Processing helix chain 'K' and resid 183 through 187 Processing helix chain 'K' and resid 191 through 196 removed outlier: 3.947A pdb=" N GLU K 195 " --> pdb=" O LEU K 191 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL K 196 " --> pdb=" O ARG K 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 191 through 196' Processing helix chain 'K' and resid 198 through 204 removed outlier: 4.047A pdb=" N TYR K 202 " --> pdb=" O ASN K 198 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER K 203 " --> pdb=" O HIS K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 216 through 220 Processing helix chain 'K' and resid 224 through 228 Processing helix chain 'K' and resid 290 through 297 Processing helix chain 'K' and resid 298 through 301 Processing helix chain 'K' and resid 304 through 321 Processing helix chain 'K' and resid 327 through 332 Processing helix chain 'K' and resid 333 through 335 No H-bonds generated for 'chain 'K' and resid 333 through 335' Processing helix chain 'K' and resid 340 through 359 removed outlier: 3.592A pdb=" N ARG K 344 " --> pdb=" O LEU K 340 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU K 350 " --> pdb=" O VAL K 346 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG K 351 " --> pdb=" O GLN K 347 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 381 Processing helix chain 'K' and resid 391 through 405 Processing helix chain 'K' and resid 445 through 455 Processing helix chain 'K' and resid 476 through 498 Processing helix chain 'K' and resid 499 through 501 No H-bonds generated for 'chain 'K' and resid 499 through 501' Processing helix chain 'K' and resid 502 through 506 Processing helix chain 'K' and resid 508 through 524 Processing helix chain 'K' and resid 529 through 548 Processing helix chain 'K' and resid 560 through 565 Processing helix chain 'K' and resid 579 through 588 Processing helix chain 'K' and resid 628 through 635 Processing helix chain 'K' and resid 644 through 653 Processing helix chain 'K' and resid 671 through 676 Processing helix chain 'K' and resid 715 through 721 removed outlier: 4.197A pdb=" N ALA K 719 " --> pdb=" O GLY K 715 " (cutoff:3.500A) Processing helix chain 'K' and resid 725 through 741 Processing helix chain 'K' and resid 756 through 760 Processing helix chain 'K' and resid 776 through 784 removed outlier: 4.028A pdb=" N ASP K 780 " --> pdb=" O GLY K 776 " (cutoff:3.500A) Processing helix chain 'K' and resid 794 through 798 Processing helix chain 'K' and resid 804 through 822 removed outlier: 3.731A pdb=" N PHE K 822 " --> pdb=" O LYS K 818 " (cutoff:3.500A) Processing helix chain 'L' and resid 219 through 223 removed outlier: 3.846A pdb=" N SER L 223 " --> pdb=" O PHE L 220 " (cutoff:3.500A) Processing helix chain 'M' and resid 1 through 5 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.061A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.677A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.781A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.765A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'K' and resid 82 through 86 removed outlier: 6.486A pdb=" N GLU K 89 " --> pdb=" O LEU K 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 139 through 141 Processing sheet with id=AB2, first strand: chain 'K' and resid 592 through 593 removed outlier: 8.207A pdb=" N GLN K 593 " --> pdb=" O VAL K 408 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL K 410 " --> pdb=" O GLN K 593 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL K 385 " --> pdb=" O THR K 409 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU K 411 " --> pdb=" O VAL K 385 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE K 387 " --> pdb=" O LEU K 411 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 423 through 424 Processing sheet with id=AB4, first strand: chain 'K' and resid 438 through 440 Processing sheet with id=AB5, first strand: chain 'K' and resid 467 through 468 removed outlier: 5.345A pdb=" N ALA K 695 " --> pdb=" O HIS K 683 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL K 696 " --> pdb=" O VAL K 712 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL K 712 " --> pdb=" O VAL K 696 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS K 751 " --> pdb=" O GLN K 665 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 617 through 620 removed outlier: 6.794A pdb=" N GLN K 599 " --> pdb=" O GLN K 638 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ASN K 640 " --> pdb=" O GLN K 599 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE K 601 " --> pdb=" O ASN K 640 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 654 through 657 612 hydrogen bonds defined for protein. 1749 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 363 hydrogen bonds 722 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 10.98 Time building geometry restraints manager: 5.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2389 1.31 - 1.44: 6635 1.44 - 1.57: 9668 1.57 - 1.70: 586 1.70 - 1.82: 81 Bond restraints: 19359 Sorted by residual: bond pdb=" O5B FAD K 901 " pdb=" PA FAD K 901 " ideal model delta sigma weight residual 1.634 1.386 0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" O3P FAD K 901 " pdb=" P FAD K 901 " ideal model delta sigma weight residual 1.660 1.470 0.190 2.00e-02 2.50e+03 9.07e+01 bond pdb=" O3P FAD K 901 " pdb=" PA FAD K 901 " ideal model delta sigma weight residual 1.633 1.454 0.179 2.00e-02 2.50e+03 8.05e+01 bond pdb=" O5' FAD K 901 " pdb=" P FAD K 901 " ideal model delta sigma weight residual 1.637 1.464 0.173 2.00e-02 2.50e+03 7.48e+01 bond pdb=" O1A FAD K 901 " pdb=" PA FAD K 901 " ideal model delta sigma weight residual 1.509 1.365 0.144 2.00e-02 2.50e+03 5.22e+01 ... (remaining 19354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 27127 3.43 - 6.86: 273 6.86 - 10.29: 18 10.29 - 13.72: 3 13.72 - 17.15: 2 Bond angle restraints: 27423 Sorted by residual: angle pdb=" C LYS K 75 " pdb=" CA LYS K 75 " pdb=" CB LYS K 75 " ideal model delta sigma weight residual 117.23 108.32 8.91 1.36e+00 5.41e-01 4.29e+01 angle pdb=" O1P FAD K 901 " pdb=" P FAD K 901 " pdb=" O2P FAD K 901 " ideal model delta sigma weight residual 122.50 105.35 17.15 3.00e+00 1.11e-01 3.27e+01 angle pdb=" C ASP L 214 " pdb=" N PRO L 215 " pdb=" CA PRO L 215 " ideal model delta sigma weight residual 119.47 125.97 -6.50 1.16e+00 7.43e-01 3.14e+01 angle pdb=" CA LYS K 75 " pdb=" C LYS K 75 " pdb=" N ASN K 76 " ideal model delta sigma weight residual 119.98 115.33 4.65 8.50e-01 1.38e+00 3.00e+01 angle pdb=" C ASP K 760 " pdb=" N PRO K 761 " pdb=" CA PRO K 761 " ideal model delta sigma weight residual 119.05 125.04 -5.99 1.11e+00 8.12e-01 2.92e+01 ... (remaining 27418 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 9220 35.91 - 71.82: 1648 71.82 - 107.73: 32 107.73 - 143.64: 1 143.64 - 179.56: 1 Dihedral angle restraints: 10902 sinusoidal: 6408 harmonic: 4494 Sorted by residual: dihedral pdb=" CD ARG A 40 " pdb=" NE ARG A 40 " pdb=" CZ ARG A 40 " pdb=" NH1 ARG A 40 " ideal model delta sinusoidal sigma weight residual 0.00 -85.61 85.61 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CD ARG G 11 " pdb=" NE ARG G 11 " pdb=" CZ ARG G 11 " pdb=" NH1 ARG G 11 " ideal model delta sinusoidal sigma weight residual 0.00 -66.88 66.88 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CD ARG H 30 " pdb=" NE ARG H 30 " pdb=" CZ ARG H 30 " pdb=" NH1 ARG H 30 " ideal model delta sinusoidal sigma weight residual 0.00 -57.45 57.45 1 1.00e+01 1.00e-02 4.43e+01 ... (remaining 10899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2312 0.062 - 0.124: 630 0.124 - 0.186: 107 0.186 - 0.247: 16 0.247 - 0.309: 3 Chirality restraints: 3068 Sorted by residual: chirality pdb=" C3' FAD K 901 " pdb=" C2' FAD K 901 " pdb=" C4' FAD K 901 " pdb=" O3' FAD K 901 " both_signs ideal model delta sigma weight residual False -2.55 -2.24 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA THR K 143 " pdb=" N THR K 143 " pdb=" C THR K 143 " pdb=" CB THR K 143 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CG LEU G 34 " pdb=" CB LEU G 34 " pdb=" CD1 LEU G 34 " pdb=" CD2 LEU G 34 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 3065 not shown) Planarity restraints: 2456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FAD K 901 " -0.396 2.00e-02 2.50e+03 2.24e-01 2.38e+03 pdb=" C10 FAD K 901 " -0.140 2.00e-02 2.50e+03 pdb=" C2 FAD K 901 " 0.214 2.00e-02 2.50e+03 pdb=" C4 FAD K 901 " 0.037 2.00e-02 2.50e+03 pdb=" C4X FAD K 901 " -0.149 2.00e-02 2.50e+03 pdb=" C5X FAD K 901 " -0.219 2.00e-02 2.50e+03 pdb=" C6 FAD K 901 " -0.124 2.00e-02 2.50e+03 pdb=" C7 FAD K 901 " 0.076 2.00e-02 2.50e+03 pdb=" C7M FAD K 901 " 0.199 2.00e-02 2.50e+03 pdb=" C8 FAD K 901 " 0.173 2.00e-02 2.50e+03 pdb=" C8M FAD K 901 " 0.382 2.00e-02 2.50e+03 pdb=" C9 FAD K 901 " 0.055 2.00e-02 2.50e+03 pdb=" C9A FAD K 901 " -0.148 2.00e-02 2.50e+03 pdb=" N1 FAD K 901 " 0.045 2.00e-02 2.50e+03 pdb=" N10 FAD K 901 " -0.262 2.00e-02 2.50e+03 pdb=" N3 FAD K 901 " 0.222 2.00e-02 2.50e+03 pdb=" N5 FAD K 901 " -0.369 2.00e-02 2.50e+03 pdb=" O2 FAD K 901 " 0.371 2.00e-02 2.50e+03 pdb=" O4 FAD K 901 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 40 " 1.099 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG A 40 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 40 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 40 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 40 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 11 " 1.007 9.50e-02 1.11e+02 4.51e-01 1.23e+02 pdb=" NE ARG G 11 " -0.061 2.00e-02 2.50e+03 pdb=" CZ ARG G 11 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG G 11 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG G 11 " 0.023 2.00e-02 2.50e+03 ... (remaining 2453 not shown) Histogram of nonbonded interaction distances: 0.54 - 1.42: 11 1.42 - 2.29: 63 2.29 - 3.16: 14531 3.16 - 4.03: 54780 4.03 - 4.90: 89241 Warning: very small nonbonded interaction distances. Nonbonded interactions: 158626 Sorted by model distance: nonbonded pdb=" NH1 ARG H 30 " pdb=" O5' DC J -46 " model vdw 0.544 3.120 nonbonded pdb=" NH2 ARG H 30 " pdb=" O3' DT J -47 " model vdw 0.796 3.120 nonbonded pdb=" CB ARG A 128 " pdb=" OE1 GLU A 133 " model vdw 0.821 3.440 nonbonded pdb=" NE ARG A 128 " pdb=" OE2 GLU A 133 " model vdw 0.827 3.120 nonbonded pdb=" NZ LYS D 28 " pdb=" O3' DA J 50 " model vdw 0.922 3.120 ... (remaining 158621 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 37 through 134) selection = (chain 'E' and resid 37 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 101) selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 120) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 26 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.780 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 54.430 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4616 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.248 19359 Z= 0.521 Angle : 1.043 17.149 27423 Z= 0.634 Chirality : 0.058 0.309 3068 Planarity : 0.023 0.492 2456 Dihedral : 25.719 179.556 8006 Min Nonbonded Distance : 0.544 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 1.25 % Allowed : 4.66 % Favored : 94.09 % Rotamer: Outliers : 6.26 % Allowed : 4.58 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.18), residues: 1524 helix: -2.27 (0.14), residues: 787 sheet: 0.51 (0.69), residues: 61 loop : -1.71 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 117 HIS 0.014 0.002 HIS B 75 PHE 0.033 0.003 PHE C 25 TYR 0.019 0.003 TYR K 767 ARG 0.016 0.001 ARG K 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 276 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8726 (mp) cc_final: 0.8345 (tp) REVERT: E 74 ILE cc_start: 0.9194 (mt) cc_final: 0.8614 (mm) REVERT: E 107 THR cc_start: 0.8394 (m) cc_final: 0.8033 (p) REVERT: F 88 TYR cc_start: 0.8176 (m-10) cc_final: 0.7941 (m-80) REVERT: K 85 LEU cc_start: 0.1545 (OUTLIER) cc_final: 0.1162 (tp) REVERT: K 204 MET cc_start: 0.2224 (mtm) cc_final: 0.1943 (ttm) REVERT: K 294 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6212 (mt) REVERT: K 458 MET cc_start: -0.1180 (mtm) cc_final: -0.3741 (mtt) REVERT: K 700 MET cc_start: -0.2175 (mmm) cc_final: -0.2801 (mmm) REVERT: M 22 THR cc_start: -0.0210 (OUTLIER) cc_final: -0.0427 (t) outliers start: 82 outliers final: 26 residues processed: 347 average time/residue: 0.4178 time to fit residues: 198.4253 Evaluate side-chains 150 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 121 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 40.0000 chunk 134 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 138 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 103 optimal weight: 0.4980 chunk 160 optimal weight: 20.0000 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 46 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 ASN K 98 HIS K 400 GLN ** K 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 218 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4844 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19359 Z= 0.311 Angle : 0.725 8.920 27423 Z= 0.408 Chirality : 0.042 0.196 3068 Planarity : 0.008 0.168 2456 Dihedral : 29.503 177.284 4968 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.67 % Favored : 96.13 % Rotamer: Outliers : 0.23 % Allowed : 2.90 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.20), residues: 1524 helix: 0.20 (0.17), residues: 802 sheet: 1.29 (0.66), residues: 61 loop : -0.95 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 762 HIS 0.007 0.001 HIS F 75 PHE 0.021 0.002 PHE C 25 TYR 0.030 0.002 TYR B 88 ARG 0.026 0.001 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 168 time to evaluate : 1.599 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: B 84 MET cc_start: 0.8083 (mmm) cc_final: 0.6741 (tpp) REVERT: H 73 GLU cc_start: 0.8150 (tp30) cc_final: 0.7737 (tp30) REVERT: K 265 MET cc_start: -0.2579 (ttt) cc_final: -0.3187 (tpt) REVERT: K 458 MET cc_start: -0.1748 (mtm) cc_final: -0.3921 (mtt) outliers start: 3 outliers final: 0 residues processed: 169 average time/residue: 0.3607 time to fit residues: 88.0485 Evaluate side-chains 111 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 109 optimal weight: 40.0000 chunk 44 optimal weight: 3.9990 chunk 161 optimal weight: 30.0000 chunk 173 optimal weight: 30.0000 chunk 143 optimal weight: 50.0000 chunk 159 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 129 optimal weight: 30.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS K 469 GLN ** K 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4926 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19359 Z= 0.259 Angle : 0.647 7.788 27423 Z= 0.370 Chirality : 0.040 0.203 3068 Planarity : 0.006 0.079 2456 Dihedral : 29.537 178.180 4968 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.35 % Favored : 96.39 % Rotamer: Outliers : 0.31 % Allowed : 3.13 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1524 helix: 0.89 (0.18), residues: 805 sheet: 1.56 (0.60), residues: 71 loop : -0.60 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 762 HIS 0.016 0.001 HIS E 39 PHE 0.018 0.001 PHE K 91 TYR 0.034 0.002 TYR B 88 ARG 0.008 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 155 time to evaluate : 1.689 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: B 84 MET cc_start: 0.8109 (mmm) cc_final: 0.7580 (tpp) REVERT: B 88 TYR cc_start: 0.8417 (m-80) cc_final: 0.7923 (m-80) REVERT: E 103 LEU cc_start: 0.8916 (tt) cc_final: 0.8635 (tt) REVERT: F 59 LYS cc_start: 0.8969 (tptp) cc_final: 0.8603 (tppt) REVERT: H 73 GLU cc_start: 0.8001 (tp30) cc_final: 0.7550 (tp30) REVERT: H 76 ARG cc_start: 0.8444 (ptp90) cc_final: 0.8199 (ptp90) REVERT: K 204 MET cc_start: 0.2357 (mtm) cc_final: 0.1844 (ttm) REVERT: K 265 MET cc_start: -0.2569 (ttt) cc_final: -0.2816 (tpt) REVERT: K 458 MET cc_start: -0.2008 (mtm) cc_final: -0.4016 (mtt) outliers start: 4 outliers final: 0 residues processed: 157 average time/residue: 0.3853 time to fit residues: 87.7755 Evaluate side-chains 106 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 108 optimal weight: 50.0000 chunk 161 optimal weight: 50.0000 chunk 171 optimal weight: 50.0000 chunk 84 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 184 HIS ** K 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5081 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 19359 Z= 0.362 Angle : 0.669 7.132 27423 Z= 0.380 Chirality : 0.040 0.176 3068 Planarity : 0.005 0.095 2456 Dihedral : 29.635 177.486 4968 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.67 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.22), residues: 1524 helix: 1.14 (0.18), residues: 810 sheet: 1.51 (0.63), residues: 72 loop : -0.47 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 762 HIS 0.014 0.002 HIS F 75 PHE 0.013 0.001 PHE K 91 TYR 0.020 0.002 TYR A 54 ARG 0.019 0.001 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.647 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: B 84 MET cc_start: 0.8232 (mmm) cc_final: 0.7956 (mmm) REVERT: E 94 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7568 (mm-30) REVERT: H 73 GLU cc_start: 0.8195 (tp30) cc_final: 0.7874 (tp30) REVERT: K 204 MET cc_start: 0.2246 (mtm) cc_final: 0.1500 (ttm) REVERT: K 265 MET cc_start: -0.2749 (ttt) cc_final: -0.3212 (tpt) REVERT: K 458 MET cc_start: -0.2204 (mtm) cc_final: -0.4354 (mtt) REVERT: M 4 MET cc_start: -0.2057 (ppp) cc_final: -0.2607 (ttt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.4126 time to fit residues: 80.5517 Evaluate side-chains 94 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 2 optimal weight: 0.0670 chunk 127 optimal weight: 40.0000 chunk 70 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 118 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 overall best weight: 5.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 31 HIS D 81 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5133 moved from start: 0.6272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 19359 Z= 0.341 Angle : 0.672 9.904 27423 Z= 0.379 Chirality : 0.040 0.189 3068 Planarity : 0.005 0.048 2456 Dihedral : 29.890 177.411 4968 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.02 % Favored : 96.78 % Rotamer: Outliers : 0.08 % Allowed : 3.21 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.22), residues: 1524 helix: 1.15 (0.18), residues: 809 sheet: 1.36 (0.62), residues: 74 loop : -0.42 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 762 HIS 0.011 0.001 HIS F 75 PHE 0.015 0.001 PHE K 91 TYR 0.035 0.002 TYR B 88 ARG 0.013 0.001 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8458 (mt-10) REVERT: C 110 ASN cc_start: 0.8805 (t0) cc_final: 0.8527 (t0) REVERT: G 104 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7685 (tp-100) REVERT: H 73 GLU cc_start: 0.8292 (tp30) cc_final: 0.7730 (tp30) REVERT: H 76 ARG cc_start: 0.8397 (ptp90) cc_final: 0.8173 (ptp90) REVERT: K 265 MET cc_start: -0.2476 (ttt) cc_final: -0.3022 (tpt) REVERT: K 458 MET cc_start: -0.2165 (mtm) cc_final: -0.4327 (mtt) REVERT: K 700 MET cc_start: -0.2103 (mmt) cc_final: -0.2443 (mmp) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.3454 time to fit residues: 64.8179 Evaluate side-chains 86 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 0.9990 chunk 154 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 171 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 104 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5035 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19359 Z= 0.189 Angle : 0.615 9.423 27423 Z= 0.346 Chirality : 0.039 0.189 3068 Planarity : 0.004 0.052 2456 Dihedral : 29.783 178.175 4968 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.69 % Favored : 97.18 % Rotamer: Outliers : 0.08 % Allowed : 1.30 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.22), residues: 1524 helix: 1.43 (0.18), residues: 802 sheet: 0.85 (0.60), residues: 84 loop : -0.23 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 762 HIS 0.008 0.001 HIS F 75 PHE 0.016 0.001 PHE G 25 TYR 0.028 0.001 TYR B 88 ARG 0.006 0.000 ARG H 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8381 (mt-10) REVERT: E 126 LEU cc_start: 0.9083 (tp) cc_final: 0.8772 (tt) REVERT: F 25 ASN cc_start: 0.8088 (OUTLIER) cc_final: 0.7765 (t0) REVERT: F 34 ILE cc_start: 0.9581 (mt) cc_final: 0.9238 (tt) REVERT: F 59 LYS cc_start: 0.9033 (mmmm) cc_final: 0.8754 (mmmm) REVERT: H 73 GLU cc_start: 0.8108 (tp30) cc_final: 0.7755 (tp30) REVERT: K 204 MET cc_start: 0.2349 (mtm) cc_final: 0.1451 (ttt) REVERT: K 265 MET cc_start: -0.2517 (ttt) cc_final: -0.3080 (tpt) REVERT: K 458 MET cc_start: -0.2129 (mtm) cc_final: -0.4297 (mtt) REVERT: M 4 MET cc_start: -0.1292 (ppp) cc_final: -0.2419 (ptm) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.3516 time to fit residues: 69.9026 Evaluate side-chains 90 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 125 optimal weight: 30.0000 chunk 96 optimal weight: 7.9990 chunk 144 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 chunk 170 optimal weight: 40.0000 chunk 106 optimal weight: 0.0370 chunk 104 optimal weight: 50.0000 chunk 78 optimal weight: 6.9990 overall best weight: 6.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5213 moved from start: 0.7043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 19359 Z= 0.415 Angle : 0.690 8.218 27423 Z= 0.394 Chirality : 0.042 0.174 3068 Planarity : 0.005 0.047 2456 Dihedral : 29.897 177.138 4968 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.22), residues: 1524 helix: 1.21 (0.18), residues: 805 sheet: 0.94 (0.63), residues: 84 loop : -0.31 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 762 HIS 0.011 0.001 HIS F 75 PHE 0.019 0.001 PHE K 753 TYR 0.021 0.002 TYR A 54 ARG 0.010 0.001 ARG K 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8370 (mt-10) REVERT: A 105 GLU cc_start: 0.8429 (pm20) cc_final: 0.8224 (pm20) REVERT: E 103 LEU cc_start: 0.9050 (tt) cc_final: 0.8756 (tp) REVERT: E 124 ILE cc_start: 0.9543 (mp) cc_final: 0.9193 (tp) REVERT: F 59 LYS cc_start: 0.9086 (mmmm) cc_final: 0.8687 (mmmm) REVERT: H 73 GLU cc_start: 0.8359 (tp30) cc_final: 0.7908 (tp30) REVERT: K 265 MET cc_start: -0.2529 (ttt) cc_final: -0.2982 (tpt) REVERT: K 458 MET cc_start: -0.2013 (mtm) cc_final: -0.4328 (mtt) REVERT: M 4 MET cc_start: -0.1554 (ppp) cc_final: -0.2369 (ptm) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3568 time to fit residues: 57.4310 Evaluate side-chains 76 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 101 optimal weight: 50.0000 chunk 51 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 135 GLN ** K 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5130 moved from start: 0.7237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19359 Z= 0.263 Angle : 0.630 9.183 27423 Z= 0.356 Chirality : 0.039 0.156 3068 Planarity : 0.004 0.046 2456 Dihedral : 29.909 178.867 4968 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.76 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.22), residues: 1524 helix: 1.45 (0.18), residues: 802 sheet: 0.92 (0.63), residues: 84 loop : -0.21 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 762 HIS 0.009 0.001 HIS F 75 PHE 0.016 0.001 PHE K 753 TYR 0.024 0.001 TYR K 99 ARG 0.007 0.000 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8314 (mt-10) REVERT: E 103 LEU cc_start: 0.9074 (tt) cc_final: 0.8763 (tp) REVERT: E 124 ILE cc_start: 0.9554 (mp) cc_final: 0.9272 (tp) REVERT: E 126 LEU cc_start: 0.9111 (tp) cc_final: 0.8798 (tt) REVERT: F 59 LYS cc_start: 0.9101 (mmmm) cc_final: 0.8628 (mmmm) REVERT: H 73 GLU cc_start: 0.8221 (tp30) cc_final: 0.7874 (tp30) REVERT: K 204 MET cc_start: 0.2517 (mtm) cc_final: 0.1635 (ttt) REVERT: K 265 MET cc_start: -0.2540 (ttt) cc_final: -0.2968 (tpt) REVERT: K 458 MET cc_start: -0.1991 (mtm) cc_final: -0.4184 (mtt) REVERT: M 4 MET cc_start: -0.1543 (ppp) cc_final: -0.2343 (ptm) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.3349 time to fit residues: 57.0842 Evaluate side-chains 81 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 40.0000 chunk 149 optimal weight: 6.9990 chunk 158 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 124 optimal weight: 30.0000 chunk 48 optimal weight: 0.9980 chunk 143 optimal weight: 50.0000 chunk 150 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 168 optimal weight: 30.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5203 moved from start: 0.7640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 19359 Z= 0.360 Angle : 0.669 8.409 27423 Z= 0.379 Chirality : 0.040 0.162 3068 Planarity : 0.005 0.064 2456 Dihedral : 29.927 177.794 4968 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.35 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.22), residues: 1524 helix: 1.39 (0.18), residues: 797 sheet: 0.98 (0.63), residues: 81 loop : -0.27 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 762 HIS 0.011 0.001 HIS F 75 PHE 0.016 0.001 PHE K 753 TYR 0.019 0.002 TYR B 88 ARG 0.011 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8298 (mt-10) REVERT: F 59 LYS cc_start: 0.9125 (mmmm) cc_final: 0.8726 (mmmm) REVERT: H 73 GLU cc_start: 0.8303 (tp30) cc_final: 0.7440 (tp30) REVERT: H 76 ARG cc_start: 0.8356 (ptp90) cc_final: 0.8082 (ptp90) REVERT: K 131 MET cc_start: 0.4619 (mpp) cc_final: 0.4336 (mpp) REVERT: K 265 MET cc_start: -0.2541 (ttt) cc_final: -0.2987 (tpt) REVERT: K 458 MET cc_start: -0.2040 (mtm) cc_final: -0.4263 (mtt) REVERT: M 4 MET cc_start: -0.1273 (ppp) cc_final: -0.2076 (ptm) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.3267 time to fit residues: 50.8504 Evaluate side-chains 74 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 50.0000 chunk 79 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 176 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 111 optimal weight: 20.0000 chunk 149 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5227 moved from start: 0.8062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 19359 Z= 0.378 Angle : 0.684 8.653 27423 Z= 0.387 Chirality : 0.041 0.203 3068 Planarity : 0.005 0.057 2456 Dihedral : 30.071 178.689 4968 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.15 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.22), residues: 1524 helix: 1.32 (0.18), residues: 794 sheet: 0.84 (0.62), residues: 81 loop : -0.22 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 318 HIS 0.010 0.001 HIS F 75 PHE 0.023 0.002 PHE A 104 TYR 0.020 0.002 TYR B 88 ARG 0.009 0.001 ARG E 131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8263 (mt-10) REVERT: H 73 GLU cc_start: 0.8347 (tp30) cc_final: 0.7482 (tp30) REVERT: H 76 ARG cc_start: 0.8389 (ptp90) cc_final: 0.8171 (ptp90) REVERT: K 265 MET cc_start: -0.2480 (ttt) cc_final: -0.2976 (tpt) REVERT: K 458 MET cc_start: -0.1937 (mtm) cc_final: -0.3584 (mtp) REVERT: M 4 MET cc_start: -0.1292 (ppp) cc_final: -0.1945 (ptm) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.3339 time to fit residues: 50.1963 Evaluate side-chains 71 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 123 optimal weight: 20.0000 chunk 8 optimal weight: 0.0970 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 106 HIS E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 539 HIS ** K 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.065504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.026769 restraints weight = 140205.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.027090 restraints weight = 89118.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.027306 restraints weight = 69871.729| |-----------------------------------------------------------------------------| r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.7980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19359 Z= 0.185 Angle : 0.620 10.620 27423 Z= 0.347 Chirality : 0.039 0.181 3068 Planarity : 0.004 0.060 2456 Dihedral : 29.707 179.697 4968 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.56 % Favored : 97.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.22), residues: 1524 helix: 1.66 (0.18), residues: 792 sheet: 1.26 (0.63), residues: 71 loop : -0.16 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 318 HIS 0.006 0.001 HIS F 75 PHE 0.017 0.001 PHE A 104 TYR 0.015 0.001 TYR B 88 ARG 0.005 0.000 ARG H 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3115.63 seconds wall clock time: 57 minutes 28.20 seconds (3448.20 seconds total)