Starting phenix.real_space_refine on Sat Sep 28 06:35:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r25_4710/09_2024/6r25_4710.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r25_4710/09_2024/6r25_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r25_4710/09_2024/6r25_4710.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r25_4710/09_2024/6r25_4710.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r25_4710/09_2024/6r25_4710.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r25_4710/09_2024/6r25_4710.cif" } resolution = 4.61 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 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 11.04, per 1000 atoms: 0.59 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: 4.98 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 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: 8.41 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: 12.29 Time building geometry restraints manager: 5.72 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: 1.670 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: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 56.480 Find NCS groups from input model: 0.390 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: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.390 ------------------------------------------------------------------------------- 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 0.248 19304 Z= 0.498 Angle : 1.047 17.201 27349 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 : 12.86 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 (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: -2.97 (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 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 0.018 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) ************************************************ 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 fitting. rotamer outliers: 74 poor density : 215 time to evaluate : 1.723 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: K 119 SER cc_start: 0.1979 (OUTLIER) cc_final: 0.1571 (t) REVERT: K 230 MET cc_start: 0.5295 (mtm) cc_final: 0.4207 (ttt) REVERT: K 265 MET cc_start: -0.0069 (ttm) cc_final: -0.0396 (tpp) REVERT: K 267 ARG cc_start: 0.4737 (OUTLIER) cc_final: 0.4250 (mpp-170) REVERT: K 458 MET cc_start: -0.1116 (mtm) cc_final: -0.1592 (mtt) REVERT: M 4 MET cc_start: -0.5283 (tpp) cc_final: -0.5670 (tpt) REVERT: M 18 LYS cc_start: 0.0005 (OUTLIER) cc_final: -0.0263 (pttt) REVERT: D 38 VAL cc_start: 0.9645 (t) cc_final: 0.9423 (m) REVERT: E 65 LEU cc_start: 0.8813 (mt) cc_final: 0.8353 (mt) REVERT: F 25 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8090 (t0) REVERT: F 62 LEU cc_start: 0.9357 (mt) cc_final: 0.8943 (tt) REVERT: G 72 ASP cc_start: 0.8589 (m-30) cc_final: 0.8368 (p0) REVERT: G 112 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8071 (mm-40) outliers start: 74 outliers final: 14 residues processed: 282 average time/residue: 0.4723 time to fit residues: 179.4091 Evaluate side-chains 118 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 71 optimal weight: 30.0000 chunk 137 optimal weight: 8.9990 chunk 53 optimal weight: 30.0000 chunk 83 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 L 218 HIS ** M 19 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** H 46 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4731 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 19304 Z= 0.300 Angle : 0.712 8.748 27349 Z= 0.402 Chirality : 0.042 0.217 3059 Planarity : 0.007 0.074 2447 Dihedral : 29.545 179.446 4960 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.75 % Favored : 96.05 % Rotamer: Outliers : 0.15 % Allowed : 1.84 % Favored : 98.01 % 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: -0.29 (0.21), residues: 1518 helix: 0.31 (0.17), residues: 794 sheet: 1.23 (0.66), residues: 61 loop : -0.87 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 201 HIS 0.006 0.001 HIS B 75 PHE 0.024 0.002 PHE C 25 TYR 0.018 0.002 TYR D 37 ARG 0.017 0.001 ARG A 40 *********************** 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 133 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 1.694 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: K 171 MET cc_start: -0.3958 (ttp) cc_final: -0.4297 (ptm) REVERT: K 230 MET cc_start: 0.4872 (mtm) cc_final: 0.4017 (ttt) REVERT: K 458 MET cc_start: -0.0972 (mtm) cc_final: -0.2001 (mtt) REVERT: M 4 MET cc_start: -0.5498 (tpp) cc_final: -0.5796 (tpt) REVERT: H 56 MET cc_start: 0.8324 (tpp) cc_final: 0.8112 (tpp) REVERT: H 59 MET cc_start: 0.8377 (tpt) cc_final: 0.7914 (tpp) outliers start: 2 outliers final: 1 residues processed: 132 average time/residue: 0.4425 time to fit residues: 81.3808 Evaluate side-chains 82 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 40.0000 chunk 133 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 54 optimal weight: 40.0000 chunk 128 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 469 GLN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4849 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 19304 Z= 0.314 Angle : 0.670 9.558 27349 Z= 0.384 Chirality : 0.040 0.204 3059 Planarity : 0.006 0.056 2447 Dihedral : 29.734 176.599 4960 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.29 % Favored : 96.57 % Rotamer: Outliers : 0.15 % Allowed : 2.84 % Favored : 97.01 % 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: 0.49 (0.21), residues: 1518 helix: 0.97 (0.18), residues: 800 sheet: 0.91 (0.58), residues: 81 loop : -0.50 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 762 HIS 0.015 0.002 HIS E 39 PHE 0.020 0.002 PHE K 91 TYR 0.023 0.002 TYR A 54 ARG 0.008 0.001 ARG G 20 *********************** 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 106 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 1.738 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: K 171 MET cc_start: -0.4124 (ttp) cc_final: -0.6203 (mtm) REVERT: K 230 MET cc_start: 0.5323 (mtm) cc_final: 0.4232 (ttt) REVERT: K 458 MET cc_start: -0.0216 (mtm) cc_final: -0.1090 (mtt) REVERT: M 4 MET cc_start: -0.5545 (tpp) cc_final: -0.5948 (tpt) REVERT: H 59 MET cc_start: 0.8424 (tpt) cc_final: 0.7959 (tpp) REVERT: H 73 GLU cc_start: 0.8132 (tp30) cc_final: 0.7852 (tp30) outliers start: 2 outliers final: 2 residues processed: 104 average time/residue: 0.4268 time to fit residues: 62.6761 Evaluate side-chains 74 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 141 optimal weight: 0.0970 overall best weight: 4.6186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4889 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19304 Z= 0.284 Angle : 0.642 8.520 27349 Z= 0.364 Chirality : 0.039 0.185 3059 Planarity : 0.005 0.050 2447 Dihedral : 29.801 174.493 4960 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.96 % Favored : 96.97 % Rotamer: Outliers : 0.08 % Allowed : 2.61 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.87 (0.21), residues: 1518 helix: 1.32 (0.18), residues: 803 sheet: 0.93 (0.58), residues: 81 loop : -0.38 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 762 HIS 0.009 0.001 HIS F 75 PHE 0.014 0.001 PHE K 91 TYR 0.037 0.002 TYR E 54 ARG 0.012 0.001 ARG H 76 *********************** 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 98 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 1.867 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 171 MET cc_start: -0.4216 (ttp) cc_final: -0.6100 (mtm) REVERT: K 230 MET cc_start: 0.5519 (mtm) cc_final: 0.4253 (ttt) REVERT: K 458 MET cc_start: -0.0218 (mtm) cc_final: -0.1304 (mtt) REVERT: K 483 MET cc_start: -0.4787 (ttt) cc_final: -0.5426 (ptm) REVERT: M 4 MET cc_start: -0.5271 (tpp) cc_final: -0.5716 (tpt) REVERT: H 59 MET cc_start: 0.8347 (tpt) cc_final: 0.7885 (tpp) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.4174 time to fit residues: 58.7361 Evaluate side-chains 64 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 10.0000 chunk 2 optimal weight: 30.0000 chunk 126 optimal weight: 0.9980 chunk 70 optimal weight: 30.0000 chunk 145 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 0 optimal weight: 120.0000 chunk 86 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 42 optimal weight: 30.0000 chunk 57 optimal weight: 7.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- 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** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4976 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 19304 Z= 0.338 Angle : 0.655 8.691 27349 Z= 0.374 Chirality : 0.040 0.174 3059 Planarity : 0.005 0.053 2447 Dihedral : 30.100 175.110 4960 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.29 % Favored : 96.64 % Rotamer: Outliers : 0.15 % Allowed : 1.84 % Favored : 98.01 % 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: 0.95 (0.22), residues: 1518 helix: 1.29 (0.18), residues: 801 sheet: 0.97 (0.59), residues: 81 loop : -0.17 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 762 HIS 0.010 0.001 HIS F 75 PHE 0.013 0.001 PHE K 91 TYR 0.027 0.002 TYR E 54 ARG 0.010 0.001 ARG M 2 *********************** 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 fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 1.752 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 171 MET cc_start: -0.4701 (ttp) cc_final: -0.6378 (mtm) REVERT: K 230 MET cc_start: 0.5600 (mtm) cc_final: 0.4296 (ttt) REVERT: K 458 MET cc_start: -0.0032 (mtm) cc_final: -0.1239 (mtt) REVERT: K 483 MET cc_start: -0.4655 (ttt) cc_final: -0.6011 (ttp) REVERT: M 4 MET cc_start: -0.5239 (tpp) cc_final: -0.5523 (tpt) REVERT: E 120 MET cc_start: 0.8146 (mmp) cc_final: 0.7944 (mmm) REVERT: H 59 MET cc_start: 0.8267 (tpt) cc_final: 0.7688 (tpt) outliers start: 2 outliers final: 0 residues processed: 86 average time/residue: 0.4019 time to fit residues: 50.5680 Evaluate side-chains 60 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 6.9990 chunk 33 optimal weight: 50.0000 chunk 99 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 56 optimal weight: 50.0000 chunk 89 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4928 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19304 Z= 0.257 Angle : 0.619 8.970 27349 Z= 0.352 Chirality : 0.039 0.268 3059 Planarity : 0.004 0.060 2447 Dihedral : 30.147 174.434 4960 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.10 % Favored : 96.84 % Rotamer: Outliers : 0.15 % Allowed : 1.46 % Favored : 98.39 % 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: 1.15 (0.22), residues: 1518 helix: 1.51 (0.18), residues: 797 sheet: 0.95 (0.59), residues: 81 loop : -0.13 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 762 HIS 0.008 0.001 HIS F 75 PHE 0.014 0.001 PHE C 25 TYR 0.023 0.001 TYR E 54 ARG 0.010 0.001 ARG H 76 *********************** 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 88 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 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: K 230 MET cc_start: 0.5537 (mtm) cc_final: 0.4255 (ttt) REVERT: K 450 MET cc_start: -0.4987 (ttt) cc_final: -0.5219 (ttt) REVERT: K 458 MET cc_start: 0.0304 (mtm) cc_final: -0.1011 (mtt) REVERT: K 483 MET cc_start: -0.4678 (ttt) cc_final: -0.6130 (ttp) REVERT: F 25 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8075 (t0) REVERT: F 62 LEU cc_start: 0.9266 (tt) cc_final: 0.9006 (tt) REVERT: H 59 MET cc_start: 0.8163 (tpt) cc_final: 0.7709 (tpp) outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.3960 time to fit residues: 51.0560 Evaluate side-chains 58 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 30.0000 chunk 97 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 169 optimal weight: 7.9990 chunk 106 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4828 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19304 Z= 0.174 Angle : 0.590 10.454 27349 Z= 0.331 Chirality : 0.039 0.292 3059 Planarity : 0.004 0.055 2447 Dihedral : 29.843 175.746 4960 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.10 % Favored : 96.84 % Rotamer: Outliers : 0.08 % Allowed : 1.07 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.31 (0.22), residues: 1518 helix: 1.69 (0.18), residues: 800 sheet: 0.97 (0.60), residues: 81 loop : -0.13 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 762 HIS 0.007 0.001 HIS F 75 PHE 0.014 0.001 PHE K 91 TYR 0.015 0.001 TYR C 50 ARG 0.004 0.000 ARG M 2 *********************** 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 86 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 1.755 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: K 230 MET cc_start: 0.5405 (mtm) cc_final: 0.4195 (ttt) REVERT: K 450 MET cc_start: -0.4827 (ttt) cc_final: -0.5311 (ttt) REVERT: K 458 MET cc_start: 0.0283 (mtm) cc_final: -0.1005 (mtt) REVERT: K 483 MET cc_start: -0.4779 (ttt) cc_final: -0.5934 (ttp) REVERT: H 59 MET cc_start: 0.8211 (tpt) cc_final: 0.7678 (tpp) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.3978 time to fit residues: 50.0983 Evaluate side-chains 62 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 51 optimal weight: 50.0000 chunk 33 optimal weight: 50.0000 chunk 32 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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** A 93 GLN ** C 73 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5025 moved from start: 0.6626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 19304 Z= 0.384 Angle : 0.672 9.218 27349 Z= 0.384 Chirality : 0.041 0.180 3059 Planarity : 0.005 0.058 2447 Dihedral : 30.095 176.898 4960 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.03 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: 1.09 (0.22), residues: 1518 helix: 1.35 (0.18), residues: 797 sheet: 0.95 (0.59), residues: 81 loop : -0.01 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 762 HIS 0.015 0.002 HIS F 75 PHE 0.014 0.001 PHE K 801 TYR 0.031 0.002 TYR E 54 ARG 0.006 0.001 ARG M 2 *********************** 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 72 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.720 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: 0.5582 (mtm) cc_final: 0.4008 (tmm) REVERT: K 450 MET cc_start: -0.4599 (ttt) cc_final: -0.5099 (ttt) REVERT: K 458 MET cc_start: 0.0492 (mtm) cc_final: -0.0815 (mtt) REVERT: K 483 MET cc_start: -0.3371 (ttm) cc_final: -0.3686 (ttm) REVERT: E 120 MET cc_start: 0.8037 (mmp) cc_final: 0.7816 (mmm) REVERT: H 59 MET cc_start: 0.8204 (tpt) cc_final: 0.7876 (tpp) REVERT: H 97 LEU cc_start: 0.9367 (mt) cc_final: 0.9143 (mt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.4118 time to fit residues: 43.5929 Evaluate side-chains 52 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 8.9990 chunk 148 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 50.0000 chunk 142 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4943 moved from start: 0.6726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19304 Z= 0.251 Angle : 0.620 10.745 27349 Z= 0.351 Chirality : 0.039 0.204 3059 Planarity : 0.004 0.057 2447 Dihedral : 30.223 178.075 4960 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % 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 (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: 1.19 (0.22), residues: 1518 helix: 1.48 (0.18), residues: 797 sheet: 0.92 (0.60), residues: 81 loop : -0.01 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 762 HIS 0.009 0.001 HIS F 75 PHE 0.011 0.001 PHE K 91 TYR 0.019 0.001 TYR E 54 ARG 0.009 0.001 ARG H 76 *********************** 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 74 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.699 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: 0.5554 (mtm) cc_final: 0.3921 (tmm) REVERT: K 450 MET cc_start: -0.4581 (ttt) cc_final: -0.4936 (ttt) REVERT: K 458 MET cc_start: 0.0602 (mtm) cc_final: -0.0813 (mtt) REVERT: K 483 MET cc_start: -0.3389 (ttm) cc_final: -0.3931 (ttm) REVERT: H 59 MET cc_start: 0.8346 (tpt) cc_final: 0.7819 (tpp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.3968 time to fit residues: 42.8714 Evaluate side-chains 51 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 175 optimal weight: 7.9990 chunk 161 optimal weight: 7.9990 chunk 139 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5010 moved from start: 0.7177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 19304 Z= 0.317 Angle : 0.650 9.713 27349 Z= 0.369 Chirality : 0.040 0.207 3059 Planarity : 0.005 0.059 2447 Dihedral : 30.300 177.795 4960 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % 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: 1.11 (0.22), residues: 1518 helix: 1.37 (0.18), residues: 799 sheet: 0.88 (0.60), residues: 81 loop : 0.01 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 762 HIS 0.007 0.001 HIS F 75 PHE 0.013 0.001 PHE B 61 TYR 0.025 0.001 TYR E 54 ARG 0.005 0.001 ARG D 26 ********************** 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 fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.738 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: 0.5783 (mtm) cc_final: 0.3946 (tmm) REVERT: K 450 MET cc_start: -0.4556 (ttt) cc_final: -0.4843 (ttt) REVERT: K 458 MET cc_start: 0.0356 (mtm) cc_final: 0.0146 (mtt) REVERT: K 483 MET cc_start: -0.3337 (ttm) cc_final: -0.4045 (ttm) REVERT: E 120 MET cc_start: 0.7936 (mmp) cc_final: 0.7697 (mmm) REVERT: H 59 MET cc_start: 0.8366 (tpt) cc_final: 0.7821 (tpp) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.3837 time to fit residues: 40.0512 Evaluate side-chains 53 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 8.9990 chunk 42 optimal weight: 40.0000 chunk 128 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 38 optimal weight: 20.0000 chunk 139 optimal weight: 7.9990 chunk 58 optimal weight: 30.0000 chunk 143 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 40.0000 chunk 122 optimal weight: 1.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.089487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.047690 restraints weight = 240558.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.046079 restraints weight = 192381.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.043480 restraints weight = 148206.827| |-----------------------------------------------------------------------------| r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.7705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 19304 Z= 0.345 Angle : 0.681 9.796 27349 Z= 0.385 Chirality : 0.041 0.201 3059 Planarity : 0.005 0.056 2447 Dihedral : 30.687 178.208 4960 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: 0.91 (0.22), residues: 1518 helix: 1.15 (0.18), residues: 800 sheet: 0.77 (0.59), residues: 81 loop : 0.00 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 762 HIS 0.009 0.001 HIS F 75 PHE 0.014 0.001 PHE B 61 TYR 0.045 0.002 TYR A 54 ARG 0.008 0.001 ARG H 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3296.48 seconds wall clock time: 61 minutes 10.63 seconds (3670.63 seconds total)