Starting phenix.real_space_refine on Mon Nov 18 21:18:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3x_27167/11_2024/8d3x_27167.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3x_27167/11_2024/8d3x_27167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3x_27167/11_2024/8d3x_27167.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3x_27167/11_2024/8d3x_27167.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3x_27167/11_2024/8d3x_27167.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3x_27167/11_2024/8d3x_27167.cif" } resolution = 4.1 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9217 atoms to isotropic. 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 Mg 1 5.21 5 S 61 5.16 5 C 6531 2.51 5 N 1704 2.21 5 O 1918 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10219 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2322 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 264} Chain: "G" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 246 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "A" Number of atoms: 7646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7646 Classifications: {'peptide': 989} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 947} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'MF4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.33, per 1000 atoms: 0.62 Number of scatterers: 10219 At special positions: 0 Unit cell: (146.08, 106.24, 141.93, 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) S 61 16.00 Mg 1 11.99 F 4 9.00 O 1918 8.00 N 1704 7.00 C 6531 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 239 " distance=2.04 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.4 seconds 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 9 sheets defined 46.0% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'B' and resid 33 through 60 removed outlier: 3.532A pdb=" N THR B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 152 through 156 removed outlier: 3.734A pdb=" N TRP B 155 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 58 removed outlier: 3.525A pdb=" N LEU G 55 " --> pdb=" O VAL G 51 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE G 56 " --> pdb=" O GLY G 52 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU G 57 " --> pdb=" O ILE G 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 45 removed outlier: 3.630A pdb=" N TYR A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 66 removed outlier: 3.917A pdb=" N ARG A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 88 Processing helix chain 'A' and resid 91 through 109 Processing helix chain 'A' and resid 119 through 138 Processing helix chain 'A' and resid 146 through 151 removed outlier: 3.618A pdb=" N GLU A 149 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 150 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE A 151 " --> pdb=" O MET A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 151' Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.918A pdb=" N GLU A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 304 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 326 through 343 removed outlier: 3.870A pdb=" N THR A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG A 343 " --> pdb=" O LYS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 360 removed outlier: 3.589A pdb=" N THR A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY A 358 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 418 Processing helix chain 'A' and resid 431 through 435 removed outlier: 3.726A pdb=" N ARG A 435 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 454 Processing helix chain 'A' and resid 456 through 464 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 521 through 537 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.580A pdb=" N ALA A 592 " --> pdb=" O ALA A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 622 Processing helix chain 'A' and resid 630 through 638 Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 646 through 650 Processing helix chain 'A' and resid 659 through 663 Processing helix chain 'A' and resid 664 through 675 Processing helix chain 'A' and resid 684 through 698 removed outlier: 3.699A pdb=" N GLN A 698 " --> pdb=" O GLY A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'A' and resid 729 through 735 Processing helix chain 'A' and resid 744 through 772 removed outlier: 3.870A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA A 767 " --> pdb=" O LYS A 763 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER A 772 " --> pdb=" O TYR A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 786 Proline residue: A 779 - end of helix Processing helix chain 'A' and resid 794 through 804 removed outlier: 3.520A pdb=" N LEU A 798 " --> pdb=" O THR A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 812 Processing helix chain 'A' and resid 818 through 824 removed outlier: 3.827A pdb=" N ILE A 821 " --> pdb=" O GLU A 818 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N MET A 822 " --> pdb=" O SER A 819 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG A 824 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 845 removed outlier: 3.577A pdb=" N SER A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET A 842 " --> pdb=" O ARG A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 865 Processing helix chain 'A' and resid 876 through 881 Processing helix chain 'A' and resid 897 through 928 removed outlier: 3.807A pdb=" N VAL A 904 " --> pdb=" O GLN A 900 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA A 922 " --> pdb=" O VAL A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 941 through 959 removed outlier: 3.838A pdb=" N ILE A 945 " --> pdb=" O ASN A 941 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE A 946 " --> pdb=" O LYS A 942 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 969 Processing helix chain 'A' and resid 974 through 980 Processing helix chain 'A' and resid 981 through 1002 removed outlier: 4.501A pdb=" N LEU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1012 Processing sheet with id=AA1, first strand: chain 'B' and resid 77 through 79 removed outlier: 3.567A pdb=" N THR B 78 " --> pdb=" O LYS B 179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 87 through 90 removed outlier: 5.852A pdb=" N ILE B 88 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 299 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE B 272 " --> pdb=" O ILE B 299 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 227 through 230 Processing sheet with id=AA4, first strand: chain 'A' and resid 166 through 171 removed outlier: 5.133A pdb=" N LEU A 160 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU A 180 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLU A 241 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY A 200 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N THR A 243 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA A 198 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ARG A 245 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ASP A 192 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 193 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 346 through 348 removed outlier: 6.194A pdb=" N GLY A 721 " --> pdb=" O MET A 738 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU A 740 " --> pdb=" O GLY A 721 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ALA A 723 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL A 702 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N VAL A 722 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL A 704 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N MET A 724 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N GLY A 706 " --> pdb=" O MET A 724 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE A 363 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL A 606 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N SER A 365 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL A 603 " --> pdb=" O ILE A 678 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N PHE A 680 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N MET A 605 " --> pdb=" O PHE A 680 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N CYS A 653 " --> pdb=" O VAL A 679 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 386 through 389 removed outlier: 3.536A pdb=" N HIS A 380 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP A 382 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N LEU A 573 " --> pdb=" O TYR A 549 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N TYR A 549 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE A 575 " --> pdb=" O HIS A 547 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N HIS A 547 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY A 577 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 480 " --> pdb=" O ILE A 470 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A 468 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 386 through 389 removed outlier: 3.536A pdb=" N HIS A 380 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP A 382 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE A 575 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE A 511 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N GLY A 577 " --> pdb=" O ILE A 511 " (cutoff:3.500A) removed outlier: 11.521A pdb=" N LEU A 513 " --> pdb=" O GLY A 577 " (cutoff:3.500A) removed outlier: 17.099A pdb=" N MET A 579 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 422 through 423 removed outlier: 3.984A pdb=" N VAL A 422 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA A 438 " --> pdb=" O VAL A 422 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 888 through 889 454 hydrogen bonds defined for protein. 1299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.53 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3338 1.35 - 1.47: 2328 1.47 - 1.59: 4667 1.59 - 1.71: 1 1.71 - 1.82: 94 Bond restraints: 10428 Sorted by residual: bond pdb=" CB PRO A 519 " pdb=" CG PRO A 519 " ideal model delta sigma weight residual 1.492 1.615 -0.123 5.00e-02 4.00e+02 6.05e+00 bond pdb=" F3 MF4 A2101 " pdb="MG MF4 A2101 " ideal model delta sigma weight residual 1.837 1.788 0.049 2.00e-02 2.50e+03 6.05e+00 bond pdb=" F2 MF4 A2101 " pdb="MG MF4 A2101 " ideal model delta sigma weight residual 1.836 1.788 0.048 2.00e-02 2.50e+03 5.82e+00 bond pdb=" F1 MF4 A2101 " pdb="MG MF4 A2101 " ideal model delta sigma weight residual 1.836 1.789 0.047 2.00e-02 2.50e+03 5.52e+00 bond pdb=" F4 MF4 A2101 " pdb="MG MF4 A2101 " ideal model delta sigma weight residual 1.836 1.789 0.047 2.00e-02 2.50e+03 5.50e+00 ... (remaining 10423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.64: 14121 6.64 - 13.29: 7 13.29 - 19.93: 2 19.93 - 26.57: 0 26.57 - 33.21: 1 Bond angle restraints: 14131 Sorted by residual: angle pdb=" N TYR G 32 " pdb=" CA TYR G 32 " pdb=" C TYR G 32 " ideal model delta sigma weight residual 108.20 74.99 33.21 1.71e+00 3.42e-01 3.77e+02 angle pdb=" C TYR G 32 " pdb=" CA TYR G 32 " pdb=" CB TYR G 32 " ideal model delta sigma weight residual 110.78 91.27 19.51 1.60e+00 3.91e-01 1.49e+02 angle pdb=" N ASP G 33 " pdb=" CA ASP G 33 " pdb=" C ASP G 33 " ideal model delta sigma weight residual 110.80 126.71 -15.91 2.13e+00 2.20e-01 5.58e+01 angle pdb=" CA PRO A 983 " pdb=" N PRO A 983 " pdb=" CD PRO A 983 " ideal model delta sigma weight residual 112.00 102.85 9.15 1.40e+00 5.10e-01 4.27e+01 angle pdb=" CA PRO A 519 " pdb=" N PRO A 519 " pdb=" CD PRO A 519 " ideal model delta sigma weight residual 112.00 103.32 8.68 1.40e+00 5.10e-01 3.84e+01 ... (remaining 14126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5603 17.99 - 35.98: 558 35.98 - 53.98: 96 53.98 - 71.97: 17 71.97 - 89.96: 9 Dihedral angle restraints: 6283 sinusoidal: 2530 harmonic: 3753 Sorted by residual: dihedral pdb=" C TYR G 32 " pdb=" N TYR G 32 " pdb=" CA TYR G 32 " pdb=" CB TYR G 32 " ideal model delta harmonic sigma weight residual -122.60 -85.73 -36.87 0 2.50e+00 1.60e-01 2.17e+02 dihedral pdb=" N ASP G 33 " pdb=" C ASP G 33 " pdb=" CA ASP G 33 " pdb=" CB ASP G 33 " ideal model delta harmonic sigma weight residual 122.80 154.71 -31.91 0 2.50e+00 1.60e-01 1.63e+02 dihedral pdb=" C ASP G 33 " pdb=" N ASP G 33 " pdb=" CA ASP G 33 " pdb=" CB ASP G 33 " ideal model delta harmonic sigma weight residual -122.60 -152.40 29.80 0 2.50e+00 1.60e-01 1.42e+02 ... (remaining 6280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.283: 1596 0.283 - 0.565: 1 0.565 - 0.848: 0 0.848 - 1.130: 0 1.130 - 1.413: 1 Chirality restraints: 1598 Sorted by residual: chirality pdb=" CA ASP G 33 " pdb=" N ASP G 33 " pdb=" C ASP G 33 " pdb=" CB ASP G 33 " both_signs ideal model delta sigma weight residual False 2.51 1.10 1.41 2.00e-01 2.50e+01 4.99e+01 chirality pdb=" CA TYR G 32 " pdb=" N TYR G 32 " pdb=" C TYR G 32 " pdb=" CB TYR G 32 " both_signs ideal model delta sigma weight residual False 2.51 3.05 -0.54 2.00e-01 2.50e+01 7.38e+00 chirality pdb=" CA PRO A 983 " pdb=" N PRO A 983 " pdb=" C PRO A 983 " pdb=" CB PRO A 983 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.57e-01 ... (remaining 1595 not shown) Planarity restraints: 1824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 982 " -0.073 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO A 983 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO A 983 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 983 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 825 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.76e+00 pdb=" N PRO A 826 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 826 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 826 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 71 " 0.174 9.50e-02 1.11e+02 7.79e-02 3.73e+00 pdb=" NE ARG B 71 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 71 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 71 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 71 " 0.006 2.00e-02 2.50e+03 ... (remaining 1821 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 5 2.17 - 2.86: 3631 2.86 - 3.54: 14825 3.54 - 4.22: 22382 4.22 - 4.90: 39449 Nonbonded interactions: 80292 Sorted by model distance: nonbonded pdb=" CZ PHE A 90 " pdb=" CG1 VAL A 322 " model vdw 1.492 3.760 nonbonded pdb=" O GLU B 165 " pdb=" OG1 THR B 166 " model vdw 1.982 3.040 nonbonded pdb=" CE1 PHE A 90 " pdb=" CG1 VAL A 322 " model vdw 2.051 3.760 nonbonded pdb=" O SER A 91 " pdb=" N LEU A 94 " model vdw 2.058 3.120 nonbonded pdb=" O SER A 91 " pdb=" N LEU A 93 " model vdw 2.080 3.120 ... (remaining 80287 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 25.790 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 0.003 0.123 10428 Z= 0.214 Angle : 0.693 33.213 14131 Z= 0.382 Chirality : 0.056 1.413 1598 Planarity : 0.005 0.105 1824 Dihedral : 14.473 89.962 3866 Min Nonbonded Distance : 1.492 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.39 % Favored : 95.30 % Rotamer: Outliers : 0.27 % Allowed : 0.71 % Favored : 99.02 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: -0.48 (0.23), residues: 1299 helix: 0.87 (0.23), residues: 537 sheet: -1.53 (0.40), residues: 150 loop : -1.04 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 896 HIS 0.010 0.001 HIS A 413 PHE 0.021 0.001 PHE A 136 TYR 0.012 0.001 TYR G 34 ARG 0.004 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 197 time to evaluate : 1.213 Fit side-chains REVERT: B 41 ILE cc_start: 0.7865 (tt) cc_final: 0.7617 (tt) REVERT: A 215 GLN cc_start: 0.7439 (mm110) cc_final: 0.7064 (mm110) REVERT: A 360 THR cc_start: 0.8891 (p) cc_final: 0.8671 (p) REVERT: A 409 VAL cc_start: 0.8641 (m) cc_final: 0.8209 (t) REVERT: A 419 ASN cc_start: 0.7179 (m110) cc_final: 0.6794 (m-40) REVERT: A 457 VAL cc_start: 0.8729 (t) cc_final: 0.8124 (m) REVERT: A 724 MET cc_start: 0.8665 (mmt) cc_final: 0.8244 (mmt) outliers start: 3 outliers final: 1 residues processed: 200 average time/residue: 0.1818 time to fit residues: 55.8319 Evaluate side-chains 147 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 117 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 464 ASN A 518 GLN ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 932 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10428 Z= 0.188 Angle : 0.542 7.027 14131 Z= 0.286 Chirality : 0.041 0.146 1598 Planarity : 0.004 0.049 1824 Dihedral : 4.081 21.513 1404 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: -0.30 (0.23), residues: 1299 helix: 0.93 (0.23), residues: 552 sheet: -1.45 (0.39), residues: 157 loop : -0.87 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 79 HIS 0.006 0.001 HIS A 34 PHE 0.030 0.001 PHE A 90 TYR 0.013 0.001 TYR G 32 ARG 0.003 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.205 Fit side-chains REVERT: B 41 ILE cc_start: 0.7893 (tt) cc_final: 0.7635 (tt) REVERT: A 215 GLN cc_start: 0.7139 (mm110) cc_final: 0.6878 (mm110) REVERT: A 324 GLU cc_start: 0.7503 (mp0) cc_final: 0.7296 (mp0) REVERT: A 355 GLU cc_start: 0.8083 (tp30) cc_final: 0.7730 (tp30) REVERT: A 360 THR cc_start: 0.8849 (p) cc_final: 0.8617 (p) REVERT: A 409 VAL cc_start: 0.8617 (m) cc_final: 0.8348 (t) REVERT: A 460 MET cc_start: 0.8075 (mmp) cc_final: 0.7696 (tpt) REVERT: A 865 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8847 (mm-30) REVERT: A 968 LEU cc_start: 0.8992 (tp) cc_final: 0.8762 (tp) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1702 time to fit residues: 51.4678 Evaluate side-chains 141 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 0.1980 chunk 97 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 117 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 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 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10428 Z= 0.178 Angle : 0.530 6.901 14131 Z= 0.276 Chirality : 0.040 0.139 1598 Planarity : 0.004 0.046 1824 Dihedral : 4.029 21.098 1404 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: -0.25 (0.23), residues: 1299 helix: 1.05 (0.23), residues: 547 sheet: -1.48 (0.40), residues: 146 loop : -0.91 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 977 HIS 0.004 0.001 HIS A 34 PHE 0.024 0.001 PHE A 423 TYR 0.011 0.001 TYR B 204 ARG 0.003 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.220 Fit side-chains REVERT: B 41 ILE cc_start: 0.7836 (tt) cc_final: 0.7550 (tt) REVERT: A 136 PHE cc_start: 0.8419 (t80) cc_final: 0.8114 (t80) REVERT: A 215 GLN cc_start: 0.7147 (mm110) cc_final: 0.6872 (mm110) REVERT: A 355 GLU cc_start: 0.7978 (tp30) cc_final: 0.7621 (tp30) REVERT: A 360 THR cc_start: 0.8734 (p) cc_final: 0.8502 (p) REVERT: A 409 VAL cc_start: 0.8586 (m) cc_final: 0.8247 (t) REVERT: A 419 ASN cc_start: 0.7057 (m110) cc_final: 0.6659 (m110) REVERT: A 457 VAL cc_start: 0.8976 (t) cc_final: 0.8507 (m) REVERT: A 724 MET cc_start: 0.8602 (mmt) cc_final: 0.8280 (mmt) REVERT: A 760 ASP cc_start: 0.7577 (m-30) cc_final: 0.7366 (m-30) REVERT: A 889 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6927 (tp30) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1800 time to fit residues: 56.1640 Evaluate side-chains 150 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 78 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10428 Z= 0.209 Angle : 0.544 6.993 14131 Z= 0.283 Chirality : 0.041 0.153 1598 Planarity : 0.004 0.044 1824 Dihedral : 4.067 22.228 1404 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: -0.37 (0.23), residues: 1299 helix: 0.97 (0.23), residues: 554 sheet: -1.64 (0.39), residues: 150 loop : -0.99 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 896 HIS 0.005 0.001 HIS A 909 PHE 0.020 0.001 PHE A 90 TYR 0.022 0.001 TYR B 204 ARG 0.003 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 1.258 Fit side-chains REVERT: B 41 ILE cc_start: 0.7801 (tt) cc_final: 0.7526 (tt) REVERT: A 136 PHE cc_start: 0.8515 (t80) cc_final: 0.8172 (t80) REVERT: A 215 GLN cc_start: 0.7141 (mm110) cc_final: 0.6903 (mm110) REVERT: A 324 GLU cc_start: 0.7619 (mp0) cc_final: 0.7404 (mp0) REVERT: A 355 GLU cc_start: 0.7941 (tp30) cc_final: 0.7549 (tp30) REVERT: A 360 THR cc_start: 0.8682 (p) cc_final: 0.8350 (p) REVERT: A 409 VAL cc_start: 0.8529 (m) cc_final: 0.8184 (t) REVERT: A 460 MET cc_start: 0.8113 (mmp) cc_final: 0.7782 (tpt) REVERT: A 859 TYR cc_start: 0.9186 (t80) cc_final: 0.8962 (t80) REVERT: A 889 GLU cc_start: 0.7259 (mm-30) cc_final: 0.7013 (tp30) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1880 time to fit residues: 58.3890 Evaluate side-chains 146 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10428 Z= 0.200 Angle : 0.551 6.759 14131 Z= 0.285 Chirality : 0.040 0.141 1598 Planarity : 0.004 0.085 1824 Dihedral : 4.086 22.140 1404 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: -0.34 (0.23), residues: 1299 helix: 0.98 (0.22), residues: 554 sheet: -1.55 (0.41), residues: 146 loop : -0.98 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 896 HIS 0.004 0.001 HIS A 34 PHE 0.023 0.001 PHE A 90 TYR 0.016 0.001 TYR B 204 ARG 0.003 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.492 Fit side-chains revert: symmetry clash REVERT: B 41 ILE cc_start: 0.7813 (tt) cc_final: 0.7534 (tt) REVERT: B 165 GLU cc_start: 0.6420 (pt0) cc_final: 0.6209 (pt0) REVERT: B 202 MET cc_start: 0.3527 (tpt) cc_final: 0.2995 (ttt) REVERT: A 136 PHE cc_start: 0.8598 (t80) cc_final: 0.8268 (t80) REVERT: A 215 GLN cc_start: 0.7173 (mm110) cc_final: 0.6938 (mm110) REVERT: A 324 GLU cc_start: 0.7655 (mp0) cc_final: 0.7336 (mp0) REVERT: A 355 GLU cc_start: 0.7912 (tp30) cc_final: 0.7522 (tp30) REVERT: A 409 VAL cc_start: 0.8570 (m) cc_final: 0.8234 (t) REVERT: A 859 TYR cc_start: 0.9212 (t80) cc_final: 0.8925 (t80) REVERT: A 889 GLU cc_start: 0.7286 (mm-30) cc_final: 0.7034 (tp30) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1900 time to fit residues: 60.2627 Evaluate side-chains 150 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 GLN A 419 ASN ** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10428 Z= 0.160 Angle : 0.537 6.971 14131 Z= 0.278 Chirality : 0.041 0.155 1598 Planarity : 0.004 0.042 1824 Dihedral : 4.001 21.577 1404 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: -0.24 (0.23), residues: 1299 helix: 1.05 (0.23), residues: 555 sheet: -1.49 (0.40), residues: 151 loop : -0.91 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 896 HIS 0.003 0.001 HIS A 34 PHE 0.016 0.001 PHE A 90 TYR 0.015 0.001 TYR B 204 ARG 0.003 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.221 Fit side-chains REVERT: B 41 ILE cc_start: 0.7814 (tt) cc_final: 0.7524 (tt) REVERT: B 212 GLN cc_start: 0.6645 (mm-40) cc_final: 0.6387 (mm-40) REVERT: A 136 PHE cc_start: 0.8525 (t80) cc_final: 0.8204 (t80) REVERT: A 215 GLN cc_start: 0.7129 (mm110) cc_final: 0.6906 (mm110) REVERT: A 355 GLU cc_start: 0.7938 (tp30) cc_final: 0.7541 (tp30) REVERT: A 360 THR cc_start: 0.8759 (p) cc_final: 0.8554 (p) REVERT: A 460 MET cc_start: 0.8094 (mmp) cc_final: 0.7746 (tpt) REVERT: A 738 MET cc_start: 0.8690 (ttp) cc_final: 0.8470 (ttm) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.1927 time to fit residues: 58.8232 Evaluate side-chains 145 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.0170 chunk 71 optimal weight: 0.3980 chunk 91 optimal weight: 0.0070 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN A 419 ASN ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10428 Z= 0.153 Angle : 0.535 7.389 14131 Z= 0.277 Chirality : 0.040 0.148 1598 Planarity : 0.004 0.076 1824 Dihedral : 3.933 20.576 1404 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: -0.15 (0.24), residues: 1299 helix: 1.07 (0.23), residues: 559 sheet: -1.34 (0.41), residues: 150 loop : -0.86 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 155 HIS 0.009 0.001 HIS A 413 PHE 0.013 0.001 PHE B 230 TYR 0.014 0.001 TYR B 204 ARG 0.002 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 1.172 Fit side-chains REVERT: B 41 ILE cc_start: 0.7805 (tt) cc_final: 0.7508 (tt) REVERT: B 202 MET cc_start: 0.3499 (tpt) cc_final: 0.2993 (ttt) REVERT: B 212 GLN cc_start: 0.6653 (mm-40) cc_final: 0.6327 (mm-40) REVERT: B 296 ASP cc_start: 0.7524 (t0) cc_final: 0.7228 (t0) REVERT: A 136 PHE cc_start: 0.8492 (t80) cc_final: 0.8192 (t80) REVERT: A 215 GLN cc_start: 0.7137 (mm110) cc_final: 0.6891 (mm110) REVERT: A 355 GLU cc_start: 0.7919 (tp30) cc_final: 0.7515 (tp30) REVERT: A 360 THR cc_start: 0.8711 (p) cc_final: 0.8486 (p) REVERT: A 859 TYR cc_start: 0.9241 (t80) cc_final: 0.8996 (t80) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2009 time to fit residues: 62.1153 Evaluate side-chains 150 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 84 optimal weight: 0.0020 chunk 61 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 HIS A 321 ASN A 413 HIS ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10428 Z= 0.156 Angle : 0.539 7.667 14131 Z= 0.279 Chirality : 0.040 0.140 1598 Planarity : 0.004 0.045 1824 Dihedral : 3.907 23.390 1404 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: -0.15 (0.24), residues: 1299 helix: 1.09 (0.23), residues: 559 sheet: -1.34 (0.41), residues: 150 loop : -0.86 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 155 HIS 0.008 0.001 HIS A 413 PHE 0.022 0.001 PHE A 90 TYR 0.020 0.001 TYR A 105 ARG 0.004 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 1.069 Fit side-chains REVERT: B 41 ILE cc_start: 0.7834 (tt) cc_final: 0.7526 (tt) REVERT: B 202 MET cc_start: 0.3705 (tpt) cc_final: 0.3140 (ttt) REVERT: A 105 TYR cc_start: 0.8620 (t80) cc_final: 0.8328 (t80) REVERT: A 136 PHE cc_start: 0.8459 (t80) cc_final: 0.8185 (t80) REVERT: A 215 GLN cc_start: 0.7122 (mm110) cc_final: 0.6891 (mm110) REVERT: A 355 GLU cc_start: 0.7914 (tp30) cc_final: 0.7517 (tp30) REVERT: A 360 THR cc_start: 0.8687 (p) cc_final: 0.8452 (p) REVERT: A 409 VAL cc_start: 0.8342 (t) cc_final: 0.8004 (t) REVERT: A 460 MET cc_start: 0.8069 (mmp) cc_final: 0.7741 (tpt) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1850 time to fit residues: 57.7842 Evaluate side-chains 148 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 69 optimal weight: 8.9990 chunk 50 optimal weight: 0.0040 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 104 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10428 Z= 0.160 Angle : 0.549 7.898 14131 Z= 0.282 Chirality : 0.040 0.140 1598 Planarity : 0.004 0.045 1824 Dihedral : 3.893 24.610 1404 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: -0.12 (0.24), residues: 1299 helix: 1.08 (0.23), residues: 559 sheet: -1.33 (0.42), residues: 145 loop : -0.81 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 155 HIS 0.004 0.001 HIS A 413 PHE 0.024 0.001 PHE A 90 TYR 0.016 0.001 TYR A 105 ARG 0.003 0.000 ARG A 877 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 1.065 Fit side-chains REVERT: B 41 ILE cc_start: 0.7833 (tt) cc_final: 0.7525 (tt) REVERT: B 202 MET cc_start: 0.3695 (tpt) cc_final: 0.3203 (ttt) REVERT: A 57 LYS cc_start: 0.8254 (mmpt) cc_final: 0.8047 (tppt) REVERT: A 105 TYR cc_start: 0.8636 (t80) cc_final: 0.8355 (t80) REVERT: A 136 PHE cc_start: 0.8444 (t80) cc_final: 0.8160 (t80) REVERT: A 215 GLN cc_start: 0.7106 (mm110) cc_final: 0.6862 (mm110) REVERT: A 355 GLU cc_start: 0.7923 (tp30) cc_final: 0.7492 (tp30) REVERT: A 360 THR cc_start: 0.8672 (p) cc_final: 0.8449 (p) REVERT: A 460 MET cc_start: 0.8096 (mmp) cc_final: 0.7865 (tmm) REVERT: A 859 TYR cc_start: 0.8999 (t80) cc_final: 0.8780 (t80) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1742 time to fit residues: 55.0401 Evaluate side-chains 151 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 109 optimal weight: 0.0470 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 HIS A 321 ASN ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 GLN ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10428 Z= 0.158 Angle : 0.542 7.273 14131 Z= 0.279 Chirality : 0.041 0.140 1598 Planarity : 0.004 0.046 1824 Dihedral : 3.901 21.963 1404 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: -0.09 (0.24), residues: 1299 helix: 1.11 (0.23), residues: 559 sheet: -1.33 (0.42), residues: 145 loop : -0.80 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 155 HIS 0.002 0.001 HIS A 656 PHE 0.023 0.001 PHE A 90 TYR 0.016 0.001 TYR A 105 ARG 0.003 0.000 ARG B 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 1.134 Fit side-chains REVERT: B 41 ILE cc_start: 0.7822 (tt) cc_final: 0.7516 (tt) REVERT: B 202 MET cc_start: 0.3733 (tpt) cc_final: 0.3215 (ttt) REVERT: A 105 TYR cc_start: 0.8626 (t80) cc_final: 0.8348 (t80) REVERT: A 215 GLN cc_start: 0.7106 (mm110) cc_final: 0.6879 (mm110) REVERT: A 355 GLU cc_start: 0.7943 (tp30) cc_final: 0.7545 (tp30) REVERT: A 360 THR cc_start: 0.8660 (p) cc_final: 0.8432 (p) REVERT: A 419 ASN cc_start: 0.6743 (m110) cc_final: 0.6529 (m-40) REVERT: A 460 MET cc_start: 0.8081 (mmp) cc_final: 0.7863 (tmm) REVERT: A 859 TYR cc_start: 0.8998 (t80) cc_final: 0.8722 (t80) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1912 time to fit residues: 60.4880 Evaluate side-chains 151 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 0.0770 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.134744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.106348 restraints weight = 18864.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.108966 restraints weight = 11259.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.110750 restraints weight = 7758.478| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10428 Z= 0.169 Angle : 0.550 7.414 14131 Z= 0.283 Chirality : 0.041 0.141 1598 Planarity : 0.004 0.045 1824 Dihedral : 3.904 21.647 1404 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: -0.12 (0.24), residues: 1299 helix: 1.06 (0.23), residues: 559 sheet: -1.32 (0.42), residues: 145 loop : -0.80 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 155 HIS 0.003 0.001 HIS A 199 PHE 0.024 0.001 PHE A 90 TYR 0.016 0.001 TYR A 105 ARG 0.003 0.000 ARG A 877 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2080.19 seconds wall clock time: 38 minutes 48.69 seconds (2328.69 seconds total)