Starting phenix.real_space_refine on Thu Mar 5 00:09:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d3x_27167/03_2026/8d3x_27167.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d3x_27167/03_2026/8d3x_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 { model { file = "/net/cci-nas-00/data/ceres_data/8d3x_27167/03_2026/8d3x_27167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d3x_27167/03_2026/8d3x_27167.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d3x_27167/03_2026/8d3x_27167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d3x_27167/03_2026/8d3x_27167.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.65, per 1000 atoms: 0.26 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: 0.65 Conformation dependent library (CDL) restraints added in 666.2 milliseconds 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: 0.36 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: 1.68 Time building geometry restraints manager: 0.94 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.210 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.590 ------------------------------------------------------------------------------- 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 10431 Z= 0.139 Angle : 0.695 33.213 14137 Z= 0.383 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (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 ARG 0.004 0.000 ARG B 182 TYR 0.012 0.001 TYR G 34 PHE 0.021 0.001 PHE A 136 TRP 0.007 0.001 TRP A 896 HIS 0.010 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00330 (10428) covalent geometry : angle 0.69296 (14131) SS BOND : bond 0.00384 ( 3) SS BOND : angle 2.75106 ( 6) hydrogen bonds : bond 0.14590 ( 448) hydrogen bonds : angle 6.36363 ( 1299) *********************** 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 : 0.396 Fit side-chains REVERT: B 41 ILE cc_start: 0.7864 (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: 0.6796 (m-40) REVERT: A 457 VAL cc_start: 0.8730 (t) cc_final: 0.8124 (m) REVERT: A 724 MET cc_start: 0.8664 (mmt) cc_final: 0.8244 (mmt) outliers start: 3 outliers final: 1 residues processed: 200 average time/residue: 0.0726 time to fit residues: 22.6546 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 : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.0010 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 35 optimal weight: 0.8980 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.136383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.107919 restraints weight = 18761.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.110533 restraints weight = 11278.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.112362 restraints weight = 7793.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.113636 restraints weight = 5993.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.114396 restraints weight = 4993.877| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 10431 Z= 0.109 Angle : 0.531 6.851 14137 Z= 0.279 Chirality : 0.040 0.145 1598 Planarity : 0.004 0.049 1824 Dihedral : 4.010 20.381 1404 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.23), residues: 1299 helix: 1.04 (0.23), residues: 546 sheet: -1.40 (0.39), residues: 158 loop : -0.82 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 838 TYR 0.010 0.001 TYR B 204 PHE 0.028 0.001 PHE A 90 TRP 0.006 0.001 TRP A 977 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00242 (10428) covalent geometry : angle 0.52997 (14131) SS BOND : bond 0.00275 ( 3) SS BOND : angle 1.83332 ( 6) hydrogen bonds : bond 0.03585 ( 448) hydrogen bonds : angle 4.94790 ( 1299) *********************** 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 204 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.300 Fit side-chains REVERT: B 41 ILE cc_start: 0.7904 (tt) cc_final: 0.7697 (tt) REVERT: A 215 GLN cc_start: 0.7124 (mm110) cc_final: 0.6824 (mm110) REVERT: A 324 GLU cc_start: 0.7428 (mp0) cc_final: 0.7175 (mp0) REVERT: A 355 GLU cc_start: 0.8005 (tp30) cc_final: 0.7662 (tp30) REVERT: A 360 THR cc_start: 0.8819 (p) cc_final: 0.8586 (p) REVERT: A 409 VAL cc_start: 0.8636 (m) cc_final: 0.8375 (t) REVERT: A 460 MET cc_start: 0.8133 (mmp) cc_final: 0.7642 (tpt) REVERT: A 724 MET cc_start: 0.8652 (mmt) cc_final: 0.8355 (mmt) REVERT: A 859 TYR cc_start: 0.9312 (t80) cc_final: 0.9092 (t80) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.0701 time to fit residues: 22.6252 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 : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 16 optimal weight: 4.9990 chunk 107 optimal weight: 0.1980 chunk 120 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 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 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.136397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.107701 restraints weight = 18789.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.110290 restraints weight = 11201.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.112055 restraints weight = 7758.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.113204 restraints weight = 6029.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.114051 restraints weight = 5084.054| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 10431 Z= 0.108 Angle : 0.522 6.807 14137 Z= 0.271 Chirality : 0.040 0.148 1598 Planarity : 0.004 0.045 1824 Dihedral : 3.919 21.111 1404 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.23), residues: 1299 helix: 1.06 (0.23), residues: 552 sheet: -1.32 (0.39), residues: 156 loop : -0.89 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 182 TYR 0.010 0.001 TYR B 204 PHE 0.024 0.001 PHE A 423 TRP 0.007 0.001 TRP A 977 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00245 (10428) covalent geometry : angle 0.52008 (14131) SS BOND : bond 0.00249 ( 3) SS BOND : angle 2.18359 ( 6) hydrogen bonds : bond 0.03387 ( 448) hydrogen bonds : angle 4.67554 ( 1299) *********************** 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 : 0.383 Fit side-chains REVERT: B 299 ILE cc_start: 0.8137 (mm) cc_final: 0.7918 (mp) REVERT: A 136 PHE cc_start: 0.8420 (t80) cc_final: 0.7999 (t80) REVERT: A 215 GLN cc_start: 0.7070 (mm110) cc_final: 0.6797 (mm110) REVERT: A 355 GLU cc_start: 0.7860 (tp30) cc_final: 0.7460 (tp30) REVERT: A 360 THR cc_start: 0.8693 (p) cc_final: 0.8435 (p) REVERT: A 409 VAL cc_start: 0.8609 (m) cc_final: 0.8276 (t) REVERT: A 419 ASN cc_start: 0.7053 (m110) cc_final: 0.6649 (m110) REVERT: A 457 VAL cc_start: 0.8949 (t) cc_final: 0.8584 (m) REVERT: A 460 MET cc_start: 0.8157 (mmp) cc_final: 0.7922 (tmm) REVERT: A 859 TYR cc_start: 0.9311 (t80) cc_final: 0.9050 (t80) REVERT: A 889 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7574 (tp30) REVERT: A 968 LEU cc_start: 0.8949 (tp) cc_final: 0.8677 (tp) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.0748 time to fit residues: 24.0632 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 : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 11 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 0.0970 chunk 69 optimal weight: 9.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- 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 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.130154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.101646 restraints weight = 19003.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.104128 restraints weight = 11395.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105860 restraints weight = 7938.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106899 restraints weight = 6157.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.107613 restraints weight = 5220.549| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10431 Z= 0.178 Angle : 0.576 7.218 14137 Z= 0.300 Chirality : 0.042 0.155 1598 Planarity : 0.004 0.044 1824 Dihedral : 4.115 22.857 1404 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.23), residues: 1299 helix: 0.94 (0.22), residues: 554 sheet: -1.57 (0.39), residues: 150 loop : -0.97 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 182 TYR 0.013 0.001 TYR B 204 PHE 0.028 0.002 PHE A 423 TRP 0.010 0.001 TRP A 896 HIS 0.007 0.001 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00414 (10428) covalent geometry : angle 0.57411 (14131) SS BOND : bond 0.00448 ( 3) SS BOND : angle 2.29447 ( 6) hydrogen bonds : bond 0.03645 ( 448) hydrogen bonds : angle 4.65930 ( 1299) *********************** 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 202 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.384 Fit side-chains REVERT: B 41 ILE cc_start: 0.7890 (tt) cc_final: 0.7653 (tt) REVERT: B 79 GLN cc_start: 0.7126 (pt0) cc_final: 0.6912 (pt0) REVERT: A 136 PHE cc_start: 0.8592 (t80) cc_final: 0.8205 (t80) REVERT: A 215 GLN cc_start: 0.7257 (mm110) cc_final: 0.6938 (mm110) REVERT: A 355 GLU cc_start: 0.7989 (tp30) cc_final: 0.7619 (tp30) REVERT: A 360 THR cc_start: 0.8755 (p) cc_final: 0.8418 (p) REVERT: A 409 VAL cc_start: 0.8562 (m) cc_final: 0.8211 (t) REVERT: A 419 ASN cc_start: 0.6972 (m110) cc_final: 0.6651 (m110) REVERT: A 457 VAL cc_start: 0.8949 (t) cc_final: 0.8674 (m) REVERT: A 738 MET cc_start: 0.8740 (ttp) cc_final: 0.8448 (ttm) REVERT: A 859 TYR cc_start: 0.9367 (t80) cc_final: 0.9141 (t80) REVERT: A 889 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7640 (tp30) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.0746 time to fit residues: 23.7659 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 : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 103 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.133025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.104631 restraints weight = 18843.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.107197 restraints weight = 11124.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.108943 restraints weight = 7698.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.110117 restraints weight = 5965.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.110746 restraints weight = 5015.790| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10431 Z= 0.114 Angle : 0.543 6.644 14137 Z= 0.280 Chirality : 0.040 0.143 1598 Planarity : 0.004 0.071 1824 Dihedral : 4.072 21.607 1404 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.23), residues: 1299 helix: 0.97 (0.22), residues: 559 sheet: -1.40 (0.41), residues: 145 loop : -0.96 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 182 TYR 0.022 0.001 TYR B 204 PHE 0.025 0.001 PHE A 423 TRP 0.007 0.001 TRP A 896 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00264 (10428) covalent geometry : angle 0.54076 (14131) SS BOND : bond 0.00721 ( 3) SS BOND : angle 2.18018 ( 6) hydrogen bonds : bond 0.03351 ( 448) hydrogen bonds : angle 4.50277 ( 1299) *********************** 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 212 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: B 41 ILE cc_start: 0.7873 (tt) cc_final: 0.7633 (tt) REVERT: B 202 MET cc_start: 0.3627 (tpt) cc_final: 0.3090 (ttt) REVERT: A 136 PHE cc_start: 0.8591 (t80) cc_final: 0.8169 (t80) REVERT: A 215 GLN cc_start: 0.7220 (mm110) cc_final: 0.6895 (mm110) REVERT: A 355 GLU cc_start: 0.7910 (tp30) cc_final: 0.7519 (tp30) REVERT: A 360 THR cc_start: 0.8684 (p) cc_final: 0.8323 (p) REVERT: A 409 VAL cc_start: 0.8540 (m) cc_final: 0.8220 (t) REVERT: A 419 ASN cc_start: 0.7067 (m110) cc_final: 0.6810 (m110) REVERT: A 457 VAL cc_start: 0.8922 (t) cc_final: 0.8462 (m) REVERT: A 460 MET cc_start: 0.8141 (mmp) cc_final: 0.7744 (tpt) REVERT: A 889 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7686 (tp30) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.0787 time to fit residues: 25.2617 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 : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 63 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 91 optimal weight: 0.0070 chunk 88 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.135252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.106458 restraints weight = 19081.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.109084 restraints weight = 11456.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.110861 restraints weight = 7942.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.111857 restraints weight = 6180.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.112630 restraints weight = 5287.005| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10431 Z= 0.112 Angle : 0.549 6.928 14137 Z= 0.283 Chirality : 0.041 0.141 1598 Planarity : 0.004 0.063 1824 Dihedral : 4.016 21.373 1404 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.23), residues: 1299 helix: 0.96 (0.23), residues: 553 sheet: -1.42 (0.40), residues: 151 loop : -0.90 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 182 TYR 0.017 0.001 TYR B 204 PHE 0.016 0.001 PHE A 90 TRP 0.008 0.001 TRP A 896 HIS 0.003 0.001 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00259 (10428) covalent geometry : angle 0.54554 (14131) SS BOND : bond 0.00292 ( 3) SS BOND : angle 2.89893 ( 6) hydrogen bonds : bond 0.03351 ( 448) hydrogen bonds : angle 4.51468 ( 1299) *********************** 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 200 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.387 Fit side-chains REVERT: B 41 ILE cc_start: 0.7856 (tt) cc_final: 0.7645 (tt) REVERT: B 202 MET cc_start: 0.3696 (tpt) cc_final: 0.3189 (ttt) REVERT: A 136 PHE cc_start: 0.8557 (t80) cc_final: 0.8182 (t80) REVERT: A 215 GLN cc_start: 0.7144 (mm110) cc_final: 0.6914 (mm110) REVERT: A 324 GLU cc_start: 0.7450 (mp0) cc_final: 0.7175 (mp0) REVERT: A 355 GLU cc_start: 0.7800 (tp30) cc_final: 0.7419 (tp30) REVERT: A 360 THR cc_start: 0.8768 (p) cc_final: 0.8551 (p) REVERT: A 409 VAL cc_start: 0.8528 (m) cc_final: 0.8239 (t) REVERT: A 460 MET cc_start: 0.8104 (mmp) cc_final: 0.7744 (tpt) REVERT: A 889 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7607 (tp30) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.0735 time to fit residues: 22.5097 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 : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 114 optimal weight: 0.6980 chunk 85 optimal weight: 0.0770 chunk 33 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 overall best weight: 1.2742 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.134872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.106000 restraints weight = 18902.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.108530 restraints weight = 11393.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.110294 restraints weight = 7938.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.111088 restraints weight = 6207.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.112102 restraints weight = 5404.965| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10431 Z= 0.119 Angle : 0.554 7.182 14137 Z= 0.287 Chirality : 0.041 0.169 1598 Planarity : 0.004 0.043 1824 Dihedral : 4.024 21.707 1404 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.23), residues: 1299 helix: 0.92 (0.23), residues: 560 sheet: -1.36 (0.41), residues: 150 loop : -0.87 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.016 0.001 TYR B 204 PHE 0.017 0.001 PHE A 90 TRP 0.014 0.001 TRP B 155 HIS 0.004 0.001 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00278 (10428) covalent geometry : angle 0.55131 (14131) SS BOND : bond 0.00319 ( 3) SS BOND : angle 2.45416 ( 6) hydrogen bonds : bond 0.03298 ( 448) hydrogen bonds : angle 4.46963 ( 1299) *********************** 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 198 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.372 Fit side-chains REVERT: B 41 ILE cc_start: 0.7903 (tt) cc_final: 0.7644 (tt) REVERT: B 165 GLU cc_start: 0.6441 (pt0) cc_final: 0.6211 (pt0) REVERT: A 136 PHE cc_start: 0.8558 (t80) cc_final: 0.8239 (t80) REVERT: A 215 GLN cc_start: 0.7220 (mm110) cc_final: 0.6945 (mm110) REVERT: A 355 GLU cc_start: 0.7921 (tp30) cc_final: 0.7547 (tp30) REVERT: A 360 THR cc_start: 0.8737 (p) cc_final: 0.8508 (p) REVERT: A 419 ASN cc_start: 0.7248 (m-40) cc_final: 0.7010 (m110) REVERT: A 460 MET cc_start: 0.8115 (mmp) cc_final: 0.7703 (tpt) REVERT: A 859 TYR cc_start: 0.9185 (t80) cc_final: 0.8868 (t80) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.0719 time to fit residues: 22.3054 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 : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 32 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 122 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.130338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.101712 restraints weight = 18996.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.104210 restraints weight = 11366.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.105896 restraints weight = 7908.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107134 restraints weight = 6144.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.107620 restraints weight = 5187.567| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10431 Z= 0.159 Angle : 0.587 7.132 14137 Z= 0.305 Chirality : 0.042 0.142 1598 Planarity : 0.004 0.042 1824 Dihedral : 4.203 23.098 1404 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.23), residues: 1299 helix: 0.84 (0.22), residues: 560 sheet: -1.45 (0.41), residues: 145 loop : -1.06 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 877 TYR 0.018 0.001 TYR B 204 PHE 0.023 0.001 PHE A 90 TRP 0.010 0.001 TRP A 896 HIS 0.007 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00377 (10428) covalent geometry : angle 0.58380 (14131) SS BOND : bond 0.00728 ( 3) SS BOND : angle 2.90845 ( 6) hydrogen bonds : bond 0.03553 ( 448) hydrogen bonds : angle 4.59446 ( 1299) *********************** 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 200 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.311 Fit side-chains REVERT: B 41 ILE cc_start: 0.7948 (tt) cc_final: 0.7697 (tt) REVERT: B 165 GLU cc_start: 0.6517 (pt0) cc_final: 0.6302 (pt0) REVERT: B 202 MET cc_start: 0.3616 (tpt) cc_final: 0.3108 (ttt) REVERT: B 272 ILE cc_start: 0.7133 (pt) cc_final: 0.6925 (pt) REVERT: A 136 PHE cc_start: 0.8536 (t80) cc_final: 0.8242 (t80) REVERT: A 215 GLN cc_start: 0.7289 (mm110) cc_final: 0.7080 (mm110) REVERT: A 355 GLU cc_start: 0.7945 (tp30) cc_final: 0.7602 (tp30) REVERT: A 360 THR cc_start: 0.8836 (p) cc_final: 0.8586 (p) REVERT: A 409 VAL cc_start: 0.8360 (t) cc_final: 0.8017 (t) REVERT: A 419 ASN cc_start: 0.7164 (m-40) cc_final: 0.6429 (m-40) REVERT: A 859 TYR cc_start: 0.9237 (t80) cc_final: 0.8957 (t80) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.0739 time to fit residues: 23.1414 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 : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 120 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 107 optimal weight: 0.0970 chunk 8 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 52 optimal weight: 0.4980 chunk 45 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 GLN A 321 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.132308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.103683 restraints weight = 18891.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.106318 restraints weight = 11191.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.108122 restraints weight = 7693.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109232 restraints weight = 5930.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.110076 restraints weight = 4996.808| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10431 Z= 0.121 Angle : 0.580 7.711 14137 Z= 0.300 Chirality : 0.041 0.141 1598 Planarity : 0.004 0.043 1824 Dihedral : 4.125 21.976 1404 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.09 % Allowed : 0.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.23), residues: 1299 helix: 0.91 (0.22), residues: 559 sheet: -1.40 (0.42), residues: 145 loop : -1.02 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 877 TYR 0.016 0.001 TYR B 204 PHE 0.016 0.001 PHE A 90 TRP 0.012 0.001 TRP B 155 HIS 0.003 0.001 HIS A 547 Details of bonding type rmsd covalent geometry : bond 0.00283 (10428) covalent geometry : angle 0.57828 (14131) SS BOND : bond 0.00496 ( 3) SS BOND : angle 2.41485 ( 6) hydrogen bonds : bond 0.03381 ( 448) hydrogen bonds : angle 4.51770 ( 1299) *********************** 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: 1 poor density : 201 time to evaluate : 0.244 Fit side-chains REVERT: B 41 ILE cc_start: 0.7940 (tt) cc_final: 0.7682 (tt) REVERT: B 165 GLU cc_start: 0.6449 (pt0) cc_final: 0.6249 (pt0) REVERT: B 202 MET cc_start: 0.3740 (tpt) cc_final: 0.3181 (ttt) REVERT: B 212 GLN cc_start: 0.6771 (OUTLIER) cc_final: 0.6505 (mm-40) REVERT: B 275 GLU cc_start: 0.7378 (tp30) cc_final: 0.6991 (mt-10) REVERT: A 136 PHE cc_start: 0.8520 (t80) cc_final: 0.8244 (t80) REVERT: A 355 GLU cc_start: 0.7961 (tp30) cc_final: 0.7599 (tp30) REVERT: A 360 THR cc_start: 0.8771 (p) cc_final: 0.8529 (p) REVERT: A 460 MET cc_start: 0.8097 (mmp) cc_final: 0.7639 (tpt) REVERT: A 859 TYR cc_start: 0.9232 (t80) cc_final: 0.8852 (t80) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.0763 time to fit residues: 23.4525 Evaluate side-chains 150 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 50 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.131457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.102865 restraints weight = 18817.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.105392 restraints weight = 11164.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107196 restraints weight = 7724.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.108226 restraints weight = 5988.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.108737 restraints weight = 5080.632| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10431 Z= 0.134 Angle : 0.585 7.718 14137 Z= 0.302 Chirality : 0.041 0.141 1598 Planarity : 0.004 0.042 1824 Dihedral : 4.144 22.381 1404 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.23), residues: 1299 helix: 0.83 (0.22), residues: 564 sheet: -1.45 (0.42), residues: 144 loop : -1.01 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 877 TYR 0.016 0.001 TYR B 204 PHE 0.018 0.001 PHE A 90 TRP 0.009 0.001 TRP B 155 HIS 0.004 0.001 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00319 (10428) covalent geometry : angle 0.58318 (14131) SS BOND : bond 0.00546 ( 3) SS BOND : angle 2.58376 ( 6) hydrogen bonds : bond 0.03464 ( 448) hydrogen bonds : angle 4.52463 ( 1299) ********************** 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 199 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.374 Fit side-chains REVERT: B 41 ILE cc_start: 0.7942 (tt) cc_final: 0.7685 (tt) REVERT: B 202 MET cc_start: 0.3895 (tpt) cc_final: 0.3326 (ttt) REVERT: B 275 GLU cc_start: 0.7663 (tp30) cc_final: 0.7244 (mt-10) REVERT: A 136 PHE cc_start: 0.8496 (t80) cc_final: 0.8212 (t80) REVERT: A 355 GLU cc_start: 0.7952 (tp30) cc_final: 0.7567 (tp30) REVERT: A 360 THR cc_start: 0.8757 (p) cc_final: 0.8516 (p) REVERT: A 460 MET cc_start: 0.8123 (mmp) cc_final: 0.7661 (tpt) REVERT: A 859 TYR cc_start: 0.9229 (t80) cc_final: 0.8930 (t80) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.0743 time to fit residues: 23.0783 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 : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 26 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 111 optimal weight: 0.0370 chunk 106 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.6662 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.133853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107834 restraints weight = 18876.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108415 restraints weight = 11475.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.109170 restraints weight = 7900.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.109395 restraints weight = 7123.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.109652 restraints weight = 6774.900| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10431 Z= 0.113 Angle : 0.575 8.005 14137 Z= 0.295 Chirality : 0.041 0.148 1598 Planarity : 0.004 0.043 1824 Dihedral : 4.063 21.400 1404 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.23), residues: 1299 helix: 0.99 (0.23), residues: 554 sheet: -1.47 (0.42), residues: 146 loop : -0.94 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 182 TYR 0.014 0.001 TYR B 204 PHE 0.023 0.001 PHE A 90 TRP 0.008 0.001 TRP B 155 HIS 0.002 0.001 HIS A 547 Details of bonding type rmsd covalent geometry : bond 0.00261 (10428) covalent geometry : angle 0.57288 (14131) SS BOND : bond 0.00367 ( 3) SS BOND : angle 2.47794 ( 6) hydrogen bonds : bond 0.03253 ( 448) hydrogen bonds : angle 4.45293 ( 1299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1655.19 seconds wall clock time: 29 minutes 13.55 seconds (1753.55 seconds total)