Starting phenix.real_space_refine on Sat Aug 23 11:44:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t9a_41105/08_2025/8t9a_41105.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t9a_41105/08_2025/8t9a_41105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t9a_41105/08_2025/8t9a_41105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t9a_41105/08_2025/8t9a_41105.map" model { file = "/net/cci-nas-00/data/ceres_data/8t9a_41105/08_2025/8t9a_41105.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t9a_41105/08_2025/8t9a_41105.cif" } resolution = 3.17 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 7468 2.51 5 N 2010 2.21 5 O 2248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11785 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8744 Classifications: {'peptide': 1114} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 1073} Chain breaks: 4 Chain: "B" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2998 Classifications: {'peptide': 379} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 364} Chain breaks: 4 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Time building chain proxies: 3.36, per 1000 atoms: 0.29 Number of scatterers: 11785 At special positions: 0 Unit cell: (89.112, 112.812, 146.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 2248 8.00 N 2010 7.00 C 7468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 643.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 33 sheets defined 6.8% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.578A pdb=" N SER A 256 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1059 removed outlier: 3.807A pdb=" N ASP A1053 " --> pdb=" O ASN A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1075 Processing helix chain 'A' and resid 1090 through 1096 Processing helix chain 'A' and resid 1101 through 1110 removed outlier: 3.990A pdb=" N GLU A1107 " --> pdb=" O PRO A1103 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL A1108 " --> pdb=" O LYS A1104 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A1109 " --> pdb=" O MET A1105 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA A1110 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1132 Processing helix chain 'A' and resid 1133 through 1138 Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.752A pdb=" N TYR B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 75 removed outlier: 4.016A pdb=" N GLN B 73 " --> pdb=" O GLY B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 213 through 224 removed outlier: 3.626A pdb=" N HIS B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 10 removed outlier: 6.296A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A1006 " --> pdb=" O GLY A1031 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 21 removed outlier: 3.797A pdb=" N GLY A 17 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL A 43 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 67 removed outlier: 6.993A pdb=" N ALA A 86 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N HIS A 105 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE A 88 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 94 removed outlier: 3.734A pdb=" N ASP A 99 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA6, first strand: chain 'A' and resid 164 through 168 removed outlier: 5.834A pdb=" N VAL A 164 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN A 183 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 201 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 219 through 220 Processing sheet with id=AA8, first strand: chain 'A' and resid 262 through 263 removed outlier: 7.202A pdb=" N LEU A 280 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU A 304 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N MET A 282 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL A 302 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 284 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU A 300 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLU A 286 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 315 through 318 removed outlier: 5.422A pdb=" N TYR A 316 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE A 323 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP A 318 " --> pdb=" O VAL A 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 331 through 332 Processing sheet with id=AB2, first strand: chain 'A' and resid 335 through 336 Processing sheet with id=AB3, first strand: chain 'A' and resid 374 through 379 removed outlier: 3.908A pdb=" N ILE A 390 " --> pdb=" O LEU A 375 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.669A pdb=" N SER A 690 " --> pdb=" O PRO A 681 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA A 692 " --> pdb=" O MET A 679 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N MET A 679 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA A 694 " --> pdb=" O ASN A 677 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 409 through 412 removed outlier: 4.064A pdb=" N GLY A 409 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 459 through 463 removed outlier: 3.926A pdb=" N PHE A 459 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN A 467 " --> pdb=" O VAL A 463 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER A 480 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU A 486 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 500 through 503 removed outlier: 3.601A pdb=" N VAL A 500 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 516 " --> pdb=" O HIS A 531 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N HIS A 531 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N TYR A 518 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE A 529 " --> pdb=" O TYR A 518 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.339A pdb=" N GLY A 559 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA A 557 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS A 578 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS A 570 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU A 576 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 588 through 596 removed outlier: 3.780A pdb=" N SER A 590 " --> pdb=" O ALA A 605 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N HIS A 600 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY A 615 " --> pdb=" O ASP A 625 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ASP A 625 " --> pdb=" O GLY A 615 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN A 617 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU A 623 " --> pdb=" O ASN A 617 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 637 through 643 removed outlier: 9.277A pdb=" N THR A 647 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SER A 661 " --> pdb=" O THR A 647 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 720 through 724 removed outlier: 6.505A pdb=" N LEU A 736 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE A 724 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY A 734 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N HIS A 803 " --> pdb=" O ILE A 793 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 811 through 820 removed outlier: 5.265A pdb=" N ALA A 813 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA A 834 " --> pdb=" O ALA A 813 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N THR A 827 " --> pdb=" O TYR A 853 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N TYR A 853 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 848 " --> pdb=" O GLU A 863 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU A 863 " --> pdb=" O ILE A 848 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL A 850 " --> pdb=" O VAL A 861 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 854 " --> pdb=" O LYS A 857 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 870 through 876 removed outlier: 3.985A pdb=" N SER A 872 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL A 888 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASN A 904 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A 890 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 911 through 913 removed outlier: 6.687A pdb=" N GLY A 924 " --> pdb=" O LEU A 912 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE A 920 " --> pdb=" O LYS A 917 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 911 through 913 removed outlier: 6.687A pdb=" N GLY A 924 " --> pdb=" O LEU A 912 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 921 " --> pdb=" O LEU A 933 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN A 941 " --> pdb=" O LYS A 936 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 954 through 958 removed outlier: 6.712A pdb=" N ALA A 968 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL A 957 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A 966 " --> pdb=" O VAL A 957 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1076 through 1077 Processing sheet with id=AC9, first strand: chain 'B' and resid 92 through 97 removed outlier: 6.384A pdb=" N GLY B 106 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER B 95 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL B 104 " --> pdb=" O SER B 95 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TRP B 97 " --> pdb=" O GLN B 102 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLN B 102 " --> pdb=" O TRP B 97 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN B 121 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 146 through 148 removed outlier: 3.773A pdb=" N GLU B 147 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE B 167 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 189 through 192 removed outlier: 4.335A pdb=" N SER B 189 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 255 through 257 removed outlier: 3.833A pdb=" N ALA B 257 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS B 277 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LYS B 280 " --> pdb=" O LYS B 287 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LYS B 287 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 302 through 304 removed outlier: 3.719A pdb=" N LYS B 332 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 345 through 349 Processing sheet with id=AD6, first strand: chain 'B' and resid 420 through 425 removed outlier: 7.045A pdb=" N ALA B 436 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N HIS B 424 " --> pdb=" O PHE B 434 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE B 434 " --> pdb=" O HIS B 424 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 891 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: 2.78 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3540 1.33 - 1.45: 2075 1.45 - 1.57: 6312 1.57 - 1.70: 0 1.70 - 1.82: 87 Bond restraints: 12014 Sorted by residual: bond pdb=" CA ARG A 134 " pdb=" CB ARG A 134 " ideal model delta sigma weight residual 1.539 1.346 0.193 4.88e-02 4.20e+02 1.56e+01 bond pdb=" CA TYR A 871 " pdb=" C TYR A 871 " ideal model delta sigma weight residual 1.523 1.452 0.071 1.80e-02 3.09e+03 1.56e+01 bond pdb=" CA GLU A 896 " pdb=" C GLU A 896 " ideal model delta sigma weight residual 1.524 1.440 0.084 2.25e-02 1.98e+03 1.39e+01 bond pdb=" CG ARG A 134 " pdb=" CD ARG A 134 " ideal model delta sigma weight residual 1.520 1.439 0.081 3.00e-02 1.11e+03 7.22e+00 bond pdb=" C VAL A 870 " pdb=" N TYR A 871 " ideal model delta sigma weight residual 1.331 1.288 0.043 1.62e-02 3.81e+03 7.08e+00 ... (remaining 12009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 15585 2.17 - 4.34: 609 4.34 - 6.51: 67 6.51 - 8.68: 12 8.68 - 10.85: 4 Bond angle restraints: 16277 Sorted by residual: angle pdb=" N ILE A 884 " pdb=" CA ILE A 884 " pdb=" CB ILE A 884 " ideal model delta sigma weight residual 111.41 105.70 5.71 1.25e+00 6.40e-01 2.09e+01 angle pdb=" CA TYR A 871 " pdb=" C TYR A 871 " pdb=" N SER A 872 " ideal model delta sigma weight residual 118.27 125.17 -6.90 1.59e+00 3.96e-01 1.88e+01 angle pdb=" N GLY A 393 " pdb=" CA GLY A 393 " pdb=" C GLY A 393 " ideal model delta sigma weight residual 111.56 115.91 -4.35 1.01e+00 9.80e-01 1.86e+01 angle pdb=" N TRP A 411 " pdb=" CA TRP A 411 " pdb=" C TRP A 411 " ideal model delta sigma weight residual 108.25 113.05 -4.80 1.16e+00 7.43e-01 1.71e+01 angle pdb=" C ALA A 381 " pdb=" N PHE A 382 " pdb=" CA PHE A 382 " ideal model delta sigma weight residual 121.54 129.11 -7.57 1.91e+00 2.74e-01 1.57e+01 ... (remaining 16272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 6341 17.87 - 35.74: 698 35.74 - 53.61: 125 53.61 - 71.48: 27 71.48 - 89.35: 10 Dihedral angle restraints: 7201 sinusoidal: 2878 harmonic: 4323 Sorted by residual: dihedral pdb=" CA ASN B 59 " pdb=" C ASN B 59 " pdb=" N GLU B 60 " pdb=" CA GLU B 60 " ideal model delta harmonic sigma weight residual -180.00 -152.09 -27.91 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA GLY A 274 " pdb=" C GLY A 274 " pdb=" N ASP A 275 " pdb=" CA ASP A 275 " ideal model delta harmonic sigma weight residual 180.00 -156.46 -23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA TYR B 349 " pdb=" C TYR B 349 " pdb=" N GLU B 350 " pdb=" CA GLU B 350 " ideal model delta harmonic sigma weight residual -180.00 -157.29 -22.71 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 7198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1342 0.059 - 0.117: 436 0.117 - 0.176: 67 0.176 - 0.235: 6 0.235 - 0.294: 3 Chirality restraints: 1854 Sorted by residual: chirality pdb=" CB ILE A 740 " pdb=" CA ILE A 740 " pdb=" CG1 ILE A 740 " pdb=" CG2 ILE A 740 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA ARG A 134 " pdb=" N ARG A 134 " pdb=" C ARG A 134 " pdb=" CB ARG A 134 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CG LEU B 79 " pdb=" CB LEU B 79 " pdb=" CD1 LEU B 79 " pdb=" CD2 LEU B 79 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1851 not shown) Planarity restraints: 2094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 222 " -0.052 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO A 223 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 125 " -0.037 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO A 126 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 824 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO A 825 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 825 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 825 " -0.030 5.00e-02 4.00e+02 ... (remaining 2091 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 209 2.60 - 3.18: 10516 3.18 - 3.75: 17329 3.75 - 4.33: 25103 4.33 - 4.90: 42609 Nonbonded interactions: 95766 Sorted by model distance: nonbonded pdb=" OG1 THR B 107 " pdb=" OG1 THR B 111 " model vdw 2.029 3.040 nonbonded pdb=" O GLY A 227 " pdb=" OH TYR A 239 " model vdw 2.065 3.040 nonbonded pdb=" OG SER B 95 " pdb=" OG1 THR B 423 " model vdw 2.081 3.040 nonbonded pdb=" O ASN A 617 " pdb=" N GLY A 621 " model vdw 2.132 3.120 nonbonded pdb=" O ILE A 310 " pdb=" OG SER A 326 " model vdw 2.140 3.040 ... (remaining 95761 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=0.00 max=1.00 mean=0.90 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.140 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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: 17.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 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 : 0.011 0.193 12014 Z= 0.480 Angle : 0.980 10.852 16277 Z= 0.540 Chirality : 0.056 0.294 1854 Planarity : 0.006 0.077 2094 Dihedral : 15.501 89.350 4417 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.75 % Favored : 86.25 % Rotamer: Outliers : 0.61 % Allowed : 12.80 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: -5.00 (0.17), residues: 1476 helix: -3.44 (0.35), residues: 104 sheet: -2.58 (0.19), residues: 620 loop : -4.03 (0.16), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 134 TYR 0.029 0.003 TYR B 349 PHE 0.034 0.003 PHE A 733 TRP 0.030 0.003 TRP A 207 HIS 0.009 0.002 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.01140 (12014) covalent geometry : angle 0.97987 (16277) hydrogen bonds : bond 0.14221 ( 344) hydrogen bonds : angle 9.18338 ( 891) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 86 average time/residue: 0.1116 time to fit residues: 14.5698 Evaluate side-chains 57 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 377 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS A 203 ASN A 355 ASN A 759 GLN A 803 HIS A 907 ASN A 950 ASN B 99 ASN B 224 HIS B 359 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.075308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.049091 restraints weight = 48631.604| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 5.14 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 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 : 0.004 0.080 12014 Z= 0.195 Angle : 0.689 7.619 16277 Z= 0.363 Chirality : 0.047 0.222 1854 Planarity : 0.005 0.063 2094 Dihedral : 5.767 29.335 1614 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 1.75 % Allowed : 15.32 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: -4.06 (0.19), residues: 1476 helix: -2.51 (0.43), residues: 104 sheet: -1.93 (0.19), residues: 645 loop : -3.48 (0.17), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 152 TYR 0.015 0.002 TYR B 410 PHE 0.016 0.001 PHE A1030 TRP 0.019 0.002 TRP A 207 HIS 0.008 0.001 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00435 (12014) covalent geometry : angle 0.68887 (16277) hydrogen bonds : bond 0.04038 ( 344) hydrogen bonds : angle 7.13886 ( 891) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 812 TYR cc_start: 0.8948 (m-80) cc_final: 0.8734 (m-80) REVERT: A 1105 MET cc_start: 0.9230 (mtm) cc_final: 0.8849 (mtm) REVERT: A 1120 MET cc_start: 0.6824 (tmm) cc_final: 0.6602 (tmm) REVERT: B 74 GLN cc_start: 0.8601 (mm110) cc_final: 0.8083 (mm-40) REVERT: B 78 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9040 (pp) REVERT: B 207 MET cc_start: 0.8930 (mtp) cc_final: 0.8670 (mtp) REVERT: B 329 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.7940 (p90) outliers start: 23 outliers final: 8 residues processed: 77 average time/residue: 0.1091 time to fit residues: 12.8768 Evaluate side-chains 62 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 329 TYR Chi-restraints excluded: chain B residue 349 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 25 optimal weight: 0.4980 chunk 139 optimal weight: 0.3980 chunk 123 optimal weight: 6.9990 chunk 133 optimal weight: 20.0000 chunk 92 optimal weight: 0.1980 chunk 120 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 41 optimal weight: 0.3980 chunk 134 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 112 optimal weight: 0.0770 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN A1034 ASN B 144 HIS B 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.077171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.050662 restraints weight = 47312.147| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 5.18 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12014 Z= 0.105 Angle : 0.611 7.471 16277 Z= 0.321 Chirality : 0.046 0.191 1854 Planarity : 0.004 0.056 2094 Dihedral : 4.961 19.778 1612 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.60 % Allowed : 16.39 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: -3.33 (0.20), residues: 1476 helix: -1.68 (0.48), residues: 104 sheet: -1.52 (0.20), residues: 628 loop : -2.94 (0.19), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 514 TYR 0.013 0.001 TYR B 329 PHE 0.014 0.001 PHE A1030 TRP 0.019 0.001 TRP A 207 HIS 0.005 0.001 HIS B 424 Details of bonding type rmsd covalent geometry : bond 0.00228 (12014) covalent geometry : angle 0.61088 (16277) hydrogen bonds : bond 0.03375 ( 344) hydrogen bonds : angle 6.38234 ( 891) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 ASN cc_start: 0.9275 (OUTLIER) cc_final: 0.8904 (t0) REVERT: A 276 MET cc_start: 0.8881 (mmm) cc_final: 0.8608 (mmm) REVERT: A 835 MET cc_start: 0.8518 (mmm) cc_final: 0.8049 (mmm) REVERT: A 910 MET cc_start: 0.8687 (tpp) cc_final: 0.8418 (tpp) REVERT: A 1120 MET cc_start: 0.6832 (tmm) cc_final: 0.6558 (tmm) REVERT: B 74 GLN cc_start: 0.8460 (mm110) cc_final: 0.8161 (mm-40) REVERT: B 78 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8980 (pp) REVERT: B 207 MET cc_start: 0.8971 (mtp) cc_final: 0.8649 (mtp) REVERT: B 453 SER cc_start: 0.9400 (p) cc_final: 0.9117 (p) outliers start: 21 outliers final: 5 residues processed: 87 average time/residue: 0.1098 time to fit residues: 14.5174 Evaluate side-chains 65 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 203 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 111 optimal weight: 10.0000 chunk 40 optimal weight: 0.0980 chunk 124 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 50.0000 chunk 132 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1077 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.074574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.048502 restraints weight = 48793.887| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 5.11 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 12014 Z= 0.238 Angle : 0.666 7.266 16277 Z= 0.344 Chirality : 0.045 0.186 1854 Planarity : 0.004 0.055 2094 Dihedral : 5.081 22.845 1611 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.29 % Allowed : 17.45 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: -3.19 (0.20), residues: 1476 helix: -1.58 (0.47), residues: 105 sheet: -1.44 (0.20), residues: 621 loop : -2.83 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 198 TYR 0.015 0.001 TYR A 271 PHE 0.014 0.002 PHE A1007 TRP 0.010 0.001 TRP A1073 HIS 0.005 0.001 HIS A 711 Details of bonding type rmsd covalent geometry : bond 0.00522 (12014) covalent geometry : angle 0.66553 (16277) hydrogen bonds : bond 0.03587 ( 344) hydrogen bonds : angle 6.44350 ( 891) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 49 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 282 MET cc_start: 0.9252 (tpp) cc_final: 0.8986 (tpp) REVERT: A 835 MET cc_start: 0.8717 (mmm) cc_final: 0.8243 (mmm) REVERT: A 910 MET cc_start: 0.8864 (tpp) cc_final: 0.8594 (tpt) REVERT: A 1105 MET cc_start: 0.9091 (mtp) cc_final: 0.8815 (mmm) REVERT: A 1120 MET cc_start: 0.7000 (tmm) cc_final: 0.6687 (tmm) REVERT: B 78 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9077 (pp) REVERT: B 207 MET cc_start: 0.9026 (mtp) cc_final: 0.8690 (mtp) outliers start: 30 outliers final: 18 residues processed: 76 average time/residue: 0.1051 time to fit residues: 12.4559 Evaluate side-chains 64 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 349 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 77 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 25 optimal weight: 0.1980 chunk 45 optimal weight: 0.8980 chunk 96 optimal weight: 0.0370 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN B 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.076508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.049898 restraints weight = 47545.433| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 5.16 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12014 Z= 0.096 Angle : 0.581 11.209 16277 Z= 0.301 Chirality : 0.045 0.165 1854 Planarity : 0.004 0.056 2094 Dihedral : 4.568 20.145 1611 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.91 % Allowed : 18.45 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: -2.81 (0.20), residues: 1476 helix: -1.09 (0.48), residues: 106 sheet: -1.14 (0.21), residues: 617 loop : -2.65 (0.19), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 114 TYR 0.008 0.001 TYR A 613 PHE 0.012 0.001 PHE A1030 TRP 0.016 0.001 TRP A 207 HIS 0.004 0.001 HIS B 424 Details of bonding type rmsd covalent geometry : bond 0.00210 (12014) covalent geometry : angle 0.58113 (16277) hydrogen bonds : bond 0.03067 ( 344) hydrogen bonds : angle 5.93552 ( 891) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9316 (mm) REVERT: A 282 MET cc_start: 0.9221 (tpp) cc_final: 0.8825 (tpp) REVERT: A 835 MET cc_start: 0.8567 (mmm) cc_final: 0.8101 (mmm) REVERT: A 910 MET cc_start: 0.8815 (tpp) cc_final: 0.8485 (tpp) REVERT: A 1005 ASN cc_start: 0.9041 (OUTLIER) cc_final: 0.8696 (m-40) REVERT: A 1112 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8862 (mm) REVERT: A 1120 MET cc_start: 0.6946 (tmm) cc_final: 0.6620 (tmm) REVERT: B 207 MET cc_start: 0.9058 (mtp) cc_final: 0.8731 (mtp) REVERT: B 453 SER cc_start: 0.9280 (p) cc_final: 0.8964 (p) outliers start: 25 outliers final: 12 residues processed: 80 average time/residue: 0.1068 time to fit residues: 13.2269 Evaluate side-chains 65 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 349 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 40 optimal weight: 0.0040 chunk 2 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.076298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.049563 restraints weight = 47583.328| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 5.14 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12014 Z= 0.107 Angle : 0.583 10.435 16277 Z= 0.300 Chirality : 0.045 0.238 1854 Planarity : 0.004 0.056 2094 Dihedral : 4.458 20.052 1611 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.83 % Allowed : 18.60 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: -2.62 (0.20), residues: 1476 helix: -0.89 (0.49), residues: 107 sheet: -0.96 (0.21), residues: 607 loop : -2.57 (0.19), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 111 TYR 0.017 0.001 TYR B 329 PHE 0.012 0.001 PHE A1030 TRP 0.010 0.001 TRP B 279 HIS 0.003 0.001 HIS B 424 Details of bonding type rmsd covalent geometry : bond 0.00238 (12014) covalent geometry : angle 0.58250 (16277) hydrogen bonds : bond 0.03063 ( 344) hydrogen bonds : angle 5.82015 ( 891) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 52 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.9307 (pmm) cc_final: 0.8749 (pmm) REVERT: A 145 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9327 (mm) REVERT: A 282 MET cc_start: 0.9213 (tpp) cc_final: 0.8832 (tpp) REVERT: A 382 PHE cc_start: 0.9099 (m-80) cc_final: 0.8837 (m-80) REVERT: A 835 MET cc_start: 0.8667 (mmm) cc_final: 0.8202 (mmm) REVERT: A 910 MET cc_start: 0.8845 (tpp) cc_final: 0.8560 (tpt) REVERT: A 1005 ASN cc_start: 0.9052 (OUTLIER) cc_final: 0.8726 (m-40) REVERT: A 1105 MET cc_start: 0.9067 (mmm) cc_final: 0.8810 (mmm) REVERT: A 1120 MET cc_start: 0.6943 (tmm) cc_final: 0.6596 (tmm) REVERT: B 74 GLN cc_start: 0.8993 (tp40) cc_final: 0.8564 (tp40) REVERT: B 207 MET cc_start: 0.9106 (mtp) cc_final: 0.8671 (mtp) REVERT: B 453 SER cc_start: 0.9303 (p) cc_final: 0.9020 (p) outliers start: 24 outliers final: 15 residues processed: 73 average time/residue: 0.1002 time to fit residues: 11.6618 Evaluate side-chains 65 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 348 PHE Chi-restraints excluded: chain B residue 353 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 138 optimal weight: 0.1980 chunk 30 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.076035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.049398 restraints weight = 47616.510| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 5.13 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12014 Z= 0.116 Angle : 0.581 9.598 16277 Z= 0.297 Chirality : 0.044 0.208 1854 Planarity : 0.004 0.056 2094 Dihedral : 4.359 20.302 1611 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.06 % Allowed : 19.13 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: -2.46 (0.21), residues: 1476 helix: -0.60 (0.51), residues: 107 sheet: -0.89 (0.21), residues: 607 loop : -2.46 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 111 TYR 0.015 0.001 TYR B 329 PHE 0.011 0.001 PHE A1030 TRP 0.009 0.001 TRP B 279 HIS 0.003 0.001 HIS B 424 Details of bonding type rmsd covalent geometry : bond 0.00259 (12014) covalent geometry : angle 0.58073 (16277) hydrogen bonds : bond 0.03070 ( 344) hydrogen bonds : angle 5.71971 ( 891) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 49 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.9266 (pmm) cc_final: 0.8751 (pmm) REVERT: A 145 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9331 (mm) REVERT: A 282 MET cc_start: 0.9220 (tpp) cc_final: 0.8946 (tpp) REVERT: A 382 PHE cc_start: 0.9093 (m-80) cc_final: 0.8829 (m-80) REVERT: A 835 MET cc_start: 0.8669 (mmm) cc_final: 0.8213 (mmm) REVERT: A 910 MET cc_start: 0.8826 (tpp) cc_final: 0.8599 (tpt) REVERT: A 1005 ASN cc_start: 0.9027 (OUTLIER) cc_final: 0.8696 (m-40) REVERT: A 1036 MET cc_start: 0.8252 (tpt) cc_final: 0.8045 (tpt) REVERT: A 1105 MET cc_start: 0.9124 (mmm) cc_final: 0.8828 (mpp) REVERT: A 1112 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8914 (mm) REVERT: A 1120 MET cc_start: 0.7044 (tmm) cc_final: 0.6684 (tmm) REVERT: B 154 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9314 (mm) REVERT: B 207 MET cc_start: 0.9130 (mtp) cc_final: 0.8711 (mtp) outliers start: 27 outliers final: 19 residues processed: 73 average time/residue: 0.0975 time to fit residues: 11.4850 Evaluate side-chains 72 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 348 PHE Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 417 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 73 optimal weight: 10.0000 chunk 45 optimal weight: 40.0000 chunk 82 optimal weight: 8.9990 chunk 7 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 75 optimal weight: 0.0980 chunk 106 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1113 GLN B 234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.074851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.048166 restraints weight = 48562.352| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 5.14 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12014 Z= 0.173 Angle : 0.608 8.791 16277 Z= 0.311 Chirality : 0.044 0.189 1854 Planarity : 0.004 0.057 2094 Dihedral : 4.479 22.199 1611 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.98 % Allowed : 19.21 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: -2.40 (0.21), residues: 1476 helix: -0.55 (0.51), residues: 107 sheet: -0.83 (0.21), residues: 594 loop : -2.42 (0.19), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 111 TYR 0.013 0.001 TYR B 329 PHE 0.012 0.001 PHE A1030 TRP 0.009 0.001 TRP A1073 HIS 0.004 0.001 HIS A 711 Details of bonding type rmsd covalent geometry : bond 0.00380 (12014) covalent geometry : angle 0.60760 (16277) hydrogen bonds : bond 0.03184 ( 344) hydrogen bonds : angle 5.81630 ( 891) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.9195 (pmm) cc_final: 0.8771 (pmm) REVERT: A 145 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9321 (mm) REVERT: A 282 MET cc_start: 0.9225 (tpp) cc_final: 0.8963 (tpp) REVERT: A 382 PHE cc_start: 0.9144 (m-80) cc_final: 0.8908 (m-80) REVERT: A 835 MET cc_start: 0.8766 (mmm) cc_final: 0.8289 (mmm) REVERT: A 910 MET cc_start: 0.8891 (tpp) cc_final: 0.8644 (tpt) REVERT: A 1036 MET cc_start: 0.8363 (tpt) cc_final: 0.8138 (tpt) REVERT: A 1120 MET cc_start: 0.7090 (tmm) cc_final: 0.6742 (tmm) REVERT: B 207 MET cc_start: 0.9110 (mtp) cc_final: 0.8694 (mtp) outliers start: 26 outliers final: 19 residues processed: 74 average time/residue: 0.0980 time to fit residues: 11.6729 Evaluate side-chains 70 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 348 PHE Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 417 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 75 optimal weight: 9.9990 chunk 25 optimal weight: 0.0040 chunk 44 optimal weight: 40.0000 chunk 142 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.075434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.048615 restraints weight = 47971.438| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 5.17 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12014 Z= 0.125 Angle : 0.587 10.176 16277 Z= 0.299 Chirality : 0.044 0.163 1854 Planarity : 0.004 0.057 2094 Dihedral : 4.370 21.421 1611 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.68 % Allowed : 19.97 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: -2.31 (0.21), residues: 1476 helix: -0.52 (0.50), residues: 107 sheet: -0.81 (0.21), residues: 607 loop : -2.34 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 111 TYR 0.014 0.001 TYR B 329 PHE 0.010 0.001 PHE A1030 TRP 0.011 0.001 TRP B 279 HIS 0.003 0.001 HIS B 424 Details of bonding type rmsd covalent geometry : bond 0.00278 (12014) covalent geometry : angle 0.58672 (16277) hydrogen bonds : bond 0.03063 ( 344) hydrogen bonds : angle 5.69049 ( 891) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.9218 (pmm) cc_final: 0.8752 (pmm) REVERT: A 145 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9313 (mm) REVERT: A 282 MET cc_start: 0.9231 (tpp) cc_final: 0.8965 (tpp) REVERT: A 382 PHE cc_start: 0.9105 (m-80) cc_final: 0.8897 (m-80) REVERT: A 835 MET cc_start: 0.8761 (mmm) cc_final: 0.8280 (mmm) REVERT: A 910 MET cc_start: 0.8848 (tpp) cc_final: 0.8598 (tpt) REVERT: A 1036 MET cc_start: 0.8378 (tpt) cc_final: 0.8174 (tpt) REVERT: A 1120 MET cc_start: 0.7012 (tmm) cc_final: 0.6636 (tmm) REVERT: B 203 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8723 (ttm170) REVERT: B 207 MET cc_start: 0.9140 (mtp) cc_final: 0.8751 (mtp) REVERT: B 453 SER cc_start: 0.9180 (p) cc_final: 0.8952 (p) outliers start: 22 outliers final: 18 residues processed: 71 average time/residue: 0.0962 time to fit residues: 10.9967 Evaluate side-chains 69 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 348 PHE Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 417 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 76 optimal weight: 20.0000 chunk 134 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.073748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.047033 restraints weight = 50228.786| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 5.19 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 12014 Z= 0.279 Angle : 0.700 9.870 16277 Z= 0.355 Chirality : 0.045 0.194 1854 Planarity : 0.004 0.056 2094 Dihedral : 4.852 25.049 1611 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.75 % Allowed : 19.97 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: -2.46 (0.21), residues: 1476 helix: -0.98 (0.48), residues: 114 sheet: -0.85 (0.21), residues: 585 loop : -2.41 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 111 TYR 0.015 0.002 TYR A 613 PHE 0.016 0.002 PHE A 807 TRP 0.009 0.002 TRP B 192 HIS 0.005 0.001 HIS A 711 Details of bonding type rmsd covalent geometry : bond 0.00606 (12014) covalent geometry : angle 0.70033 (16277) hydrogen bonds : bond 0.03576 ( 344) hydrogen bonds : angle 6.13280 ( 891) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 46 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.9034 (pmm) cc_final: 0.8692 (pmm) REVERT: A 145 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9290 (mm) REVERT: A 282 MET cc_start: 0.9238 (tpp) cc_final: 0.8980 (tpp) REVERT: A 835 MET cc_start: 0.8832 (mmm) cc_final: 0.8351 (mmm) REVERT: A 910 MET cc_start: 0.8956 (tpp) cc_final: 0.8707 (tpt) REVERT: A 1120 MET cc_start: 0.7244 (tmm) cc_final: 0.6908 (tmm) REVERT: B 207 MET cc_start: 0.9012 (mtp) cc_final: 0.8671 (mtp) outliers start: 23 outliers final: 19 residues processed: 67 average time/residue: 0.0905 time to fit residues: 9.8448 Evaluate side-chains 64 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 679 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 417 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 69 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 96 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 789 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.074348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.048085 restraints weight = 48500.778| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 5.08 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12014 Z= 0.175 Angle : 0.619 9.444 16277 Z= 0.316 Chirality : 0.045 0.180 1854 Planarity : 0.004 0.058 2094 Dihedral : 4.632 23.603 1611 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.68 % Allowed : 20.05 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: -2.28 (0.21), residues: 1476 helix: -0.50 (0.50), residues: 107 sheet: -0.76 (0.21), residues: 590 loop : -2.32 (0.20), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 111 TYR 0.013 0.001 TYR B 329 PHE 0.010 0.001 PHE A1030 TRP 0.010 0.001 TRP B 279 HIS 0.003 0.001 HIS B 424 Details of bonding type rmsd covalent geometry : bond 0.00387 (12014) covalent geometry : angle 0.61857 (16277) hydrogen bonds : bond 0.03232 ( 344) hydrogen bonds : angle 5.92624 ( 891) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2675.42 seconds wall clock time: 46 minutes 46.07 seconds (2806.07 seconds total)