Starting phenix.real_space_refine on Sun Aug 24 04:20:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i81_52704/08_2025/9i81_52704_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i81_52704/08_2025/9i81_52704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9i81_52704/08_2025/9i81_52704_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i81_52704/08_2025/9i81_52704_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i81_52704/08_2025/9i81_52704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i81_52704/08_2025/9i81_52704.map" } resolution = 2.98 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= 0.001 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: 5 Type Number sf(0) Gaussians S 66 5.16 5 C 5610 2.51 5 N 1443 2.21 5 O 1628 1.98 5 H 8410 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 17157 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 13552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 13552 Classifications: {'peptide': 859} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 829} Chain breaks: 4 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1731 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1113 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain: "D" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 635 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 126 Unusual residues: {'6CJ': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.51, per 1000 atoms: 0.20 Number of scatterers: 17157 At special positions: 0 Unit cell: (83.4, 94.242, 120.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 O 1628 8.00 N 1443 7.00 C 5610 6.00 H 8410 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 306 " distance=2.04 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 645 " 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: 1.57 Conformation dependent library (CDL) restraints added in 515.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2084 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 10 sheets defined 52.7% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 77 through 90 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.602A pdb=" N LYS A 159 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 248 Proline residue: A 243 - end of helix removed outlier: 3.962A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 256 removed outlier: 4.402A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.840A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.743A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 385 removed outlier: 4.454A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.579A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 4.021A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.635A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 718 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.579A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.534A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 867 removed outlier: 3.902A pdb=" N MET A 855 " --> pdb=" O ASP A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 895 removed outlier: 3.971A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 924 removed outlier: 3.988A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 118 through 125 removed outlier: 4.022A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 143 removed outlier: 3.696A pdb=" N TYR B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'C' and resid 3 through 20 removed outlier: 3.610A pdb=" N GLN C 19 " --> pdb=" O SER C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 25 through 42 Processing helix chain 'C' and resid 44 through 62 removed outlier: 4.002A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 99 Processing helix chain 'D' and resid 100 through 112 removed outlier: 4.173A pdb=" N ASP D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 100 Processing sheet with id=AA3, first strand: chain 'A' and resid 201 through 202 removed outlier: 3.556A pdb=" N VAL A 202 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 354 removed outlier: 6.510A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 387 through 390 removed outlier: 3.993A pdb=" N THR B 187 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLN B 158 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 387 through 390 removed outlier: 3.993A pdb=" N THR B 187 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLN B 158 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL B 159 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 397 through 400 removed outlier: 6.457A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA9, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AB1, first strand: chain 'A' and resid 816 through 821 437 hydrogen bonds defined for protein. 1203 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: 4.19 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 8078 1.04 - 1.24: 1391 1.24 - 1.44: 2889 1.44 - 1.63: 4904 1.63 - 1.83: 102 Bond restraints: 17364 Sorted by residual: bond pdb=" C LYS B 139 " pdb=" N ASN B 140 " ideal model delta sigma weight residual 1.332 1.211 0.121 1.52e-02 4.33e+03 6.30e+01 bond pdb=" CE3 TRP B 154 " pdb=" HE3 TRP B 154 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" NE1 TRP B 154 " pdb=" HE1 TRP B 154 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N LEU B 184 " pdb=" H LEU B 184 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" N ASP B 161 " pdb=" H ASP B 161 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 ... (remaining 17359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 30788 2.47 - 4.95: 323 4.95 - 7.42: 77 7.42 - 9.89: 1 9.89 - 12.37: 1 Bond angle restraints: 31190 Sorted by residual: angle pdb=" O LYS B 139 " pdb=" C LYS B 139 " pdb=" N ASN B 140 " ideal model delta sigma weight residual 122.09 127.03 -4.94 1.04e+00 9.25e-01 2.25e+01 angle pdb=" OE1 GLN B 158 " pdb=" CD GLN B 158 " pdb=" NE2 GLN B 158 " ideal model delta sigma weight residual 122.60 117.97 4.63 1.00e+00 1.00e+00 2.14e+01 angle pdb=" OE1 GLN B 157 " pdb=" CD GLN B 157 " pdb=" NE2 GLN B 157 " ideal model delta sigma weight residual 122.60 118.15 4.45 1.00e+00 1.00e+00 1.98e+01 angle pdb=" CA ASP B 161 " pdb=" CB ASP B 161 " pdb=" CG ASP B 161 " ideal model delta sigma weight residual 112.60 117.03 -4.43 1.00e+00 1.00e+00 1.96e+01 angle pdb=" CA LYS B 139 " pdb=" C LYS B 139 " pdb=" N ASN B 140 " ideal model delta sigma weight residual 116.97 111.86 5.11 1.20e+00 6.94e-01 1.82e+01 ... (remaining 31185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.73: 7873 23.73 - 47.46: 340 47.46 - 71.19: 81 71.19 - 94.92: 19 94.92 - 118.65: 13 Dihedral angle restraints: 8326 sinusoidal: 4439 harmonic: 3887 Sorted by residual: dihedral pdb=" CA PRO A 612 " pdb=" C PRO A 612 " pdb=" N HIS A 613 " pdb=" CA HIS A 613 " ideal model delta harmonic sigma weight residual 180.00 155.72 24.28 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CB CYS A 487 " pdb=" SG CYS A 487 " pdb=" SG CYS A 645 " pdb=" CB CYS A 645 " ideal model delta sinusoidal sigma weight residual 93.00 54.87 38.13 1 1.00e+01 1.00e-02 2.05e+01 dihedral pdb=" CA TYR A 606 " pdb=" C TYR A 606 " pdb=" N SER A 607 " pdb=" CA SER A 607 " ideal model delta harmonic sigma weight residual -180.00 -159.76 -20.24 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 8323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.029: 1359 1.029 - 2.059: 0 2.059 - 3.088: 0 3.088 - 4.118: 0 4.118 - 5.147: 3 Chirality restraints: 1362 Sorted by residual: chirality pdb=" C9 6CJ A1002 " pdb=" C10 6CJ A1002 " pdb=" C14 6CJ A1002 " pdb=" O3 6CJ A1002 " both_signs ideal model delta sigma weight residual False -2.51 2.64 -5.15 2.00e-01 2.50e+01 6.62e+02 chirality pdb=" C9 6CJ A1003 " pdb=" C10 6CJ A1003 " pdb=" C14 6CJ A1003 " pdb=" O3 6CJ A1003 " both_signs ideal model delta sigma weight residual False -2.51 2.61 -5.12 2.00e-01 2.50e+01 6.55e+02 chirality pdb=" C9 6CJ A1001 " pdb=" C10 6CJ A1001 " pdb=" C14 6CJ A1001 " pdb=" O3 6CJ A1001 " both_signs ideal model delta sigma weight residual False -2.51 2.60 -5.11 2.00e-01 2.50e+01 6.53e+02 ... (remaining 1359 not shown) Planarity restraints: 2581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C15 6CJ A1003 " 0.054 2.00e-02 2.50e+03 1.25e-01 6.64e+02 pdb=" C16 6CJ A1003 " 0.115 2.00e-02 2.50e+03 pdb=" C17 6CJ A1003 " 0.120 2.00e-02 2.50e+03 pdb=" C18 6CJ A1003 " -0.081 2.00e-02 2.50e+03 pdb=" C19 6CJ A1003 " -0.167 2.00e-02 2.50e+03 pdb=" C2 6CJ A1003 " -0.046 2.00e-02 2.50e+03 pdb=" C20 6CJ A1003 " -0.193 2.00e-02 2.50e+03 pdb=" C3 6CJ A1003 " -0.049 2.00e-02 2.50e+03 pdb=" C4 6CJ A1003 " 0.106 2.00e-02 2.50e+03 pdb=" C5 6CJ A1003 " 0.063 2.00e-02 2.50e+03 pdb=" C6 6CJ A1003 " -0.052 2.00e-02 2.50e+03 pdb=" C7 6CJ A1003 " -0.117 2.00e-02 2.50e+03 pdb=" C8 6CJ A1003 " -0.059 2.00e-02 2.50e+03 pdb=" N1 6CJ A1003 " 0.139 2.00e-02 2.50e+03 pdb=" O3 6CJ A1003 " -0.173 2.00e-02 2.50e+03 pdb=" O4 6CJ A1003 " 0.261 2.00e-02 2.50e+03 pdb=" S 6CJ A1003 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 6CJ A1002 " 0.055 2.00e-02 2.50e+03 1.08e-01 4.98e+02 pdb=" C16 6CJ A1002 " -0.045 2.00e-02 2.50e+03 pdb=" C17 6CJ A1002 " -0.067 2.00e-02 2.50e+03 pdb=" C18 6CJ A1002 " 0.004 2.00e-02 2.50e+03 pdb=" C19 6CJ A1002 " 0.099 2.00e-02 2.50e+03 pdb=" C2 6CJ A1002 " 0.182 2.00e-02 2.50e+03 pdb=" C20 6CJ A1002 " -0.034 2.00e-02 2.50e+03 pdb=" C3 6CJ A1002 " 0.093 2.00e-02 2.50e+03 pdb=" C4 6CJ A1002 " -0.012 2.00e-02 2.50e+03 pdb=" C5 6CJ A1002 " -0.124 2.00e-02 2.50e+03 pdb=" C6 6CJ A1002 " -0.113 2.00e-02 2.50e+03 pdb=" C7 6CJ A1002 " -0.005 2.00e-02 2.50e+03 pdb=" C8 6CJ A1002 " 0.066 2.00e-02 2.50e+03 pdb=" N1 6CJ A1002 " -0.019 2.00e-02 2.50e+03 pdb=" O3 6CJ A1002 " 0.234 2.00e-02 2.50e+03 pdb=" O4 6CJ A1002 " -0.173 2.00e-02 2.50e+03 pdb=" S 6CJ A1002 " -0.138 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 6CJ A1001 " -0.033 2.00e-02 2.50e+03 5.59e-02 1.33e+02 pdb=" C16 6CJ A1001 " -0.046 2.00e-02 2.50e+03 pdb=" C17 6CJ A1001 " -0.048 2.00e-02 2.50e+03 pdb=" C18 6CJ A1001 " 0.035 2.00e-02 2.50e+03 pdb=" C19 6CJ A1001 " 0.065 2.00e-02 2.50e+03 pdb=" C2 6CJ A1001 " 0.029 2.00e-02 2.50e+03 pdb=" C20 6CJ A1001 " 0.099 2.00e-02 2.50e+03 pdb=" C3 6CJ A1001 " 0.006 2.00e-02 2.50e+03 pdb=" C4 6CJ A1001 " -0.084 2.00e-02 2.50e+03 pdb=" C5 6CJ A1001 " -0.008 2.00e-02 2.50e+03 pdb=" C6 6CJ A1001 " 0.058 2.00e-02 2.50e+03 pdb=" C7 6CJ A1001 " 0.071 2.00e-02 2.50e+03 pdb=" C8 6CJ A1001 " 0.011 2.00e-02 2.50e+03 pdb=" N1 6CJ A1001 " -0.077 2.00e-02 2.50e+03 pdb=" O3 6CJ A1001 " 0.044 2.00e-02 2.50e+03 pdb=" O4 6CJ A1001 " -0.081 2.00e-02 2.50e+03 pdb=" S 6CJ A1001 " -0.040 2.00e-02 2.50e+03 ... (remaining 2578 not shown) Histogram of nonbonded interaction distances: 1.21 - 1.89: 70 1.89 - 2.57: 16274 2.57 - 3.24: 53058 3.24 - 3.92: 67249 3.92 - 4.60: 106379 Nonbonded interactions: 243030 Sorted by model distance: nonbonded pdb=" HE1 TYR B 135 " pdb="HG21 ILE B 172 " model vdw 1.212 2.270 nonbonded pdb=" OE1 GLU A 665 " pdb=" H GLU A 665 " model vdw 1.501 2.450 nonbonded pdb=" HH TYR A 294 " pdb=" OD1 ASN A 314 " model vdw 1.560 2.450 nonbonded pdb="HH12 ARG A 836 " pdb=" O 6CJ A1002 " model vdw 1.575 2.450 nonbonded pdb=" O ASP A 235 " pdb=" HG SER A 239 " model vdw 1.582 2.450 ... (remaining 243025 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 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.310 Find NCS groups from input model: 0.060 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:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 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 : 0.005 0.121 8956 Z= 0.267 Angle : 0.715 7.802 12174 Z= 0.391 Chirality : 0.245 5.147 1362 Planarity : 0.006 0.125 1539 Dihedral : 14.905 118.649 3279 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.09 (0.26), residues: 1068 helix: 0.62 (0.23), residues: 503 sheet: -0.85 (0.50), residues: 109 loop : -0.18 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.077 0.002 TYR B 149 PHE 0.013 0.001 PHE C 49 TRP 0.100 0.006 TRP B 182 HIS 0.010 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 8954) covalent geometry : angle 0.71446 (12170) SS BOND : bond 0.00833 ( 2) SS BOND : angle 1.62210 ( 4) hydrogen bonds : bond 0.22769 ( 425) hydrogen bonds : angle 7.31762 ( 1203) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.8460 (pt) cc_final: 0.8198 (pp) REVERT: B 112 ASP cc_start: 0.7309 (p0) cc_final: 0.6974 (p0) REVERT: B 151 SER cc_start: 0.8635 (t) cc_final: 0.8375 (t) REVERT: C 34 GLN cc_start: 0.7904 (tp40) cc_final: 0.7144 (OUTLIER) outliers start: 0 outliers final: 1 residues processed: 134 average time/residue: 1.1957 time to fit residues: 172.4041 Evaluate side-chains 92 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 GLN B 108 ASN B 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.113499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.086754 restraints weight = 44556.689| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.54 r_work: 0.3027 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8956 Z= 0.172 Angle : 0.565 7.173 12174 Z= 0.302 Chirality : 0.041 0.154 1362 Planarity : 0.004 0.034 1539 Dihedral : 7.942 90.348 1304 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.16 % Allowed : 8.03 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.34 (0.26), residues: 1068 helix: 1.09 (0.23), residues: 514 sheet: -0.91 (0.50), residues: 96 loop : -0.41 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 735 TYR 0.011 0.001 TYR A 884 PHE 0.014 0.001 PHE A 753 TRP 0.009 0.001 TRP A 290 HIS 0.010 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8954) covalent geometry : angle 0.56473 (12170) SS BOND : bond 0.00743 ( 2) SS BOND : angle 1.66939 ( 4) hydrogen bonds : bond 0.05229 ( 425) hydrogen bonds : angle 5.00376 ( 1203) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.8017 (pt) cc_final: 0.7726 (pp) REVERT: B 112 ASP cc_start: 0.7777 (p0) cc_final: 0.7369 (p0) REVERT: B 151 SER cc_start: 0.9106 (t) cc_final: 0.8881 (t) REVERT: C 34 GLN cc_start: 0.8035 (tp40) cc_final: 0.7647 (tp40) REVERT: C 47 GLU cc_start: 0.7996 (mp0) cc_final: 0.7537 (mp0) REVERT: D 90 MET cc_start: 0.7647 (mmp) cc_final: 0.7080 (ttp) outliers start: 11 outliers final: 6 residues processed: 107 average time/residue: 1.1817 time to fit residues: 136.6494 Evaluate side-chains 97 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain C residue 50 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 24 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 58 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 543 ASN A 568 ASN ** A 705 ASN ** 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 = 0.3613 r_free = 0.3613 target = 0.115714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.089555 restraints weight = 44509.291| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.50 r_work: 0.3091 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8956 Z= 0.108 Angle : 0.494 6.182 12174 Z= 0.259 Chirality : 0.039 0.150 1362 Planarity : 0.003 0.032 1539 Dihedral : 6.868 85.539 1304 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.48 % Allowed : 8.35 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.75 (0.26), residues: 1068 helix: 1.53 (0.24), residues: 507 sheet: -0.89 (0.48), residues: 96 loop : -0.27 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 553 TYR 0.009 0.001 TYR A 674 PHE 0.014 0.001 PHE A 753 TRP 0.007 0.001 TRP A 290 HIS 0.008 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8954) covalent geometry : angle 0.49346 (12170) SS BOND : bond 0.00458 ( 2) SS BOND : angle 1.21570 ( 4) hydrogen bonds : bond 0.03780 ( 425) hydrogen bonds : angle 4.45065 ( 1203) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.8029 (pt) cc_final: 0.7749 (pp) REVERT: B 83 VAL cc_start: 0.8054 (p) cc_final: 0.7785 (m) REVERT: B 112 ASP cc_start: 0.7766 (p0) cc_final: 0.7381 (p0) REVERT: B 151 SER cc_start: 0.9149 (t) cc_final: 0.8937 (t) REVERT: C 34 GLN cc_start: 0.8105 (tp40) cc_final: 0.7711 (tp40) REVERT: C 47 GLU cc_start: 0.8089 (mp0) cc_final: 0.7684 (mp0) outliers start: 14 outliers final: 5 residues processed: 117 average time/residue: 1.1091 time to fit residues: 140.4448 Evaluate side-chains 104 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain C residue 50 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 83 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 543 ASN A 705 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.113586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.086510 restraints weight = 44679.308| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.57 r_work: 0.3021 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8956 Z= 0.180 Angle : 0.526 7.175 12174 Z= 0.279 Chirality : 0.040 0.149 1362 Planarity : 0.003 0.032 1539 Dihedral : 6.867 87.272 1304 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.59 % Allowed : 10.04 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.61 (0.26), residues: 1068 helix: 1.38 (0.24), residues: 510 sheet: -0.91 (0.48), residues: 96 loop : -0.32 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 467 TYR 0.012 0.001 TYR A 653 PHE 0.016 0.001 PHE A 741 TRP 0.012 0.001 TRP A 290 HIS 0.008 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 8954) covalent geometry : angle 0.52517 (12170) SS BOND : bond 0.00715 ( 2) SS BOND : angle 1.72817 ( 4) hydrogen bonds : bond 0.04150 ( 425) hydrogen bonds : angle 4.43123 ( 1203) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.7948 (pt) cc_final: 0.7659 (pp) REVERT: B 83 VAL cc_start: 0.8043 (p) cc_final: 0.7774 (m) REVERT: B 112 ASP cc_start: 0.7822 (p0) cc_final: 0.7444 (p0) REVERT: B 151 SER cc_start: 0.9177 (t) cc_final: 0.8972 (t) REVERT: C 47 GLU cc_start: 0.8112 (mp0) cc_final: 0.7618 (mp0) outliers start: 15 outliers final: 8 residues processed: 110 average time/residue: 1.0118 time to fit residues: 120.6819 Evaluate side-chains 103 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain C residue 50 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 102 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 722 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.114107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.087674 restraints weight = 44344.446| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.53 r_work: 0.3039 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8956 Z= 0.137 Angle : 0.500 6.579 12174 Z= 0.263 Chirality : 0.039 0.142 1362 Planarity : 0.003 0.033 1539 Dihedral : 6.771 86.034 1304 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.48 % Allowed : 10.36 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.70 (0.26), residues: 1068 helix: 1.49 (0.24), residues: 508 sheet: -0.86 (0.48), residues: 96 loop : -0.31 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 569 TYR 0.010 0.001 TYR A 289 PHE 0.014 0.001 PHE A 741 TRP 0.010 0.001 TRP A 290 HIS 0.005 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8954) covalent geometry : angle 0.49908 (12170) SS BOND : bond 0.00584 ( 2) SS BOND : angle 1.46775 ( 4) hydrogen bonds : bond 0.03727 ( 425) hydrogen bonds : angle 4.30327 ( 1203) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.7908 (pt) cc_final: 0.7611 (pp) REVERT: B 83 VAL cc_start: 0.8012 (p) cc_final: 0.7742 (m) REVERT: B 112 ASP cc_start: 0.7817 (p0) cc_final: 0.7417 (p0) REVERT: B 151 SER cc_start: 0.9197 (t) cc_final: 0.8984 (t) REVERT: C 34 GLN cc_start: 0.7973 (tp40) cc_final: 0.7593 (tp40) REVERT: C 47 GLU cc_start: 0.8111 (mp0) cc_final: 0.7658 (mp0) REVERT: D 90 MET cc_start: 0.7471 (mmp) cc_final: 0.6937 (ttt) outliers start: 14 outliers final: 9 residues processed: 108 average time/residue: 1.0542 time to fit residues: 123.2175 Evaluate side-chains 105 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain C residue 50 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 68 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.113864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.086927 restraints weight = 44439.234| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.56 r_work: 0.3029 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8956 Z= 0.154 Angle : 0.511 6.798 12174 Z= 0.269 Chirality : 0.040 0.153 1362 Planarity : 0.003 0.033 1539 Dihedral : 6.719 85.713 1304 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.90 % Allowed : 10.68 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.68 (0.26), residues: 1068 helix: 1.43 (0.24), residues: 510 sheet: -0.50 (0.50), residues: 87 loop : -0.39 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 569 TYR 0.010 0.001 TYR A 732 PHE 0.016 0.001 PHE A 741 TRP 0.010 0.001 TRP A 290 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8954) covalent geometry : angle 0.50988 (12170) SS BOND : bond 0.00648 ( 2) SS BOND : angle 1.59552 ( 4) hydrogen bonds : bond 0.03802 ( 425) hydrogen bonds : angle 4.27546 ( 1203) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: A 223 ILE cc_start: 0.7910 (pt) cc_final: 0.7616 (pp) REVERT: B 83 VAL cc_start: 0.8041 (p) cc_final: 0.7763 (m) REVERT: B 112 ASP cc_start: 0.7798 (p0) cc_final: 0.7408 (p0) REVERT: B 151 SER cc_start: 0.9185 (t) cc_final: 0.8982 (t) REVERT: B 169 LEU cc_start: 0.8139 (mm) cc_final: 0.7918 (mm) REVERT: C 47 GLU cc_start: 0.8161 (mp0) cc_final: 0.7693 (mp0) REVERT: D 90 MET cc_start: 0.7468 (mmp) cc_final: 0.6829 (ttp) outliers start: 18 outliers final: 9 residues processed: 110 average time/residue: 0.9350 time to fit residues: 112.7384 Evaluate side-chains 103 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain C residue 50 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 83 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 102 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.113300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.086841 restraints weight = 44522.251| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.53 r_work: 0.3027 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8956 Z= 0.165 Angle : 0.518 6.958 12174 Z= 0.274 Chirality : 0.040 0.164 1362 Planarity : 0.003 0.034 1539 Dihedral : 6.718 85.973 1304 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.01 % Allowed : 9.83 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.64 (0.26), residues: 1068 helix: 1.39 (0.24), residues: 510 sheet: -0.52 (0.50), residues: 87 loop : -0.40 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 836 TYR 0.010 0.001 TYR A 732 PHE 0.017 0.001 PHE A 741 TRP 0.010 0.001 TRP A 290 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 8954) covalent geometry : angle 0.51740 (12170) SS BOND : bond 0.00685 ( 2) SS BOND : angle 1.65892 ( 4) hydrogen bonds : bond 0.03863 ( 425) hydrogen bonds : angle 4.28959 ( 1203) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.6906 (ttm-80) cc_final: 0.6645 (ttm-80) REVERT: A 144 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: A 223 ILE cc_start: 0.7841 (pt) cc_final: 0.7534 (pp) REVERT: B 83 VAL cc_start: 0.8010 (p) cc_final: 0.7730 (m) REVERT: B 112 ASP cc_start: 0.7820 (p0) cc_final: 0.7407 (p0) REVERT: B 169 LEU cc_start: 0.8178 (mm) cc_final: 0.7959 (mm) REVERT: C 47 GLU cc_start: 0.8161 (mp0) cc_final: 0.7675 (mp0) REVERT: D 90 MET cc_start: 0.7495 (mmp) cc_final: 0.6860 (ttp) outliers start: 19 outliers final: 10 residues processed: 108 average time/residue: 0.9559 time to fit residues: 112.4739 Evaluate side-chains 103 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain C residue 50 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 46 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.113331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.086332 restraints weight = 44841.135| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.58 r_work: 0.3020 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8956 Z= 0.179 Angle : 0.530 8.109 12174 Z= 0.281 Chirality : 0.040 0.169 1362 Planarity : 0.003 0.035 1539 Dihedral : 6.748 86.635 1304 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.59 % Allowed : 10.89 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.55 (0.26), residues: 1068 helix: 1.32 (0.24), residues: 509 sheet: -0.54 (0.50), residues: 87 loop : -0.45 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 569 TYR 0.011 0.001 TYR A 732 PHE 0.017 0.001 PHE A 741 TRP 0.011 0.001 TRP A 290 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 8954) covalent geometry : angle 0.52869 (12170) SS BOND : bond 0.01369 ( 2) SS BOND : angle 2.10650 ( 4) hydrogen bonds : bond 0.03961 ( 425) hydrogen bonds : angle 4.30263 ( 1203) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.7898 (pt) cc_final: 0.7611 (pp) REVERT: B 112 ASP cc_start: 0.7811 (p0) cc_final: 0.7418 (p0) REVERT: B 169 LEU cc_start: 0.8205 (mm) cc_final: 0.7987 (mm) REVERT: C 47 GLU cc_start: 0.8182 (mp0) cc_final: 0.7648 (mp0) REVERT: D 89 THR cc_start: 0.7873 (p) cc_final: 0.7653 (p) REVERT: D 90 MET cc_start: 0.7495 (mmp) cc_final: 0.6862 (ttp) REVERT: D 129 MET cc_start: 0.3926 (OUTLIER) cc_final: 0.3504 (tpt) outliers start: 15 outliers final: 11 residues processed: 101 average time/residue: 1.0650 time to fit residues: 117.2385 Evaluate side-chains 103 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 129 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 106 optimal weight: 0.0570 chunk 54 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 543 ASN A 773 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.115696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.089003 restraints weight = 44592.487| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.56 r_work: 0.3060 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8956 Z= 0.100 Angle : 0.484 8.028 12174 Z= 0.254 Chirality : 0.039 0.180 1362 Planarity : 0.003 0.035 1539 Dihedral : 6.565 83.845 1304 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.27 % Allowed : 11.42 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.86 (0.26), residues: 1068 helix: 1.68 (0.24), residues: 506 sheet: -0.54 (0.48), residues: 87 loop : -0.37 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 640 TYR 0.007 0.001 TYR A 149 PHE 0.013 0.001 PHE A 753 TRP 0.005 0.001 TRP A 290 HIS 0.004 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 8954) covalent geometry : angle 0.48384 (12170) SS BOND : bond 0.00788 ( 2) SS BOND : angle 1.46884 ( 4) hydrogen bonds : bond 0.03253 ( 425) hydrogen bonds : angle 4.10792 ( 1203) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.6962 (ttm-80) cc_final: 0.6683 (ttm-80) REVERT: B 112 ASP cc_start: 0.7779 (p0) cc_final: 0.7405 (p0) REVERT: B 169 LEU cc_start: 0.8175 (mm) cc_final: 0.7942 (mm) REVERT: C 47 GLU cc_start: 0.8170 (mp0) cc_final: 0.7683 (mp0) REVERT: D 90 MET cc_start: 0.7499 (mmp) cc_final: 0.6980 (ttt) REVERT: D 129 MET cc_start: 0.3803 (ppp) cc_final: 0.3523 (tpt) outliers start: 12 outliers final: 7 residues processed: 103 average time/residue: 1.0769 time to fit residues: 120.6972 Evaluate side-chains 97 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain C residue 50 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN D 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.114232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.087296 restraints weight = 44287.335| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.58 r_work: 0.3034 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8956 Z= 0.149 Angle : 0.512 7.649 12174 Z= 0.271 Chirality : 0.040 0.139 1362 Planarity : 0.003 0.033 1539 Dihedral : 6.621 84.780 1304 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.95 % Allowed : 12.16 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.77 (0.26), residues: 1068 helix: 1.55 (0.24), residues: 509 sheet: -0.52 (0.49), residues: 87 loop : -0.38 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 836 TYR 0.010 0.001 TYR A 289 PHE 0.016 0.001 PHE A 741 TRP 0.010 0.001 TRP A 290 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8954) covalent geometry : angle 0.51150 (12170) SS BOND : bond 0.00857 ( 2) SS BOND : angle 1.82201 ( 4) hydrogen bonds : bond 0.03643 ( 425) hydrogen bonds : angle 4.18209 ( 1203) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.6966 (ttm-80) cc_final: 0.6680 (ttm-80) REVERT: B 112 ASP cc_start: 0.7788 (p0) cc_final: 0.7395 (p0) REVERT: B 169 LEU cc_start: 0.8142 (mm) cc_final: 0.7910 (mm) REVERT: C 47 GLU cc_start: 0.8184 (mp0) cc_final: 0.7677 (mp0) REVERT: D 89 THR cc_start: 0.7785 (p) cc_final: 0.7576 (p) REVERT: D 90 MET cc_start: 0.7539 (mmp) cc_final: 0.6964 (ttt) REVERT: D 129 MET cc_start: 0.3886 (ppp) cc_final: 0.3553 (tpt) outliers start: 9 outliers final: 7 residues processed: 99 average time/residue: 1.1191 time to fit residues: 120.1178 Evaluate side-chains 98 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain C residue 50 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 43 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 61 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 chunk 2 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.115864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.088866 restraints weight = 44612.396| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.63 r_work: 0.3063 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8956 Z= 0.101 Angle : 0.479 7.515 12174 Z= 0.252 Chirality : 0.039 0.140 1362 Planarity : 0.003 0.034 1539 Dihedral : 6.514 83.331 1304 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.95 % Allowed : 12.47 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.90 (0.26), residues: 1068 helix: 1.67 (0.24), residues: 514 sheet: -0.55 (0.48), residues: 87 loop : -0.33 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.007 0.001 TYR A 149 PHE 0.014 0.001 PHE C 49 TRP 0.006 0.001 TRP B 154 HIS 0.003 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8954) covalent geometry : angle 0.47866 (12170) SS BOND : bond 0.00623 ( 2) SS BOND : angle 1.37555 ( 4) hydrogen bonds : bond 0.03159 ( 425) hydrogen bonds : angle 4.06440 ( 1203) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5495.19 seconds wall clock time: 93 minutes 57.65 seconds (5637.65 seconds total)