Starting phenix.real_space_refine on Sun May 18 11:36:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i81_52704/05_2025/9i81_52704_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i81_52704/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9i81_52704/05_2025/9i81_52704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i81_52704/05_2025/9i81_52704.map" model { file = "/net/cci-nas-00/data/ceres_data/9i81_52704/05_2025/9i81_52704_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i81_52704/05_2025/9i81_52704_trim.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'GLU:plan': 1, 'ARG:plan': 2, '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: {'ARG:plan': 1, 'ASP: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: 8.77, per 1000 atoms: 0.51 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: 5.15 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.36 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: 6.40 Time building geometry restraints manager: 6.04 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: 0.640 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: 0.280 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 39.280 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 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:10.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.960 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.26), 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 TRP 0.100 0.006 TRP B 182 HIS 0.010 0.001 HIS A 613 PHE 0.013 0.001 PHE C 49 TYR 0.077 0.002 TYR B 149 ARG 0.005 0.000 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.22769 ( 425) hydrogen bonds : angle 7.31762 ( 1203) SS BOND : bond 0.00833 ( 2) SS BOND : angle 1.62210 ( 4) covalent geometry : bond 0.00523 ( 8954) covalent geometry : angle 0.71446 (12170) *********************** 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 : 1.447 Fit side-chains 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: 0.6970 (p0) REVERT: B 151 SER cc_start: 0.8635 (t) cc_final: 0.8376 (t) REVERT: C 34 GLN cc_start: 0.7904 (tp40) cc_final: 0.7163 (OUTLIER) outliers start: 0 outliers final: 1 residues processed: 134 average time/residue: 2.1515 time to fit residues: 312.2229 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 : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 ASN A 822 GLN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.112531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.085750 restraints weight = 44612.422| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.53 r_work: 0.3009 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8956 Z= 0.220 Angle : 0.586 5.905 12174 Z= 0.314 Chirality : 0.042 0.155 1362 Planarity : 0.004 0.035 1539 Dihedral : 8.091 92.137 1304 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.37 % Allowed : 8.14 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.26), residues: 1068 helix: 0.97 (0.23), residues: 514 sheet: -0.88 (0.48), residues: 109 loop : -0.47 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 290 HIS 0.010 0.001 HIS A 613 PHE 0.014 0.001 PHE A 652 TYR 0.011 0.001 TYR A 884 ARG 0.003 0.001 ARG A 735 Details of bonding type rmsd hydrogen bonds : bond 0.05453 ( 425) hydrogen bonds : angle 5.04437 ( 1203) SS BOND : bond 0.00860 ( 2) SS BOND : angle 1.91960 ( 4) covalent geometry : bond 0.00492 ( 8954) covalent geometry : angle 0.58555 (12170) *********************** 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 112 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.7025 (ttm-80) cc_final: 0.6764 (ttm-80) REVERT: A 223 ILE cc_start: 0.8010 (pt) cc_final: 0.7676 (pp) REVERT: B 112 ASP cc_start: 0.7808 (p0) cc_final: 0.7420 (p0) REVERT: B 151 SER cc_start: 0.9109 (t) cc_final: 0.8904 (t) REVERT: C 34 GLN cc_start: 0.8037 (tp40) cc_final: 0.7704 (tp40) REVERT: C 47 GLU cc_start: 0.8025 (mp0) cc_final: 0.7532 (mp0) REVERT: D 90 MET cc_start: 0.7650 (mmp) cc_final: 0.7084 (ttp) outliers start: 13 outliers final: 6 residues processed: 108 average time/residue: 2.1129 time to fit residues: 247.7271 Evaluate side-chains 98 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 1.393 ------------------------------------------------------------------------------- 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 40 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 568 ASN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.114301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.087585 restraints weight = 44098.846| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.55 r_work: 0.3041 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8956 Z= 0.137 Angle : 0.515 7.183 12174 Z= 0.272 Chirality : 0.039 0.142 1362 Planarity : 0.003 0.035 1539 Dihedral : 7.065 89.197 1304 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.80 % Allowed : 7.93 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.26), residues: 1068 helix: 1.31 (0.24), residues: 509 sheet: -1.01 (0.48), residues: 96 loop : -0.36 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 290 HIS 0.008 0.001 HIS A 613 PHE 0.014 0.001 PHE A 753 TYR 0.009 0.001 TYR A 289 ARG 0.002 0.000 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 425) hydrogen bonds : angle 4.55345 ( 1203) SS BOND : bond 0.00592 ( 2) SS BOND : angle 1.48851 ( 4) covalent geometry : bond 0.00306 ( 8954) covalent geometry : angle 0.51486 (12170) *********************** 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 123 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.7945 (pt) cc_final: 0.7620 (pp) REVERT: B 83 VAL cc_start: 0.8009 (p) cc_final: 0.7727 (m) REVERT: B 112 ASP cc_start: 0.7772 (p0) cc_final: 0.7348 (p0) REVERT: B 151 SER cc_start: 0.9149 (t) cc_final: 0.8934 (t) REVERT: B 165 LYS cc_start: 0.7558 (mptt) cc_final: 0.7343 (tttm) REVERT: C 34 GLN cc_start: 0.8028 (tp40) cc_final: 0.7644 (tp40) REVERT: C 47 GLU cc_start: 0.8076 (mp0) cc_final: 0.7632 (mp0) REVERT: C 62 MET cc_start: 0.8073 (ttt) cc_final: 0.7869 (ttp) outliers start: 17 outliers final: 7 residues processed: 117 average time/residue: 2.0559 time to fit residues: 261.2586 Evaluate side-chains 106 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 1.405 ------------------------------------------------------------------------------- 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 447 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 92 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.112409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.085659 restraints weight = 44494.963| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.47 r_work: 0.2993 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 8956 Z= 0.250 Angle : 0.573 7.829 12174 Z= 0.307 Chirality : 0.042 0.194 1362 Planarity : 0.004 0.037 1539 Dihedral : 7.211 92.041 1304 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.26), residues: 1068 helix: 1.02 (0.23), residues: 509 sheet: -1.00 (0.47), residues: 109 loop : -0.49 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 290 HIS 0.011 0.001 HIS C 36 PHE 0.019 0.002 PHE A 741 TYR 0.014 0.002 TYR A 653 ARG 0.003 0.001 ARG A 467 Details of bonding type rmsd hydrogen bonds : bond 0.04741 ( 425) hydrogen bonds : angle 4.63523 ( 1203) SS BOND : bond 0.00942 ( 2) SS BOND : angle 2.19431 ( 4) covalent geometry : bond 0.00565 ( 8954) covalent geometry : angle 0.57176 (12170) *********************** 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 118 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.7961 (pt) cc_final: 0.7639 (pp) REVERT: B 83 VAL cc_start: 0.8078 (p) cc_final: 0.7796 (m) REVERT: B 96 ARG cc_start: 0.8188 (mmt-90) cc_final: 0.7846 (mmt-90) REVERT: B 109 ASN cc_start: 0.7829 (m-40) cc_final: 0.7433 (m110) REVERT: B 112 ASP cc_start: 0.7820 (p0) cc_final: 0.7454 (p0) REVERT: B 151 SER cc_start: 0.9173 (t) cc_final: 0.8972 (t) REVERT: B 169 LEU cc_start: 0.8073 (mm) cc_final: 0.7869 (mm) REVERT: C 34 GLN cc_start: 0.8057 (tp40) cc_final: 0.7783 (tp40) REVERT: C 47 GLU cc_start: 0.8041 (mp0) cc_final: 0.7584 (mp0) outliers start: 19 outliers final: 10 residues processed: 112 average time/residue: 1.9429 time to fit residues: 237.5633 Evaluate side-chains 107 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 60 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 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 381 HIS ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.113570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.086730 restraints weight = 44867.210| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.56 r_work: 0.3024 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8956 Z= 0.141 Angle : 0.516 6.811 12174 Z= 0.272 Chirality : 0.040 0.141 1362 Planarity : 0.003 0.039 1539 Dihedral : 6.937 89.159 1304 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.26), residues: 1068 helix: 1.22 (0.24), residues: 510 sheet: -0.97 (0.47), residues: 96 loop : -0.43 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 290 HIS 0.005 0.001 HIS C 36 PHE 0.015 0.001 PHE A 753 TYR 0.009 0.001 TYR A 732 ARG 0.001 0.000 ARG A 467 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 425) hydrogen bonds : angle 4.39808 ( 1203) SS BOND : bond 0.00852 ( 2) SS BOND : angle 1.93344 ( 4) covalent geometry : bond 0.00315 ( 8954) covalent geometry : angle 0.51443 (12170) *********************** 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 115 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: A 223 ILE cc_start: 0.7878 (pt) cc_final: 0.7551 (pp) REVERT: B 83 VAL cc_start: 0.7987 (p) cc_final: 0.7701 (m) REVERT: B 112 ASP cc_start: 0.7835 (p0) cc_final: 0.7461 (p0) REVERT: B 151 SER cc_start: 0.9202 (t) cc_final: 0.8985 (t) REVERT: C 34 GLN cc_start: 0.8007 (tp40) cc_final: 0.7667 (tp40) REVERT: C 47 GLU cc_start: 0.8115 (mp0) cc_final: 0.7605 (mp0) outliers start: 15 outliers final: 9 residues processed: 112 average time/residue: 2.0516 time to fit residues: 249.8417 Evaluate side-chains 107 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 44 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 B 108 ASN D 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.115345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.088597 restraints weight = 44420.173| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.55 r_work: 0.3058 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8956 Z= 0.103 Angle : 0.483 6.849 12174 Z= 0.252 Chirality : 0.039 0.156 1362 Planarity : 0.003 0.035 1539 Dihedral : 6.657 84.266 1304 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.27 % Allowed : 11.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1068 helix: 1.53 (0.24), residues: 507 sheet: -0.60 (0.48), residues: 87 loop : -0.36 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 290 HIS 0.004 0.001 HIS A 613 PHE 0.015 0.001 PHE A 753 TYR 0.007 0.001 TYR A 732 ARG 0.001 0.000 ARG A 624 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 425) hydrogen bonds : angle 4.17002 ( 1203) SS BOND : bond 0.00615 ( 2) SS BOND : angle 1.44973 ( 4) covalent geometry : bond 0.00232 ( 8954) covalent geometry : angle 0.48256 (12170) *********************** 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 113 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.7909 (pt) cc_final: 0.7615 (pp) REVERT: B 83 VAL cc_start: 0.7994 (p) cc_final: 0.7715 (m) REVERT: B 112 ASP cc_start: 0.7776 (p0) cc_final: 0.7388 (p0) REVERT: B 151 SER cc_start: 0.9166 (t) cc_final: 0.8962 (t) REVERT: C 34 GLN cc_start: 0.8010 (tp40) cc_final: 0.7654 (tp40) REVERT: C 47 GLU cc_start: 0.8156 (mp0) cc_final: 0.7689 (mp0) REVERT: D 90 MET cc_start: 0.7508 (mmp) cc_final: 0.6960 (ttt) outliers start: 12 outliers final: 8 residues processed: 109 average time/residue: 1.9349 time to fit residues: 230.5721 Evaluate side-chains 105 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.113192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.086176 restraints weight = 44459.167| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.58 r_work: 0.3015 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2279 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= 0.181 Angle : 0.526 7.124 12174 Z= 0.278 Chirality : 0.040 0.139 1362 Planarity : 0.003 0.035 1539 Dihedral : 6.744 86.400 1304 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.90 % Allowed : 10.89 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.26), residues: 1068 helix: 1.35 (0.24), residues: 509 sheet: -0.65 (0.49), residues: 87 loop : -0.42 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 290 HIS 0.007 0.001 HIS C 36 PHE 0.016 0.001 PHE A 741 TYR 0.011 0.001 TYR A 653 ARG 0.003 0.000 ARG A 467 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 425) hydrogen bonds : angle 4.28546 ( 1203) SS BOND : bond 0.00817 ( 2) SS BOND : angle 1.89835 ( 4) covalent geometry : bond 0.00410 ( 8954) covalent geometry : angle 0.52467 (12170) *********************** 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 117 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: A 223 ILE cc_start: 0.7883 (pt) cc_final: 0.7575 (pp) REVERT: B 109 ASN cc_start: 0.7790 (m-40) cc_final: 0.7417 (m110) REVERT: B 112 ASP cc_start: 0.7795 (p0) cc_final: 0.7393 (p0) REVERT: C 47 GLU cc_start: 0.8166 (mp0) cc_final: 0.7690 (mp0) REVERT: D 90 MET cc_start: 0.7522 (mmp) cc_final: 0.6849 (ttp) outliers start: 18 outliers final: 9 residues processed: 111 average time/residue: 1.9025 time to fit residues: 230.9896 Evaluate side-chains 106 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 1.340 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 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 = 0.114159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.087847 restraints weight = 44570.691| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.50 r_work: 0.3041 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8956 Z= 0.126 Angle : 0.503 8.975 12174 Z= 0.262 Chirality : 0.039 0.139 1362 Planarity : 0.003 0.036 1539 Dihedral : 6.641 85.280 1304 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.27 % Allowed : 12.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1068 helix: 1.52 (0.24), residues: 508 sheet: -0.68 (0.48), residues: 87 loop : -0.37 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 290 HIS 0.004 0.001 HIS C 36 PHE 0.013 0.001 PHE A 652 TYR 0.008 0.001 TYR A 732 ARG 0.001 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 425) hydrogen bonds : angle 4.18707 ( 1203) SS BOND : bond 0.00605 ( 2) SS BOND : angle 1.51556 ( 4) covalent geometry : bond 0.00283 ( 8954) covalent geometry : angle 0.50229 (12170) *********************** 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 111 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 1.352 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: 0.7881 (pt) cc_final: 0.7581 (pp) REVERT: B 112 ASP cc_start: 0.7772 (p0) cc_final: 0.7370 (p0) REVERT: B 169 LEU cc_start: 0.8193 (mm) cc_final: 0.7967 (mm) REVERT: C 47 GLU cc_start: 0.8193 (mp0) cc_final: 0.7705 (mp0) REVERT: D 90 MET cc_start: 0.7541 (mmp) cc_final: 0.6882 (ttp) REVERT: D 129 MET cc_start: 0.3786 (ppp) cc_final: 0.3372 (tpt) outliers start: 12 outliers final: 10 residues processed: 107 average time/residue: 2.0055 time to fit residues: 234.2576 Evaluate side-chains 105 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 89 optimal weight: 0.4980 chunk 92 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.115502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.088837 restraints weight = 44687.051| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.55 r_work: 0.3062 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8956 Z= 0.103 Angle : 0.485 8.429 12174 Z= 0.252 Chirality : 0.039 0.141 1362 Planarity : 0.003 0.034 1539 Dihedral : 6.509 83.642 1304 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.27 % Allowed : 12.68 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.26), residues: 1068 helix: 1.72 (0.24), residues: 506 sheet: -0.69 (0.47), residues: 87 loop : -0.34 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 268 HIS 0.003 0.001 HIS A 613 PHE 0.013 0.001 PHE A 753 TYR 0.007 0.001 TYR A 732 ARG 0.001 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03161 ( 425) hydrogen bonds : angle 4.07698 ( 1203) SS BOND : bond 0.00499 ( 2) SS BOND : angle 1.29038 ( 4) covalent geometry : bond 0.00234 ( 8954) covalent geometry : angle 0.48463 (12170) *********************** 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 108 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.6978 (ttm-80) cc_final: 0.6731 (ttm-80) REVERT: A 223 ILE cc_start: 0.7886 (pt) cc_final: 0.7597 (pp) REVERT: B 112 ASP cc_start: 0.7761 (p0) cc_final: 0.7361 (p0) REVERT: B 165 LYS cc_start: 0.7882 (mptt) cc_final: 0.7608 (tttm) REVERT: B 169 LEU cc_start: 0.8163 (mm) cc_final: 0.7921 (mm) REVERT: C 47 GLU cc_start: 0.8160 (mp0) cc_final: 0.7741 (mp0) REVERT: D 89 THR cc_start: 0.7855 (p) cc_final: 0.7646 (p) REVERT: D 90 MET cc_start: 0.7505 (mmp) cc_final: 0.7004 (ttt) REVERT: D 129 MET cc_start: 0.3781 (ppp) cc_final: 0.3444 (tpt) outliers start: 12 outliers final: 9 residues processed: 105 average time/residue: 1.9713 time to fit residues: 225.4899 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 : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 9 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 D 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.115614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.088717 restraints weight = 44447.388| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.59 r_work: 0.3057 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2660 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= 0.103 Angle : 0.482 8.259 12174 Z= 0.252 Chirality : 0.039 0.145 1362 Planarity : 0.003 0.033 1539 Dihedral : 6.442 84.504 1304 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.06 % Allowed : 13.11 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1068 helix: 1.67 (0.24), residues: 514 sheet: -0.64 (0.47), residues: 87 loop : -0.32 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 290 HIS 0.004 0.001 HIS A 613 PHE 0.013 0.001 PHE C 49 TYR 0.007 0.001 TYR A 732 ARG 0.001 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03157 ( 425) hydrogen bonds : angle 4.04131 ( 1203) SS BOND : bond 0.00484 ( 2) SS BOND : angle 1.28442 ( 4) covalent geometry : bond 0.00234 ( 8954) covalent geometry : angle 0.48187 (12170) ********************** 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 105 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 879 ASP cc_start: 0.8262 (t70) cc_final: 0.7545 (t0) REVERT: B 112 ASP cc_start: 0.7736 (p0) cc_final: 0.7328 (p0) REVERT: B 165 LYS cc_start: 0.7840 (mptt) cc_final: 0.7584 (tttm) REVERT: B 169 LEU cc_start: 0.8141 (mm) cc_final: 0.7904 (mm) REVERT: B 171 GLU cc_start: 0.7228 (pt0) cc_final: 0.7007 (pt0) REVERT: C 47 GLU cc_start: 0.8152 (mp0) cc_final: 0.7736 (mp0) REVERT: D 90 MET cc_start: 0.7497 (mmp) cc_final: 0.6955 (ttt) REVERT: D 129 MET cc_start: 0.3875 (ppp) cc_final: 0.3569 (tpt) outliers start: 10 outliers final: 8 residues processed: 102 average time/residue: 1.9347 time to fit residues: 215.5597 Evaluate side-chains 100 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 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 91 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.114795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.088463 restraints weight = 44599.416| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.53 r_work: 0.3052 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8956 Z= 0.117 Angle : 0.490 7.940 12174 Z= 0.256 Chirality : 0.039 0.139 1362 Planarity : 0.003 0.033 1539 Dihedral : 6.439 84.275 1304 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.16 % Allowed : 13.11 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1068 helix: 1.67 (0.24), residues: 514 sheet: -0.58 (0.47), residues: 87 loop : -0.31 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 290 HIS 0.004 0.001 HIS C 36 PHE 0.015 0.001 PHE C 49 TYR 0.008 0.001 TYR A 884 ARG 0.001 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 425) hydrogen bonds : angle 4.06467 ( 1203) SS BOND : bond 0.00558 ( 2) SS BOND : angle 1.42086 ( 4) covalent geometry : bond 0.00264 ( 8954) covalent geometry : angle 0.48959 (12170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10838.29 seconds wall clock time: 186 minutes 6.65 seconds (11166.65 seconds total)