Starting phenix.real_space_refine on Sun Jun 15 04:41:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i81_52704/06_2025/9i81_52704_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i81_52704/06_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_52704/06_2025/9i81_52704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i81_52704/06_2025/9i81_52704.map" model { file = "/net/cci-nas-00/data/ceres_data/9i81_52704/06_2025/9i81_52704_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i81_52704/06_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-5710/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: 8.23, per 1000 atoms: 0.48 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: 4.89 Conformation dependent library (CDL) restraints added in 1.5 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: 1.62 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: 6.81 Time building geometry restraints manager: 5.58 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: 0.550 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: 0.310 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 38.660 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:13.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.010 ------------------------------------------------------------------------------- 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 : 1.411 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: 2.1739 time to fit residues: 315.2742 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 : 1.360 ------------------------------------------------------------------------------- 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 = 0.085751 restraints weight = 44612.420| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.53 r_work: 0.3010 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1419 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 5.904 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 0.58556 (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 : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.7015 (ttm-80) cc_final: 0.6754 (ttm-80) REVERT: A 223 ILE cc_start: 0.8002 (pt) cc_final: 0.7667 (pp) REVERT: B 112 ASP cc_start: 0.7805 (p0) cc_final: 0.7417 (p0) REVERT: B 151 SER cc_start: 0.9111 (t) cc_final: 0.8907 (t) REVERT: C 34 GLN cc_start: 0.8036 (tp40) cc_final: 0.7704 (tp40) REVERT: C 47 GLU cc_start: 0.8022 (mp0) cc_final: 0.7529 (mp0) REVERT: D 90 MET cc_start: 0.7645 (mmp) cc_final: 0.7079 (ttp) outliers start: 13 outliers final: 6 residues processed: 108 average time/residue: 2.3986 time to fit residues: 282.1549 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 : 1.767 ------------------------------------------------------------------------------- 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: 2.9990 chunk 45 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.114801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.088581 restraints weight = 43965.429| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.48 r_work: 0.3075 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8956 Z= 0.118 Angle : 0.504 6.709 12174 Z= 0.266 Chirality : 0.039 0.145 1362 Planarity : 0.003 0.033 1539 Dihedral : 7.029 88.033 1304 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.59 % Allowed : 8.03 % Favored : 90.38 % 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: 0.61 (0.26), residues: 1068 helix: 1.40 (0.24), residues: 507 sheet: -0.99 (0.48), residues: 96 loop : -0.33 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 290 HIS 0.008 0.001 HIS A 613 PHE 0.014 0.001 PHE A 753 TYR 0.008 0.001 TYR A 674 ARG 0.001 0.000 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 425) hydrogen bonds : angle 4.53075 ( 1203) SS BOND : bond 0.00513 ( 2) SS BOND : angle 1.34250 ( 4) covalent geometry : bond 0.00262 ( 8954) covalent geometry : angle 0.50388 (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: 15 poor density : 108 time to evaluate : 1.435 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: 0.8018 (pt) cc_final: 0.7695 (pp) REVERT: B 83 VAL cc_start: 0.8052 (p) cc_final: 0.7779 (m) REVERT: B 112 ASP cc_start: 0.7779 (p0) cc_final: 0.7353 (p0) REVERT: B 151 SER cc_start: 0.9132 (t) cc_final: 0.8930 (t) REVERT: B 165 LYS cc_start: 0.7556 (mptt) cc_final: 0.7353 (tttm) REVERT: C 34 GLN cc_start: 0.8124 (tp40) cc_final: 0.7741 (tp40) REVERT: C 47 GLU cc_start: 0.8107 (mp0) cc_final: 0.7679 (mp0) outliers start: 15 outliers final: 6 residues processed: 118 average time/residue: 2.0667 time to fit residues: 265.4178 Evaluate side-chains 105 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 85 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.113642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.086692 restraints weight = 44301.056| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.55 r_work: 0.3025 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1988 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= 0.167 Angle : 0.519 7.010 12174 Z= 0.275 Chirality : 0.040 0.152 1362 Planarity : 0.003 0.034 1539 Dihedral : 6.937 88.274 1304 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.59 % Allowed : 9.20 % Favored : 89.22 % 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: 0.56 (0.26), residues: 1068 helix: 1.34 (0.24), residues: 510 sheet: -0.94 (0.48), residues: 96 loop : -0.35 (0.29), residues: 462 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 0.014 0.001 PHE A 741 TYR 0.011 0.001 TYR A 653 ARG 0.002 0.000 ARG A 467 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 425) hydrogen bonds : angle 4.43828 ( 1203) SS BOND : bond 0.00686 ( 2) SS BOND : angle 1.68742 ( 4) covalent geometry : bond 0.00378 ( 8954) covalent geometry : angle 0.51771 (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 115 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.7942 (pt) cc_final: 0.7624 (pp) REVERT: B 83 VAL cc_start: 0.8026 (p) cc_final: 0.7739 (m) REVERT: B 96 ARG cc_start: 0.8169 (mmt-90) cc_final: 0.7802 (mmt-90) REVERT: B 112 ASP cc_start: 0.7829 (p0) cc_final: 0.7455 (p0) REVERT: B 151 SER cc_start: 0.9175 (t) cc_final: 0.8960 (t) REVERT: C 34 GLN cc_start: 0.7999 (tp40) cc_final: 0.7706 (tp40) REVERT: C 47 GLU cc_start: 0.8122 (mp0) cc_final: 0.7633 (mp0) outliers start: 15 outliers final: 9 residues processed: 111 average time/residue: 2.2879 time to fit residues: 277.6929 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 : 1.376 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.113486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.086510 restraints weight = 44906.367| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.57 r_work: 0.3019 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2085 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= 0.168 Angle : 0.521 7.157 12174 Z= 0.275 Chirality : 0.040 0.146 1362 Planarity : 0.003 0.035 1539 Dihedral : 6.884 87.852 1304 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.80 % Allowed : 9.94 % Favored : 88.27 % 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: 0.51 (0.26), residues: 1068 helix: 1.31 (0.24), residues: 510 sheet: -0.92 (0.48), residues: 96 loop : -0.39 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 290 HIS 0.007 0.001 HIS C 36 PHE 0.016 0.001 PHE A 741 TYR 0.010 0.001 TYR A 732 ARG 0.002 0.000 ARG A 569 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 425) hydrogen bonds : angle 4.38136 ( 1203) SS BOND : bond 0.00696 ( 2) SS BOND : angle 1.70389 ( 4) covalent geometry : bond 0.00379 ( 8954) covalent geometry : angle 0.52054 (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 117 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.7929 (pt) cc_final: 0.7631 (pp) REVERT: B 83 VAL cc_start: 0.8031 (p) cc_final: 0.7750 (m) REVERT: B 112 ASP cc_start: 0.7832 (p0) cc_final: 0.7460 (p0) REVERT: B 151 SER cc_start: 0.9196 (t) cc_final: 0.8988 (t) REVERT: C 34 GLN cc_start: 0.8013 (tp40) cc_final: 0.7691 (tp40) REVERT: C 47 GLU cc_start: 0.8141 (mp0) cc_final: 0.7624 (mp0) REVERT: D 90 MET cc_start: 0.7466 (mmp) cc_final: 0.6817 (ttp) outliers start: 17 outliers final: 10 residues processed: 111 average time/residue: 2.0409 time to fit residues: 246.9401 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 : 1.379 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 52 optimal weight: 0.2980 chunk 37 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 ** 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 = 0.3582 r_free = 0.3582 target = 0.114174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.087892 restraints weight = 44498.497| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.52 r_work: 0.3042 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2240 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= 0.124 Angle : 0.494 6.354 12174 Z= 0.260 Chirality : 0.039 0.155 1362 Planarity : 0.003 0.034 1539 Dihedral : 6.709 85.638 1304 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.59 % Allowed : 10.57 % Favored : 87.84 % 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: 0.73 (0.26), residues: 1068 helix: 1.49 (0.24), residues: 508 sheet: -0.57 (0.49), residues: 87 loop : -0.36 (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 A 613 PHE 0.014 0.001 PHE A 753 TYR 0.008 0.001 TYR A 732 ARG 0.001 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 425) hydrogen bonds : angle 4.22982 ( 1203) SS BOND : bond 0.00539 ( 2) SS BOND : angle 1.42762 ( 4) covalent geometry : bond 0.00278 ( 8954) covalent geometry : angle 0.49305 (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: 15 poor density : 98 time to evaluate : 1.301 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: 0.8254 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: A 223 ILE cc_start: 0.7882 (pt) cc_final: 0.7584 (pp) REVERT: B 83 VAL cc_start: 0.7977 (p) cc_final: 0.7693 (m) REVERT: B 112 ASP cc_start: 0.7828 (p0) cc_final: 0.7431 (p0) REVERT: B 151 SER cc_start: 0.9172 (t) cc_final: 0.8967 (t) REVERT: B 169 LEU cc_start: 0.8183 (mm) cc_final: 0.7961 (mm) REVERT: C 34 GLN cc_start: 0.7991 (tp40) cc_final: 0.7688 (tp40) REVERT: C 47 GLU cc_start: 0.8159 (mp0) cc_final: 0.7695 (mp0) REVERT: D 90 MET cc_start: 0.7499 (mmp) cc_final: 0.6934 (ttt) outliers start: 15 outliers final: 9 residues processed: 108 average time/residue: 1.9591 time to fit residues: 231.2989 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 : 1.263 ------------------------------------------------------------------------------- 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 8 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 43 optimal weight: 0.0270 chunk 83 optimal weight: 4.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- 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 ** 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 = 0.3561 r_free = 0.3561 target = 0.112815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.085936 restraints weight = 44513.140| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.56 r_work: 0.3014 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8956 Z= 0.194 Angle : 0.537 7.362 12174 Z= 0.284 Chirality : 0.040 0.139 1362 Planarity : 0.003 0.035 1539 Dihedral : 6.809 87.353 1304 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.11 % Allowed : 10.36 % 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: 0.54 (0.26), residues: 1068 helix: 1.32 (0.24), residues: 509 sheet: -0.57 (0.50), residues: 87 loop : -0.45 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 290 HIS 0.008 0.001 HIS C 36 PHE 0.018 0.001 PHE A 741 TYR 0.011 0.001 TYR A 732 ARG 0.002 0.000 ARG A 569 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 425) hydrogen bonds : angle 4.33275 ( 1203) SS BOND : bond 0.00798 ( 2) SS BOND : angle 1.87055 ( 4) covalent geometry : bond 0.00439 ( 8954) covalent geometry : angle 0.53612 (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 118 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: A 223 ILE cc_start: 0.7933 (pt) cc_final: 0.7640 (pp) REVERT: B 83 VAL cc_start: 0.8070 (p) cc_final: 0.7786 (m) REVERT: B 109 ASN cc_start: 0.7789 (m-40) cc_final: 0.7418 (m110) REVERT: B 112 ASP cc_start: 0.7788 (p0) cc_final: 0.7391 (p0) REVERT: B 169 LEU cc_start: 0.8207 (mm) cc_final: 0.8001 (mm) REVERT: C 47 GLU cc_start: 0.8168 (mp0) cc_final: 0.7639 (mp0) REVERT: D 90 MET cc_start: 0.7463 (mmp) cc_final: 0.6781 (ttp) outliers start: 20 outliers final: 11 residues processed: 110 average time/residue: 2.0558 time to fit residues: 249.6975 Evaluate side-chains 106 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 1.519 ------------------------------------------------------------------------------- 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 105 ASN 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: 3.9990 chunk 86 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 44 optimal weight: 0.0870 chunk 55 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 overall best weight: 1.1562 ------------------------------------------------------------------------------- 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 ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.114561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.087769 restraints weight = 44659.572| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.58 r_work: 0.3043 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8956 Z= 0.119 Angle : 0.494 6.763 12174 Z= 0.259 Chirality : 0.039 0.138 1362 Planarity : 0.003 0.036 1539 Dihedral : 6.644 85.379 1304 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.48 % Allowed : 11.31 % 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: 0.77 (0.26), residues: 1068 helix: 1.54 (0.24), residues: 508 sheet: -0.57 (0.49), residues: 87 loop : -0.36 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 290 HIS 0.003 0.001 HIS A 613 PHE 0.013 0.001 PHE A 652 TYR 0.010 0.001 TYR A 289 ARG 0.001 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 425) hydrogen bonds : angle 4.17298 ( 1203) SS BOND : bond 0.00870 ( 2) SS BOND : angle 1.65764 ( 4) covalent geometry : bond 0.00268 ( 8954) covalent geometry : angle 0.49361 (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: 14 poor density : 97 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.7895 (pt) cc_final: 0.7609 (pp) REVERT: B 109 ASN cc_start: 0.7816 (m-40) cc_final: 0.7467 (m110) REVERT: B 112 ASP cc_start: 0.7788 (p0) cc_final: 0.7377 (p0) REVERT: B 165 LYS cc_start: 0.7862 (mptt) cc_final: 0.7578 (tttm) REVERT: B 169 LEU cc_start: 0.8209 (mm) cc_final: 0.8002 (mm) REVERT: C 31 GLN cc_start: 0.7427 (tp40) cc_final: 0.6955 (tp40) REVERT: C 47 GLU cc_start: 0.8198 (mp0) cc_final: 0.7714 (mp0) REVERT: D 90 MET cc_start: 0.7449 (mmp) cc_final: 0.6829 (ttp) outliers start: 14 outliers final: 10 residues processed: 105 average time/residue: 2.0225 time to fit residues: 232.0471 Evaluate side-chains 104 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 1.386 ------------------------------------------------------------------------------- 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: 0.5980 chunk 92 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 773 GLN B 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.115280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.088520 restraints weight = 44736.072| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.60 r_work: 0.3056 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8956 Z= 0.105 Angle : 0.493 8.577 12174 Z= 0.256 Chirality : 0.039 0.141 1362 Planarity : 0.003 0.034 1539 Dihedral : 6.530 83.385 1304 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.27 % Allowed : 11.95 % Favored : 86.79 % 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: 0.88 (0.26), residues: 1068 helix: 1.69 (0.24), residues: 507 sheet: -0.60 (0.48), residues: 87 loop : -0.35 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 0.03227 ( 425) hydrogen bonds : angle 4.07340 ( 1203) SS BOND : bond 0.00859 ( 2) SS BOND : angle 1.52856 ( 4) covalent geometry : bond 0.00239 ( 8954) covalent geometry : angle 0.49227 (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 110 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 1.529 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: 0.7890 (pt) cc_final: 0.7593 (pp) REVERT: B 109 ASN cc_start: 0.7824 (m-40) cc_final: 0.7459 (m110) REVERT: B 112 ASP cc_start: 0.7754 (p0) cc_final: 0.7354 (p0) REVERT: B 165 LYS cc_start: 0.7846 (mptt) cc_final: 0.7591 (tttm) REVERT: B 169 LEU cc_start: 0.8165 (mm) cc_final: 0.7942 (mm) REVERT: C 47 GLU cc_start: 0.8137 (mp0) cc_final: 0.7693 (mp0) REVERT: D 90 MET cc_start: 0.7431 (mmp) cc_final: 0.6832 (ttp) REVERT: D 129 MET cc_start: 0.3764 (ppp) cc_final: 0.3433 (tpt) outliers start: 12 outliers final: 9 residues processed: 106 average time/residue: 2.6644 time to fit residues: 310.4260 Evaluate side-chains 101 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 1.418 ------------------------------------------------------------------------------- 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: 2.9990 chunk 16 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.113524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.087246 restraints weight = 44588.264| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.53 r_work: 0.3030 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8956 Z= 0.155 Angle : 0.522 7.097 12174 Z= 0.274 Chirality : 0.040 0.139 1362 Planarity : 0.003 0.033 1539 Dihedral : 6.595 84.122 1304 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.27 % Allowed : 12.05 % Favored : 86.68 % 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: 0.77 (0.26), residues: 1068 helix: 1.56 (0.24), residues: 508 sheet: -0.63 (0.49), residues: 87 loop : -0.36 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 290 HIS 0.006 0.001 HIS C 36 PHE 0.016 0.001 PHE A 741 TYR 0.010 0.001 TYR A 884 ARG 0.002 0.000 ARG A 836 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 425) hydrogen bonds : angle 4.16819 ( 1203) SS BOND : bond 0.00881 ( 2) SS BOND : angle 1.86726 ( 4) covalent geometry : bond 0.00351 ( 8954) covalent geometry : angle 0.52065 (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 106 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.7842 (pt) cc_final: 0.7543 (pp) REVERT: B 109 ASN cc_start: 0.7782 (m-40) cc_final: 0.7413 (m110) REVERT: B 112 ASP cc_start: 0.7805 (p0) cc_final: 0.7408 (p0) REVERT: B 169 LEU cc_start: 0.8165 (mm) cc_final: 0.7928 (mm) REVERT: B 171 GLU cc_start: 0.7347 (pt0) cc_final: 0.7060 (pt0) REVERT: C 47 GLU cc_start: 0.8144 (mp0) cc_final: 0.7686 (mp0) REVERT: D 90 MET cc_start: 0.7425 (mmp) cc_final: 0.6812 (ttp) REVERT: D 129 MET cc_start: 0.3845 (ppp) cc_final: 0.3560 (tpt) outliers start: 12 outliers final: 9 residues processed: 103 average time/residue: 2.4830 time to fit residues: 280.4427 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 : 1.553 ------------------------------------------------------------------------------- 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 91 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 C 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.114599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.088403 restraints weight = 44554.134| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.53 r_work: 0.3053 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8956 Z= 0.115 Angle : 0.498 8.977 12174 Z= 0.260 Chirality : 0.039 0.141 1362 Planarity : 0.003 0.034 1539 Dihedral : 6.527 83.217 1304 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.27 % Allowed : 12.26 % Favored : 86.47 % 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: 0.83 (0.26), residues: 1068 helix: 1.59 (0.24), residues: 514 sheet: -0.63 (0.48), residues: 87 loop : -0.32 (0.28), 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 0.008 0.001 TYR A 732 ARG 0.001 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 425) hydrogen bonds : angle 4.08717 ( 1203) SS BOND : bond 0.00710 ( 2) SS BOND : angle 1.52785 ( 4) covalent geometry : bond 0.00261 ( 8954) covalent geometry : angle 0.49766 (12170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11622.77 seconds wall clock time: 206 minutes 29.20 seconds (12389.20 seconds total)