Starting phenix.real_space_refine on Sat Aug 23 15:55:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rl9_19335/08_2025/8rl9_19335.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rl9_19335/08_2025/8rl9_19335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rl9_19335/08_2025/8rl9_19335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rl9_19335/08_2025/8rl9_19335.map" model { file = "/net/cci-nas-00/data/ceres_data/8rl9_19335/08_2025/8rl9_19335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rl9_19335/08_2025/8rl9_19335.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 39 5.16 5 C 4263 2.51 5 N 1177 2.21 5 O 1281 1.98 5 H 6425 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13186 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 3361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3361 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 4, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1686 Classifications: {'peptide': 114} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "K" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1782 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 6356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 6356 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 17, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 9, 'GLU:plan': 7, 'ASP:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 96 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12677 SG CYS A 411 24.708 62.176 78.460 1.00111.07 S ATOM 12912 SG CYS A 427 23.274 58.652 78.682 1.00 98.41 S ATOM 12946 SG CYS A 431 24.022 60.722 81.852 1.00 77.03 S ATOM 12985 SG CYS A 434 21.135 61.678 79.484 1.00 81.91 S Time building chain proxies: 2.78, per 1000 atoms: 0.21 Number of scatterers: 13186 At special positions: 0 Unit cell: (72.21, 90.47, 122.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 39 16.00 O 1281 8.00 N 1177 7.00 C 4263 6.00 H 6425 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 11 " - pdb=" SG CYS K 11 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 95 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 272 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 412.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 411 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 434 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 427 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 431 " Number of angles added : 6 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1656 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 9 sheets defined 30.8% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'B' and resid 56 through 65 removed outlier: 3.688A pdb=" N LEU B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR B 62 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 82 removed outlier: 5.432A pdb=" N ARG B 80 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.751A pdb=" N THR D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 removed outlier: 3.525A pdb=" N LYS K 64 " --> pdb=" O ASP K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'A' and resid 13 through 23 Processing helix chain 'A' and resid 31 through 44 Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.782A pdb=" N CYS A 61 " --> pdb=" O GLY A 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 105 through 118 Processing helix chain 'A' and resid 129 through 135 Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 170 through 182 removed outlier: 4.202A pdb=" N LEU A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 207 Processing helix chain 'A' and resid 237 through 252 Processing helix chain 'A' and resid 268 through 283 Processing helix chain 'A' and resid 294 through 307 Processing helix chain 'A' and resid 339 through 349 removed outlier: 4.204A pdb=" N ARG A 349 " --> pdb=" O GLN A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 386 Processing helix chain 'A' and resid 388 through 408 Processing helix chain 'A' and resid 411 through 421 Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'A' and resid 436 through 451 Processing sheet with id=AA1, first strand: chain 'B' and resid 11 through 22 removed outlier: 3.821A pdb=" N ARG B 30 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 47 " --> pdb=" O ARG B 30 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASN B 149 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LYS B 166 " --> pdb=" O ASN B 149 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY B 104 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N LEU B 119 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N ASN B 121 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU B 15 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N ILE B 123 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLU B 17 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LEU B 125 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP B 19 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLY B 127 " --> pdb=" O ASP B 19 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ASP B 21 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.584A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.901A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLY D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N MET D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL D 107 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'K' and resid 56 through 59 removed outlier: 3.684A pdb=" N SER K 56 " --> pdb=" O THR K 52 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N MET K 34 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR K 52 " --> pdb=" O ASN K 32 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ASN K 32 " --> pdb=" O THR K 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 56 through 59 removed outlier: 3.684A pdb=" N SER K 56 " --> pdb=" O THR K 52 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N MET K 34 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR K 52 " --> pdb=" O ASN K 32 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ASN K 32 " --> pdb=" O THR K 52 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER K 30 " --> pdb=" O TYR K 101 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY K 99 " --> pdb=" O ASN K 32 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 108 through 110 removed outlier: 6.600A pdb=" N VAL A 48 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N THR A 192 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL A 50 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 154 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LEU A 191 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL A 156 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER A 98 " --> pdb=" O TYR A 127 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 225 through 226 removed outlier: 6.235A pdb=" N PHE A 226 " --> pdb=" O CYS A 359 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU A 361 " --> pdb=" O PHE A 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 225 through 226 removed outlier: 6.235A pdb=" N PHE A 226 " --> pdb=" O CYS A 359 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU A 361 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLY A 262 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ALA A 315 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL A 264 " --> pdb=" O ALA A 315 " (cutoff:3.500A) 339 hydrogen bonds defined for protein. 939 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: 3.20 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6413 1.03 - 1.23: 16 1.23 - 1.42: 2923 1.42 - 1.62: 3920 1.62 - 1.81: 54 Bond restraints: 13326 Sorted by residual: bond pdb=" N ASP K 89 " pdb=" CA ASP K 89 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.16e+00 bond pdb=" N ASP K 89 " pdb=" H ASP K 89 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.84e+00 bond pdb=" N THR K 106 " pdb=" H THR K 106 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.77e+00 bond pdb=" C GLU K 88 " pdb=" N ASP K 89 " ideal model delta sigma weight residual 1.332 1.369 -0.036 1.40e-02 5.10e+03 6.76e+00 bond pdb=" N GLN K 1 " pdb=" CA GLN K 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.84e+00 ... (remaining 13321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 22870 1.12 - 2.24: 1008 2.24 - 3.36: 65 3.36 - 4.47: 23 4.47 - 5.59: 3 Bond angle restraints: 23969 Sorted by residual: angle pdb=" N THR K 106 " pdb=" CA THR K 106 " pdb=" C THR K 106 " ideal model delta sigma weight residual 111.36 107.21 4.15 1.09e+00 8.42e-01 1.45e+01 angle pdb=" CA ASP K 89 " pdb=" CB ASP K 89 " pdb=" CG ASP K 89 " ideal model delta sigma weight residual 112.60 109.14 3.46 1.00e+00 1.00e+00 1.20e+01 angle pdb=" CA THR K 106 " pdb=" C THR K 106 " pdb=" O THR K 106 " ideal model delta sigma weight residual 120.42 117.37 3.05 1.06e+00 8.90e-01 8.29e+00 angle pdb=" N GLY D 97 " pdb=" CA GLY D 97 " pdb=" C GLY D 97 " ideal model delta sigma weight residual 110.97 106.07 4.90 1.92e+00 2.71e-01 6.51e+00 angle pdb=" C ASN B 164 " pdb=" N PHE B 165 " pdb=" CA PHE B 165 " ideal model delta sigma weight residual 121.87 116.28 5.59 2.24e+00 1.99e-01 6.23e+00 ... (remaining 23964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5775 17.93 - 35.86: 425 35.86 - 53.79: 110 53.79 - 71.73: 40 71.73 - 89.66: 7 Dihedral angle restraints: 6357 sinusoidal: 3335 harmonic: 3022 Sorted by residual: dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 95 " pdb=" CB CYS K 95 " ideal model delta sinusoidal sigma weight residual 93.00 154.14 -61.14 1 1.00e+01 1.00e-02 4.97e+01 dihedral pdb=" CB CYS D 11 " pdb=" SG CYS D 11 " pdb=" SG CYS K 11 " pdb=" CB CYS K 11 " ideal model delta sinusoidal sigma weight residual -86.00 -125.94 39.94 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CB CYS A 266 " pdb=" SG CYS A 266 " pdb=" SG CYS A 272 " pdb=" CB CYS A 272 " ideal model delta sinusoidal sigma weight residual -86.00 -51.76 -34.24 1 1.00e+01 1.00e-02 1.66e+01 ... (remaining 6354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 681 0.030 - 0.060: 241 0.060 - 0.091: 64 0.091 - 0.121: 58 0.121 - 0.151: 7 Chirality restraints: 1051 Sorted by residual: chirality pdb=" CA VAL B 112 " pdb=" N VAL B 112 " pdb=" C VAL B 112 " pdb=" CB VAL B 112 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA ILE B 98 " pdb=" N ILE B 98 " pdb=" C ILE B 98 " pdb=" CB ILE B 98 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA VAL A 312 " pdb=" N VAL A 312 " pdb=" C VAL A 312 " pdb=" CB VAL A 312 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1048 not shown) Planarity restraints: 2077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 66 " 0.214 9.50e-02 1.11e+02 7.16e-02 5.89e+00 pdb=" NE ARG K 66 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG K 66 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG K 66 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG K 66 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG K 66 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG K 66 " -0.008 2.00e-02 2.50e+03 pdb="HH21 ARG K 66 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG K 66 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP K 89 " -0.008 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" CG ASP K 89 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP K 89 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP K 89 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 99 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C SER B 99 " 0.029 2.00e-02 2.50e+03 pdb=" O SER B 99 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE B 100 " -0.010 2.00e-02 2.50e+03 ... (remaining 2074 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 284 2.11 - 2.74: 23449 2.74 - 3.36: 38044 3.36 - 3.98: 48510 3.98 - 4.60: 74039 Nonbonded interactions: 184326 Sorted by model distance: nonbonded pdb=" OE1 GLU A 308 " pdb=" H GLU A 308 " model vdw 1.493 2.450 nonbonded pdb="HD21 ASN B 144 " pdb=" OD1 ASN D 95 " model vdw 1.630 2.450 nonbonded pdb=" OH TYR A 62 " pdb=" HH TYR A 127 " model vdw 1.674 2.450 nonbonded pdb=" OD1 ASN K 7 " pdb=" H GLY K 8 " model vdw 1.731 2.450 nonbonded pdb=" OE2 GLU B 115 " pdb="HH22 ARG B 122 " model vdw 1.732 2.450 ... (remaining 184321 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=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: 3.280 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: 0.090 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.200 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 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 : 0.002 0.037 6909 Z= 0.109 Angle : 0.495 5.592 9385 Z= 0.271 Chirality : 0.041 0.151 1051 Planarity : 0.005 0.093 1219 Dihedral : 14.190 89.657 2439 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.28), residues: 888 helix: 2.25 (0.35), residues: 246 sheet: -0.43 (0.28), residues: 292 loop : -0.14 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 66 TYR 0.011 0.001 TYR D 32 PHE 0.017 0.001 PHE B 100 TRP 0.006 0.001 TRP A 358 HIS 0.003 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 6901) covalent geometry : angle 0.49219 ( 9371) SS BOND : bond 0.00036 ( 4) SS BOND : angle 0.90357 ( 8) hydrogen bonds : bond 0.12475 ( 333) hydrogen bonds : angle 5.90629 ( 939) metal coordination : bond 0.00169 ( 4) metal coordination : angle 1.79039 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.336 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: symmetry clash 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: symmetry clash REVERT: B 82 ASP cc_start: 0.7467 (t0) cc_final: 0.6818 (t0) REVERT: D 43 LYS cc_start: 0.8586 (mtmm) cc_final: 0.8352 (mttm) REVERT: D 58 SER cc_start: 0.8636 (t) cc_final: 0.8378 (t) REVERT: K 77 THR cc_start: 0.7731 (p) cc_final: 0.7519 (p) REVERT: K 108 GLU cc_start: 0.7431 (mp0) cc_final: 0.7041 (mp0) REVERT: K 110 GLU cc_start: 0.7299 (tp30) cc_final: 0.7098 (tp30) REVERT: A 224 ASN cc_start: 0.7924 (t0) cc_final: 0.7579 (t0) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2245 time to fit residues: 63.0980 Evaluate side-chains 197 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN B 146 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN D 95 ASN K 32 ASN A 333 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.128601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.114592 restraints weight = 34401.144| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.96 r_work: 0.3612 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6909 Z= 0.194 Angle : 0.558 5.100 9385 Z= 0.301 Chirality : 0.042 0.170 1051 Planarity : 0.005 0.052 1219 Dihedral : 4.063 17.459 970 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.16 % Allowed : 10.55 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.28), residues: 888 helix: 2.33 (0.34), residues: 240 sheet: -0.43 (0.29), residues: 285 loop : -0.18 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 19 TYR 0.011 0.002 TYR K 94 PHE 0.017 0.002 PHE A 399 TRP 0.011 0.002 TRP A 358 HIS 0.010 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 6901) covalent geometry : angle 0.54904 ( 9371) SS BOND : bond 0.00235 ( 4) SS BOND : angle 1.10140 ( 8) hydrogen bonds : bond 0.03930 ( 333) hydrogen bonds : angle 5.39223 ( 939) metal coordination : bond 0.00518 ( 4) metal coordination : angle 3.81949 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 201 time to evaluate : 0.413 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 ASP cc_start: 0.7707 (t0) cc_final: 0.7309 (t0) REVERT: D 43 LYS cc_start: 0.8664 (mtmm) cc_final: 0.8450 (mttm) REVERT: A 224 ASN cc_start: 0.7940 (t0) cc_final: 0.7707 (t0) outliers start: 8 outliers final: 4 residues processed: 204 average time/residue: 0.2059 time to fit residues: 53.9827 Evaluate side-chains 197 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 193 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain D residue 11 CYS Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain A residue 113 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 70 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 ASN A 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.126977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.113145 restraints weight = 34804.482| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.94 r_work: 0.3589 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6909 Z= 0.178 Angle : 0.525 5.795 9385 Z= 0.279 Chirality : 0.041 0.149 1051 Planarity : 0.004 0.050 1219 Dihedral : 4.066 17.104 970 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.46 % Allowed : 11.85 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.28), residues: 888 helix: 2.30 (0.34), residues: 240 sheet: -0.45 (0.29), residues: 292 loop : -0.19 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 19 TYR 0.017 0.001 TYR B 200 PHE 0.011 0.001 PHE B 84 TRP 0.007 0.001 TRP A 358 HIS 0.003 0.001 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 6901) covalent geometry : angle 0.51387 ( 9371) SS BOND : bond 0.00177 ( 4) SS BOND : angle 1.10691 ( 8) hydrogen bonds : bond 0.03592 ( 333) hydrogen bonds : angle 5.33498 ( 939) metal coordination : bond 0.00555 ( 4) metal coordination : angle 4.10125 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 0.239 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 ASP cc_start: 0.7691 (t0) cc_final: 0.7417 (t0) REVERT: B 135 ASN cc_start: 0.6472 (m-40) cc_final: 0.6080 (m-40) REVERT: D 43 LYS cc_start: 0.8693 (mtmm) cc_final: 0.8481 (mttm) REVERT: A 408 GLU cc_start: 0.7376 (tm-30) cc_final: 0.6764 (tm-30) outliers start: 17 outliers final: 15 residues processed: 211 average time/residue: 0.2235 time to fit residues: 59.9704 Evaluate side-chains 216 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain D residue 11 CYS Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 406 CYS Chi-restraints excluded: chain A residue 422 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 ASN A 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.122029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.108257 restraints weight = 34987.208| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.90 r_work: 0.3518 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 6909 Z= 0.250 Angle : 0.593 7.912 9385 Z= 0.317 Chirality : 0.043 0.155 1051 Planarity : 0.005 0.054 1219 Dihedral : 4.510 18.028 970 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.18 % Allowed : 12.86 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.28), residues: 888 helix: 2.04 (0.34), residues: 240 sheet: -0.74 (0.29), residues: 289 loop : -0.35 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 19 TYR 0.015 0.002 TYR B 200 PHE 0.018 0.002 PHE A 231 TRP 0.012 0.002 TRP A 358 HIS 0.006 0.002 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 6901) covalent geometry : angle 0.57697 ( 9371) SS BOND : bond 0.00225 ( 4) SS BOND : angle 1.61173 ( 8) hydrogen bonds : bond 0.03906 ( 333) hydrogen bonds : angle 5.51274 ( 939) metal coordination : bond 0.00733 ( 4) metal coordination : angle 5.12545 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.374 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 ASN cc_start: 0.6699 (m-40) cc_final: 0.6493 (m-40) REVERT: D 43 LYS cc_start: 0.8787 (mtmm) cc_final: 0.8551 (mttm) REVERT: K 110 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7100 (mp0) outliers start: 22 outliers final: 14 residues processed: 213 average time/residue: 0.2334 time to fit residues: 63.1515 Evaluate side-chains 211 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain D residue 11 CYS Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 31 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN A 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.122688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.108857 restraints weight = 34854.739| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.90 r_work: 0.3526 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6909 Z= 0.189 Angle : 0.545 6.780 9385 Z= 0.289 Chirality : 0.042 0.163 1051 Planarity : 0.005 0.052 1219 Dihedral : 4.427 18.427 970 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.75 % Allowed : 15.17 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.29), residues: 888 helix: 2.15 (0.35), residues: 240 sheet: -0.74 (0.28), residues: 310 loop : -0.21 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 96 TYR 0.018 0.002 TYR D 32 PHE 0.011 0.002 PHE B 165 TRP 0.010 0.001 TRP B 57 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 6901) covalent geometry : angle 0.53272 ( 9371) SS BOND : bond 0.00179 ( 4) SS BOND : angle 1.25808 ( 8) hydrogen bonds : bond 0.03458 ( 333) hydrogen bonds : angle 5.37681 ( 939) metal coordination : bond 0.00649 ( 4) metal coordination : angle 4.44840 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 0.353 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 ASP cc_start: 0.7777 (t0) cc_final: 0.7568 (t0) REVERT: B 135 ASN cc_start: 0.6669 (m-40) cc_final: 0.6447 (m-40) REVERT: D 43 LYS cc_start: 0.8742 (mtmm) cc_final: 0.8505 (mttm) REVERT: D 101 TRP cc_start: 0.7869 (m100) cc_final: 0.7559 (m100) REVERT: K 64 LYS cc_start: 0.8420 (tptp) cc_final: 0.7852 (tppt) outliers start: 19 outliers final: 15 residues processed: 213 average time/residue: 0.2302 time to fit residues: 62.2863 Evaluate side-chains 218 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 285 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 46 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.122495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.109108 restraints weight = 35219.649| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.85 r_work: 0.3536 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6909 Z= 0.183 Angle : 0.548 6.701 9385 Z= 0.289 Chirality : 0.042 0.164 1051 Planarity : 0.004 0.051 1219 Dihedral : 4.379 18.256 970 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.89 % Allowed : 16.04 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.29), residues: 888 helix: 2.22 (0.35), residues: 240 sheet: -0.81 (0.29), residues: 307 loop : -0.26 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 19 TYR 0.014 0.002 TYR A 363 PHE 0.010 0.002 PHE A 231 TRP 0.006 0.001 TRP A 305 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 6901) covalent geometry : angle 0.53705 ( 9371) SS BOND : bond 0.00246 ( 4) SS BOND : angle 1.42825 ( 8) hydrogen bonds : bond 0.03410 ( 333) hydrogen bonds : angle 5.26317 ( 939) metal coordination : bond 0.00562 ( 4) metal coordination : angle 4.04354 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 213 time to evaluate : 0.453 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 LYS cc_start: 0.8751 (mtmm) cc_final: 0.8508 (mttm) REVERT: D 82 MET cc_start: 0.7078 (mmt) cc_final: 0.6761 (tpp) REVERT: D 101 TRP cc_start: 0.7842 (m100) cc_final: 0.7558 (m100) REVERT: K 64 LYS cc_start: 0.8352 (tptp) cc_final: 0.7801 (tppt) REVERT: A 408 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7288 (tm-30) outliers start: 20 outliers final: 14 residues processed: 218 average time/residue: 0.2366 time to fit residues: 65.6333 Evaluate side-chains 219 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 285 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 60 optimal weight: 0.0000 chunk 48 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 41 optimal weight: 0.0070 chunk 11 optimal weight: 0.2980 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.124011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.110576 restraints weight = 35027.847| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.87 r_work: 0.3553 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6909 Z= 0.131 Angle : 0.526 7.449 9385 Z= 0.276 Chirality : 0.041 0.166 1051 Planarity : 0.004 0.051 1219 Dihedral : 4.261 18.019 970 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.88 % Allowed : 17.63 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.29), residues: 888 helix: 2.38 (0.35), residues: 240 sheet: -0.63 (0.29), residues: 302 loop : -0.17 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 19 TYR 0.012 0.001 TYR A 363 PHE 0.011 0.001 PHE B 165 TRP 0.007 0.001 TRP A 305 HIS 0.001 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6901) covalent geometry : angle 0.51755 ( 9371) SS BOND : bond 0.00293 ( 4) SS BOND : angle 1.05403 ( 8) hydrogen bonds : bond 0.03097 ( 333) hydrogen bonds : angle 5.13435 ( 939) metal coordination : bond 0.00472 ( 4) metal coordination : angle 3.65830 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 208 time to evaluate : 0.362 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 81 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7471 (tt0) REVERT: D 82 MET cc_start: 0.7058 (mmt) cc_final: 0.6771 (tpp) REVERT: D 101 TRP cc_start: 0.7795 (m100) cc_final: 0.7544 (m100) REVERT: K 64 LYS cc_start: 0.8314 (tptp) cc_final: 0.7776 (tppt) outliers start: 13 outliers final: 11 residues processed: 210 average time/residue: 0.2216 time to fit residues: 59.4864 Evaluate side-chains 217 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 205 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 284 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 18 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.121681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.108328 restraints weight = 35074.894| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.86 r_work: 0.3518 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6909 Z= 0.208 Angle : 0.565 7.591 9385 Z= 0.299 Chirality : 0.042 0.172 1051 Planarity : 0.004 0.048 1219 Dihedral : 4.432 18.144 970 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.31 % Allowed : 17.92 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.29), residues: 888 helix: 2.20 (0.34), residues: 241 sheet: -0.76 (0.29), residues: 305 loop : -0.23 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 19 TYR 0.012 0.002 TYR B 92 PHE 0.012 0.002 PHE A 231 TRP 0.008 0.002 TRP B 57 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 6901) covalent geometry : angle 0.55342 ( 9371) SS BOND : bond 0.00151 ( 4) SS BOND : angle 1.21435 ( 8) hydrogen bonds : bond 0.03440 ( 333) hydrogen bonds : angle 5.22626 ( 939) metal coordination : bond 0.00615 ( 4) metal coordination : angle 4.28683 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 0.365 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 81 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7528 (tt0) REVERT: D 82 MET cc_start: 0.7118 (mmt) cc_final: 0.6741 (tpp) REVERT: K 64 LYS cc_start: 0.8408 (tptp) cc_final: 0.7870 (tppt) REVERT: A 408 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7381 (tm-30) outliers start: 16 outliers final: 15 residues processed: 207 average time/residue: 0.2410 time to fit residues: 63.1542 Evaluate side-chains 213 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 284 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN A 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.122583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.109136 restraints weight = 35200.974| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.89 r_work: 0.3530 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6909 Z= 0.161 Angle : 0.545 8.962 9385 Z= 0.287 Chirality : 0.042 0.172 1051 Planarity : 0.004 0.052 1219 Dihedral : 4.354 18.126 970 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.31 % Allowed : 18.06 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.29), residues: 888 helix: 2.34 (0.35), residues: 241 sheet: -0.71 (0.30), residues: 295 loop : -0.25 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 19 TYR 0.011 0.001 TYR A 363 PHE 0.009 0.001 PHE A 226 TRP 0.007 0.001 TRP B 57 HIS 0.002 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 6901) covalent geometry : angle 0.53538 ( 9371) SS BOND : bond 0.00159 ( 4) SS BOND : angle 1.02655 ( 8) hydrogen bonds : bond 0.03232 ( 333) hydrogen bonds : angle 5.13669 ( 939) metal coordination : bond 0.00538 ( 4) metal coordination : angle 3.97757 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.253 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 81 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: D 82 MET cc_start: 0.7073 (mmt) cc_final: 0.6770 (tpp) REVERT: K 64 LYS cc_start: 0.8406 (tptp) cc_final: 0.7856 (tppt) REVERT: A 86 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7615 (mm110) REVERT: A 278 GLU cc_start: 0.7661 (tp30) cc_final: 0.7416 (tp30) REVERT: A 408 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7245 (tm-30) outliers start: 16 outliers final: 14 residues processed: 202 average time/residue: 0.2288 time to fit residues: 58.4298 Evaluate side-chains 212 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 197 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 285 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 36 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 43 optimal weight: 0.3980 chunk 15 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.122503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.109013 restraints weight = 34662.738| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.90 r_work: 0.3527 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6909 Z= 0.152 Angle : 0.537 9.510 9385 Z= 0.284 Chirality : 0.042 0.172 1051 Planarity : 0.004 0.054 1219 Dihedral : 4.316 18.010 970 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.31 % Allowed : 18.35 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.29), residues: 888 helix: 2.41 (0.34), residues: 241 sheet: -0.76 (0.29), residues: 304 loop : -0.08 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 19 TYR 0.012 0.001 TYR B 200 PHE 0.009 0.001 PHE A 405 TRP 0.007 0.001 TRP A 305 HIS 0.002 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6901) covalent geometry : angle 0.52903 ( 9371) SS BOND : bond 0.00130 ( 4) SS BOND : angle 0.96469 ( 8) hydrogen bonds : bond 0.03159 ( 333) hydrogen bonds : angle 5.07358 ( 939) metal coordination : bond 0.00489 ( 4) metal coordination : angle 3.66799 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 0.447 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 MET cc_start: 0.7061 (mmt) cc_final: 0.6768 (tpp) REVERT: K 64 LYS cc_start: 0.8383 (tptp) cc_final: 0.7843 (tppt) REVERT: A 278 GLU cc_start: 0.7664 (tp30) cc_final: 0.7407 (tp30) REVERT: A 408 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7219 (tm-30) outliers start: 16 outliers final: 14 residues processed: 207 average time/residue: 0.2315 time to fit residues: 60.8599 Evaluate side-chains 212 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 284 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN A 86 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.121053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.107599 restraints weight = 34684.569| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.87 r_work: 0.3508 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6909 Z= 0.201 Angle : 0.571 9.396 9385 Z= 0.304 Chirality : 0.043 0.172 1051 Planarity : 0.005 0.060 1219 Dihedral : 4.478 18.645 970 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.46 % Allowed : 19.08 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.29), residues: 888 helix: 2.22 (0.34), residues: 241 sheet: -0.75 (0.29), residues: 292 loop : -0.33 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 19 TYR 0.012 0.002 TYR K 59 PHE 0.020 0.002 PHE A 399 TRP 0.009 0.001 TRP K 115 HIS 0.003 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 6901) covalent geometry : angle 0.56052 ( 9371) SS BOND : bond 0.00144 ( 4) SS BOND : angle 1.15960 ( 8) hydrogen bonds : bond 0.03426 ( 333) hydrogen bonds : angle 5.21074 ( 939) metal coordination : bond 0.00621 ( 4) metal coordination : angle 4.27280 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3411.18 seconds wall clock time: 58 minutes 40.72 seconds (3520.72 seconds total)