Starting phenix.real_space_refine on Thu May 15 12:35:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rl9_19335/05_2025/8rl9_19335.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rl9_19335/05_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_19335/05_2025/8rl9_19335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rl9_19335/05_2025/8rl9_19335.map" model { file = "/net/cci-nas-00/data/ceres_data/8rl9_19335/05_2025/8rl9_19335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rl9_19335/05_2025/8rl9_19335.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 9} 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: 7.14, per 1000 atoms: 0.54 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: 3.40 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.32 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: 5.14 Time building geometry restraints manager: 4.08 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: 2.670 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: 0.230 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 36.840 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.320 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.28), 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 TRP 0.006 0.001 TRP A 358 HIS 0.003 0.001 HIS B 181 PHE 0.017 0.001 PHE B 100 TYR 0.011 0.001 TYR D 32 ARG 0.009 0.001 ARG K 66 Details of bonding type rmsd hydrogen bonds : bond 0.12475 ( 333) hydrogen bonds : angle 5.90629 ( 939) metal coordination : bond 0.00169 ( 4) metal coordination : angle 1.79039 ( 6) SS BOND : bond 0.00036 ( 4) SS BOND : angle 0.90357 ( 8) covalent geometry : bond 0.00223 ( 6901) covalent geometry : angle 0.49219 ( 9371) *********************** 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 : 1.103 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) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.4293 time to fit residues: 120.8587 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 : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 41 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.129414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.115121 restraints weight = 34292.874| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 3.05 r_work: 0.3618 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6909 Z= 0.190 Angle : 0.546 5.113 9385 Z= 0.294 Chirality : 0.042 0.169 1051 Planarity : 0.005 0.052 1219 Dihedral : 3.985 17.228 970 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.16 % Allowed : 10.69 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.28), residues: 888 helix: 2.39 (0.35), residues: 240 sheet: -0.42 (0.29), residues: 286 loop : -0.17 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 358 HIS 0.010 0.001 HIS B 181 PHE 0.017 0.002 PHE A 399 TYR 0.010 0.001 TYR A 419 ARG 0.004 0.001 ARG K 19 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 333) hydrogen bonds : angle 5.37856 ( 939) metal coordination : bond 0.00522 ( 4) metal coordination : angle 3.56557 ( 6) SS BOND : bond 0.00173 ( 4) SS BOND : angle 1.06412 ( 8) covalent geometry : bond 0.00423 ( 6901) covalent geometry : angle 0.53764 ( 9371) *********************** 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 208 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 200 time to evaluate : 1.127 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: D 43 LYS cc_start: 0.8649 (mtmm) cc_final: 0.8432 (mttm) outliers start: 8 outliers final: 3 residues processed: 204 average time/residue: 0.4596 time to fit residues: 120.3494 Evaluate side-chains 197 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 194 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 ASN 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 63 optimal weight: 0.8980 chunk 45 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 77 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.128044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.114107 restraints weight = 34508.183| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.99 r_work: 0.3601 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6909 Z= 0.162 Angle : 0.514 5.246 9385 Z= 0.272 Chirality : 0.041 0.146 1051 Planarity : 0.004 0.051 1219 Dihedral : 3.991 16.830 970 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.46 % Allowed : 11.99 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.28), residues: 888 helix: 2.44 (0.35), residues: 240 sheet: -0.39 (0.29), residues: 289 loop : -0.15 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 358 HIS 0.003 0.001 HIS B 169 PHE 0.010 0.001 PHE B 84 TYR 0.019 0.001 TYR B 200 ARG 0.002 0.000 ARG K 19 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 333) hydrogen bonds : angle 5.25935 ( 939) metal coordination : bond 0.00513 ( 4) metal coordination : angle 3.80665 ( 6) SS BOND : bond 0.00157 ( 4) SS BOND : angle 1.09418 ( 8) covalent geometry : bond 0.00361 ( 6901) covalent geometry : angle 0.50416 ( 9371) *********************** 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 : 0.980 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: B 82 ASP cc_start: 0.7666 (t0) cc_final: 0.7249 (t0) REVERT: B 135 ASN cc_start: 0.6412 (m-40) cc_final: 0.5988 (m-40) REVERT: D 43 LYS cc_start: 0.8685 (mtmm) cc_final: 0.8468 (mttm) REVERT: A 408 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6710 (tm-30) outliers start: 17 outliers final: 14 residues processed: 212 average time/residue: 0.4574 time to fit residues: 123.4072 Evaluate side-chains 215 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 61 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 0.0770 chunk 59 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.126036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.112221 restraints weight = 34242.232| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.91 r_work: 0.3573 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6909 Z= 0.165 Angle : 0.514 5.492 9385 Z= 0.273 Chirality : 0.041 0.165 1051 Planarity : 0.004 0.051 1219 Dihedral : 4.069 16.958 970 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.89 % Allowed : 12.14 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.29), residues: 888 helix: 2.40 (0.34), residues: 240 sheet: -0.53 (0.29), residues: 297 loop : -0.02 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 358 HIS 0.003 0.001 HIS B 169 PHE 0.013 0.002 PHE A 231 TYR 0.015 0.001 TYR B 200 ARG 0.004 0.000 ARG K 19 Details of bonding type rmsd hydrogen bonds : bond 0.03303 ( 333) hydrogen bonds : angle 5.19713 ( 939) metal coordination : bond 0.00508 ( 4) metal coordination : angle 3.91194 ( 6) SS BOND : bond 0.00192 ( 4) SS BOND : angle 1.16342 ( 8) covalent geometry : bond 0.00367 ( 6901) covalent geometry : angle 0.50365 ( 9371) *********************** 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 230 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 0.970 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: K 110 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7257 (mp0) outliers start: 20 outliers final: 16 residues processed: 216 average time/residue: 0.4653 time to fit residues: 128.3259 Evaluate side-chains 215 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 ASP 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 57 THR Chi-restraints excluded: chain K residue 89 ASP 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 406 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 0.0030 chunk 45 optimal weight: 0.0970 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 0.0970 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 HIS ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 ASN A 86 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.126591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.112700 restraints weight = 34541.017| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.92 r_work: 0.3579 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6909 Z= 0.128 Angle : 0.492 4.601 9385 Z= 0.259 Chirality : 0.041 0.154 1051 Planarity : 0.004 0.050 1219 Dihedral : 3.987 17.016 970 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.60 % Allowed : 12.14 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.29), residues: 888 helix: 2.66 (0.35), residues: 238 sheet: -0.49 (0.29), residues: 309 loop : 0.08 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 305 HIS 0.013 0.001 HIS B 181 PHE 0.010 0.001 PHE B 83 TYR 0.014 0.001 TYR D 32 ARG 0.003 0.000 ARG K 19 Details of bonding type rmsd hydrogen bonds : bond 0.03089 ( 333) hydrogen bonds : angle 5.08291 ( 939) metal coordination : bond 0.00401 ( 4) metal coordination : angle 3.35833 ( 6) SS BOND : bond 0.00234 ( 4) SS BOND : angle 1.10330 ( 8) covalent geometry : bond 0.00286 ( 6901) covalent geometry : angle 0.48387 ( 9371) *********************** 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: 18 poor density : 209 time to evaluate : 1.086 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: B 82 ASP cc_start: 0.7749 (t0) cc_final: 0.7504 (t0) REVERT: B 135 ASN cc_start: 0.6486 (m-40) cc_final: 0.6254 (m-40) REVERT: K 110 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7221 (mp0) outliers start: 18 outliers final: 15 residues processed: 213 average time/residue: 0.4480 time to fit residues: 122.6554 Evaluate side-chains 217 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 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 89 ASP Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 77 SER 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3832 r_free = 0.3832 target = 0.123127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.109361 restraints weight = 35060.111| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.90 r_work: 0.3530 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6909 Z= 0.208 Angle : 0.547 6.483 9385 Z= 0.291 Chirality : 0.042 0.152 1051 Planarity : 0.004 0.057 1219 Dihedral : 4.276 17.593 970 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.89 % Allowed : 13.29 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.29), residues: 888 helix: 2.36 (0.35), residues: 240 sheet: -0.65 (0.28), residues: 311 loop : -0.05 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 358 HIS 0.006 0.001 HIS B 181 PHE 0.011 0.002 PHE A 231 TYR 0.012 0.002 TYR D 32 ARG 0.004 0.000 ARG K 19 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 333) hydrogen bonds : angle 5.25202 ( 939) metal coordination : bond 0.00583 ( 4) metal coordination : angle 4.18134 ( 6) SS BOND : bond 0.00225 ( 4) SS BOND : angle 1.47194 ( 8) covalent geometry : bond 0.00466 ( 6901) covalent geometry : angle 0.53586 ( 9371) *********************** 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 226 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 1.083 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: B 82 ASP cc_start: 0.7819 (t0) cc_final: 0.7610 (t0) REVERT: D 101 TRP cc_start: 0.7863 (m100) cc_final: 0.7435 (m100) REVERT: K 110 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7143 (mp0) outliers start: 20 outliers final: 16 residues processed: 211 average time/residue: 0.4862 time to fit residues: 130.5242 Evaluate side-chains 219 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 132 GLU 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 73 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.123618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.110194 restraints weight = 35155.262| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.87 r_work: 0.3551 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6909 Z= 0.172 Angle : 0.535 6.305 9385 Z= 0.283 Chirality : 0.042 0.152 1051 Planarity : 0.004 0.055 1219 Dihedral : 4.229 17.936 970 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.75 % Allowed : 16.04 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.29), residues: 888 helix: 2.42 (0.35), residues: 240 sheet: -0.63 (0.29), residues: 304 loop : -0.07 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 305 HIS 0.006 0.001 HIS B 181 PHE 0.010 0.001 PHE A 231 TYR 0.014 0.002 TYR A 363 ARG 0.003 0.000 ARG K 19 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 333) hydrogen bonds : angle 5.17572 ( 939) metal coordination : bond 0.00550 ( 4) metal coordination : angle 3.94734 ( 6) SS BOND : bond 0.00106 ( 4) SS BOND : angle 1.19037 ( 8) covalent geometry : bond 0.00387 ( 6901) covalent geometry : angle 0.52459 ( 9371) *********************** 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 225 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 1.023 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: 0.7825 (t0) cc_final: 0.7622 (t0) REVERT: D 101 TRP cc_start: 0.7817 (m100) cc_final: 0.7402 (m100) outliers start: 19 outliers final: 11 residues processed: 210 average time/residue: 0.4792 time to fit residues: 128.0256 Evaluate side-chains 209 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 106 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 77 SER 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 44 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3785 r_free = 0.3785 target = 0.119988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.106720 restraints weight = 35432.171| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.83 r_work: 0.3492 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 6909 Z= 0.289 Angle : 0.628 8.359 9385 Z= 0.336 Chirality : 0.044 0.154 1051 Planarity : 0.005 0.060 1219 Dihedral : 4.655 18.602 970 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.32 % Allowed : 15.03 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.28), residues: 888 helix: 1.89 (0.34), residues: 241 sheet: -0.72 (0.29), residues: 294 loop : -0.46 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 115 HIS 0.006 0.001 HIS A 160 PHE 0.016 0.002 PHE A 231 TYR 0.020 0.002 TYR B 143 ARG 0.005 0.001 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 333) hydrogen bonds : angle 5.45852 ( 939) metal coordination : bond 0.00822 ( 4) metal coordination : angle 5.13925 ( 6) SS BOND : bond 0.00208 ( 4) SS BOND : angle 1.70866 ( 8) covalent geometry : bond 0.00646 ( 6901) covalent geometry : angle 0.61263 ( 9371) *********************** 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 219 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 1.027 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: A 139 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7806 (mm-40) REVERT: A 157 ASP cc_start: 0.6936 (t0) cc_final: 0.6715 (t0) outliers start: 23 outliers final: 18 residues processed: 202 average time/residue: 0.4608 time to fit residues: 118.6370 Evaluate side-chains 210 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 132 GLU 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 69 ILE 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 101 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 4 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 73 optimal weight: 0.0470 chunk 71 optimal weight: 0.6980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.121982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.108748 restraints weight = 35087.831| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.82 r_work: 0.3529 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3762 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= 0.170 Angle : 0.550 7.043 9385 Z= 0.291 Chirality : 0.042 0.155 1051 Planarity : 0.004 0.060 1219 Dihedral : 4.435 18.552 970 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.46 % Allowed : 16.91 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.29), residues: 888 helix: 2.23 (0.35), residues: 241 sheet: -0.61 (0.29), residues: 301 loop : -0.20 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 305 HIS 0.006 0.001 HIS B 181 PHE 0.009 0.001 PHE A 226 TYR 0.014 0.002 TYR A 363 ARG 0.003 0.000 ARG K 19 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 333) hydrogen bonds : angle 5.21440 ( 939) metal coordination : bond 0.00583 ( 4) metal coordination : angle 4.37007 ( 6) SS BOND : bond 0.00175 ( 4) SS BOND : angle 1.11206 ( 8) covalent geometry : bond 0.00382 ( 6901) covalent geometry : angle 0.53870 ( 9371) *********************** 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 221 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 1.005 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 101 TRP cc_start: 0.7855 (m100) cc_final: 0.7510 (m100) REVERT: A 139 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7753 (mm-40) outliers start: 17 outliers final: 15 residues processed: 207 average time/residue: 0.4674 time to fit residues: 123.1532 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 : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 GLU 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 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 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 65 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 86 optimal weight: 0.0050 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 85 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.122977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.109742 restraints weight = 34850.344| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.82 r_work: 0.3542 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 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 : 0.003 0.035 6909 Z= 0.133 Angle : 0.535 8.940 9385 Z= 0.282 Chirality : 0.042 0.150 1051 Planarity : 0.004 0.061 1219 Dihedral : 4.315 19.108 970 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.88 % Allowed : 17.92 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.29), residues: 888 helix: 2.40 (0.35), residues: 241 sheet: -0.56 (0.29), residues: 301 loop : -0.07 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 305 HIS 0.006 0.001 HIS B 181 PHE 0.010 0.001 PHE B 46 TYR 0.014 0.002 TYR A 363 ARG 0.003 0.000 ARG K 19 Details of bonding type rmsd hydrogen bonds : bond 0.03096 ( 333) hydrogen bonds : angle 5.05155 ( 939) metal coordination : bond 0.00453 ( 4) metal coordination : angle 3.59831 ( 6) SS BOND : bond 0.00151 ( 4) SS BOND : angle 0.95850 ( 8) covalent geometry : bond 0.00307 ( 6901) covalent geometry : angle 0.52673 ( 9371) ********************** 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 212 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 1.026 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: A 139 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7696 (mm-40) outliers start: 13 outliers final: 13 residues processed: 202 average time/residue: 0.4684 time to fit residues: 120.5238 Evaluate side-chains 205 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 192 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 73 THR Chi-restraints excluded: chain A residue 77 SER 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 21 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 81 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3807 r_free = 0.3807 target = 0.121589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.108193 restraints weight = 34981.994| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.85 r_work: 0.3515 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6909 Z= 0.196 Angle : 0.575 9.620 9385 Z= 0.304 Chirality : 0.043 0.291 1051 Planarity : 0.005 0.061 1219 Dihedral : 4.468 18.595 970 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.17 % Allowed : 18.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.29), residues: 888 helix: 2.11 (0.34), residues: 241 sheet: -0.64 (0.29), residues: 301 loop : -0.11 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 115 HIS 0.016 0.001 HIS B 181 PHE 0.013 0.002 PHE B 100 TYR 0.012 0.002 TYR B 143 ARG 0.003 0.000 ARG K 19 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 333) hydrogen bonds : angle 5.21463 ( 939) metal coordination : bond 0.00626 ( 4) metal coordination : angle 4.30710 ( 6) SS BOND : bond 0.00181 ( 4) SS BOND : angle 1.26816 ( 8) covalent geometry : bond 0.00443 ( 6901) covalent geometry : angle 0.56384 ( 9371) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6320.02 seconds wall clock time: 109 minutes 13.57 seconds (6553.57 seconds total)