Starting phenix.real_space_refine on Thu Jul 2 05:55:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xn6_33312/07_2026/7xn6_33312.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xn6_33312/07_2026/7xn6_33312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7xn6_33312/07_2026/7xn6_33312.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xn6_33312/07_2026/7xn6_33312.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xn6_33312/07_2026/7xn6_33312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xn6_33312/07_2026/7xn6_33312.map" model { file = "/net/cci-nas-00/data/ceres_data/7xn6_33312/07_2026/7xn6_33312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xn6_33312/07_2026/7xn6_33312.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 38 5.16 5 C 4346 2.51 5 N 1211 2.21 5 O 1277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6874 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1714 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3256 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain: "C" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1394 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 6, 'TRANS': 163} Chain breaks: 5 Chain: "D" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 466 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'APR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NCA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.55, per 1000 atoms: 0.23 Number of scatterers: 6874 At special positions: 0 Unit cell: (107.776, 96.83, 76.622, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 2 15.00 O 1277 8.00 N 1211 7.00 C 4346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 394.2 milliseconds 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1606 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 42.3% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 67 through 80 Processing helix chain 'A' and resid 92 through 105 Processing helix chain 'A' and resid 136 through 141 removed outlier: 3.541A pdb=" N THR A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 214 through 226 removed outlier: 4.355A pdb=" N CYS A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'B' and resid 52 through 74 removed outlier: 4.209A pdb=" N PHE B 58 " --> pdb=" O LYS B 54 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU B 70 " --> pdb=" O GLN B 66 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N MET B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 82 removed outlier: 3.547A pdb=" N GLU B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 114 removed outlier: 3.927A pdb=" N LEU B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 128 Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.568A pdb=" N LEU B 175 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 171 through 176' Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.570A pdb=" N CYS B 221 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 222 " --> pdb=" O PRO B 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 218 through 222' Processing helix chain 'B' and resid 244 through 251 removed outlier: 3.715A pdb=" N VAL B 248 " --> pdb=" O HIS B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.035A pdb=" N GLY B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA B 256 " --> pdb=" O PRO B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 251 through 256' Processing helix chain 'B' and resid 280 through 292 removed outlier: 4.028A pdb=" N ALA B 284 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.882A pdb=" N TYR B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 322 removed outlier: 3.800A pdb=" N SER B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 355 through 363 removed outlier: 3.821A pdb=" N GLY B 361 " --> pdb=" O PRO B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 378 removed outlier: 4.148A pdb=" N THR B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP B 378 " --> pdb=" O TRP B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 392 Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'B' and resid 420 through 431 Processing helix chain 'B' and resid 447 through 456 Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'C' and resid 69 through 80 removed outlier: 3.783A pdb=" N GLU C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 107 through 111 removed outlier: 4.015A pdb=" N LYS C 110 " --> pdb=" O ASP C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 213 through 226 Processing helix chain 'C' and resid 231 through 246 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 102 through 112 removed outlier: 3.628A pdb=" N THR D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN D 111 " --> pdb=" O HIS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 128 removed outlier: 4.042A pdb=" N GLU D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.208A pdb=" N LEU A 46 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL A 117 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE A 48 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU A 119 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE A 50 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE A 114 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ILE A 159 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N CYS A 116 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS A 156 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ALA A 196 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE A 158 " --> pdb=" O ALA A 196 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 128 Processing sheet with id=AA3, first strand: chain 'B' and resid 225 through 227 Processing sheet with id=AA4, first strand: chain 'B' and resid 149 through 152 Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 87 removed outlier: 7.079A pdb=" N CYS C 47 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU C 46 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL C 117 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE C 48 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU C 119 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE C 50 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 194 " --> pdb=" O LYS C 156 " (cutoff:3.500A) 227 hydrogen bonds defined for protein. 654 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: 0.79 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1150 1.29 - 1.42: 1879 1.42 - 1.55: 3918 1.55 - 1.68: 6 1.68 - 1.81: 64 Bond restraints: 7017 Sorted by residual: bond pdb=" C2D APR A1001 " pdb=" O2D APR A1001 " ideal model delta sigma weight residual 1.397 1.573 -0.176 2.00e-02 2.50e+03 7.77e+01 bond pdb=" CA TYR B 68 " pdb=" C TYR B 68 " ideal model delta sigma weight residual 1.522 1.413 0.109 1.34e-02 5.57e+03 6.65e+01 bond pdb=" C1D APR A1001 " pdb=" C2D APR A1001 " ideal model delta sigma weight residual 1.529 1.675 -0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" CA ALA B 141 " pdb=" C ALA B 141 " ideal model delta sigma weight residual 1.528 1.449 0.080 1.39e-02 5.18e+03 3.28e+01 bond pdb=" CA SER B 139 " pdb=" C SER B 139 " ideal model delta sigma weight residual 1.522 1.453 0.070 1.23e-02 6.61e+03 3.20e+01 ... (remaining 7012 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.61: 9408 4.61 - 9.23: 28 9.23 - 13.84: 4 13.84 - 18.46: 3 18.46 - 23.07: 4 Bond angle restraints: 9447 Sorted by residual: angle pdb=" O3A APR A1001 " pdb=" PB APR A1001 " pdb=" O5D APR A1001 " ideal model delta sigma weight residual 101.31 124.38 -23.07 3.00e+00 1.11e-01 5.91e+01 angle pdb=" C1D APR A1001 " pdb=" C2D APR A1001 " pdb=" O2D APR A1001 " ideal model delta sigma weight residual 110.00 87.63 22.37 3.00e+00 1.11e-01 5.56e+01 angle pdb=" N TYR B 68 " pdb=" CA TYR B 68 " pdb=" C TYR B 68 " ideal model delta sigma weight residual 113.38 105.51 7.87 1.23e+00 6.61e-01 4.09e+01 angle pdb=" C5D APR A1001 " pdb=" C4D APR A1001 " pdb=" O4D APR A1001 " ideal model delta sigma weight residual 111.97 130.75 -18.78 3.00e+00 1.11e-01 3.92e+01 angle pdb=" O3A APR A1001 " pdb=" PA APR A1001 " pdb=" O5' APR A1001 " ideal model delta sigma weight residual 102.36 121.10 -18.74 3.00e+00 1.11e-01 3.90e+01 ... (remaining 9442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 3668 17.82 - 35.64: 407 35.64 - 53.46: 80 53.46 - 71.28: 9 71.28 - 89.09: 10 Dihedral angle restraints: 4174 sinusoidal: 1686 harmonic: 2488 Sorted by residual: dihedral pdb=" CA GLU D 140 " pdb=" C GLU D 140 " pdb=" N PHE D 141 " pdb=" CA PHE D 141 " ideal model delta harmonic sigma weight residual 180.00 -152.49 -27.51 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA LYS B 300 " pdb=" C LYS B 300 " pdb=" N ALA B 301 " pdb=" CA ALA B 301 " ideal model delta harmonic sigma weight residual -180.00 -154.71 -25.29 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" C ASN B 355 " pdb=" N ASN B 355 " pdb=" CA ASN B 355 " pdb=" CB ASN B 355 " ideal model delta harmonic sigma weight residual -122.60 -110.04 -12.56 0 2.50e+00 1.60e-01 2.52e+01 ... (remaining 4171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.185: 1002 0.185 - 0.370: 5 0.370 - 0.556: 1 0.556 - 0.741: 0 0.741 - 0.926: 2 Chirality restraints: 1010 Sorted by residual: chirality pdb=" C2D APR A1001 " pdb=" C1D APR A1001 " pdb=" C3D APR A1001 " pdb=" O2D APR A1001 " both_signs ideal model delta sigma weight residual False -2.45 -3.38 0.93 2.00e-01 2.50e+01 2.14e+01 chirality pdb=" C3D APR A1001 " pdb=" C2D APR A1001 " pdb=" C4D APR A1001 " pdb=" O3D APR A1001 " both_signs ideal model delta sigma weight residual False -2.71 -1.96 -0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" C4D APR A1001 " pdb=" C3D APR A1001 " pdb=" C5D APR A1001 " pdb=" O4D APR A1001 " both_signs ideal model delta sigma weight residual False -2.49 -2.04 -0.45 2.00e-01 2.50e+01 5.05e+00 ... (remaining 1007 not shown) Planarity restraints: 1221 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' APR A1001 " -0.124 2.00e-02 2.50e+03 5.80e-02 9.25e+01 pdb=" C2 APR A1001 " 0.007 2.00e-02 2.50e+03 pdb=" C4 APR A1001 " 0.060 2.00e-02 2.50e+03 pdb=" C5 APR A1001 " 0.057 2.00e-02 2.50e+03 pdb=" C6 APR A1001 " -0.001 2.00e-02 2.50e+03 pdb=" C8 APR A1001 " 0.016 2.00e-02 2.50e+03 pdb=" N1 APR A1001 " -0.024 2.00e-02 2.50e+03 pdb=" N3 APR A1001 " 0.051 2.00e-02 2.50e+03 pdb=" N6 APR A1001 " -0.095 2.00e-02 2.50e+03 pdb=" N7 APR A1001 " 0.046 2.00e-02 2.50e+03 pdb=" N9 APR A1001 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 66 " 0.024 2.00e-02 2.50e+03 4.77e-02 2.27e+01 pdb=" C GLN B 66 " -0.082 2.00e-02 2.50e+03 pdb=" O GLN B 66 " 0.030 2.00e-02 2.50e+03 pdb=" N SER B 67 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 443 " -0.016 2.00e-02 2.50e+03 3.08e-02 9.48e+00 pdb=" C ASN B 443 " 0.053 2.00e-02 2.50e+03 pdb=" O ASN B 443 " -0.019 2.00e-02 2.50e+03 pdb=" N SER B 444 " -0.018 2.00e-02 2.50e+03 ... (remaining 1218 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 4 2.26 - 2.92: 2852 2.92 - 3.58: 9411 3.58 - 4.24: 15202 4.24 - 4.90: 26010 Nonbonded interactions: 53479 Sorted by model distance: nonbonded pdb=" NE ARG A 207 " pdb=" C1D APR A1001 " model vdw 1.596 3.550 nonbonded pdb=" C3D APR A1001 " pdb=" O5D APR A1001 " model vdw 2.029 2.776 nonbonded pdb=" CZ ARG A 207 " pdb=" C1D APR A1001 " model vdw 2.227 2.960 nonbonded pdb=" OH TYR A 37 " pdb=" O GLY A 153 " model vdw 2.238 3.040 nonbonded pdb=" O PHE B 72 " pdb=" N LEU B 85 " model vdw 2.261 3.120 ... (remaining 53474 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.250 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.800 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 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 : 0.007 0.176 7018 Z= 0.402 Angle : 0.965 23.071 9447 Z= 0.518 Chirality : 0.061 0.926 1010 Planarity : 0.006 0.069 1221 Dihedral : 15.576 89.095 2568 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.70 % Allowed : 0.98 % Favored : 98.33 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.27), residues: 839 helix: -0.96 (0.28), residues: 342 sheet: -2.81 (0.47), residues: 119 loop : -2.98 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 75 TYR 0.016 0.001 TYR B 68 PHE 0.007 0.001 PHE A 78 TRP 0.033 0.002 TRP B 261 HIS 0.007 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00664 / 0.40 ( 7017) covalent geometry : angle 0.96466 / 0.52 ( 9447) hydrogen bonds : bond 0.16424 / 10.09 ( 227) hydrogen bonds : angle 6.52226 / 4.55 ( 654) Misc. bond : bond 0.03089 / 1.63 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: B 306 GLN cc_start: 0.6926 (pp30) cc_final: 0.6716 (pp30) REVERT: B 332 MET cc_start: 0.8470 (tmm) cc_final: 0.8254 (tmm) REVERT: C 89 ASN cc_start: 0.7856 (p0) cc_final: 0.7637 (p0) REVERT: C 102 ASP cc_start: 0.7464 (m-30) cc_final: 0.6305 (m-30) outliers start: 5 outliers final: 2 residues processed: 135 average time/residue: 0.0786 time to fit residues: 14.2307 Evaluate side-chains 106 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain B residue 139 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 HIS A 121 HIS A 208 ASN A 217 GLN B 140 ASN B 200 HIS B 210 ASN B 309 GLN B 443 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.139078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.110331 restraints weight = 12368.298| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.86 r_work: 0.3366 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7018 Z= 0.135 Angle : 0.572 5.930 9447 Z= 0.305 Chirality : 0.042 0.150 1010 Planarity : 0.005 0.065 1221 Dihedral : 6.426 78.948 943 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 1.53 % Allowed : 8.51 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.28), residues: 839 helix: -0.57 (0.28), residues: 342 sheet: -2.71 (0.47), residues: 120 loop : -2.66 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 75 TYR 0.017 0.001 TYR A 37 PHE 0.030 0.001 PHE A 247 TRP 0.019 0.001 TRP B 261 HIS 0.004 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 7017) covalent geometry : angle 0.57201 / 0.31 ( 9447) hydrogen bonds : bond 0.03732 / 2.30 ( 227) hydrogen bonds : angle 4.93230 / 3.46 ( 654) Misc. bond : bond 0.00085 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 TRP cc_start: 0.4546 (OUTLIER) cc_final: 0.4062 (m100) REVERT: B 302 TYR cc_start: 0.7600 (t80) cc_final: 0.7120 (t80) REVERT: C 89 ASN cc_start: 0.8160 (p0) cc_final: 0.7926 (p0) REVERT: D 140 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7702 (mm-30) outliers start: 11 outliers final: 8 residues processed: 116 average time/residue: 0.0884 time to fit residues: 13.6795 Evaluate side-chains 117 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 60 optimal weight: 0.0010 chunk 77 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 32 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.0970 chunk 30 optimal weight: 4.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 HIS ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.139686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.113195 restraints weight = 12229.889| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.98 r_work: 0.3355 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7018 Z= 0.122 Angle : 0.545 6.169 9447 Z= 0.291 Chirality : 0.041 0.141 1010 Planarity : 0.004 0.062 1221 Dihedral : 6.193 78.176 942 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 1.39 % Allowed : 11.85 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.28), residues: 839 helix: -0.40 (0.28), residues: 345 sheet: -2.56 (0.47), residues: 122 loop : -2.51 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 330 TYR 0.017 0.001 TYR A 37 PHE 0.009 0.001 PHE B 299 TRP 0.013 0.001 TRP B 261 HIS 0.004 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 7017) covalent geometry : angle 0.54508 / 0.29 ( 9447) hydrogen bonds : bond 0.03236 / 1.95 ( 227) hydrogen bonds : angle 4.68094 / 3.30 ( 654) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 TRP cc_start: 0.4516 (OUTLIER) cc_final: 0.3997 (m100) REVERT: A 228 ASP cc_start: 0.8388 (p0) cc_final: 0.7644 (p0) REVERT: A 229 LYS cc_start: 0.8950 (mmmt) cc_final: 0.8689 (mmmt) REVERT: B 302 TYR cc_start: 0.7743 (t80) cc_final: 0.7226 (t80) REVERT: C 89 ASN cc_start: 0.8158 (p0) cc_final: 0.7863 (p0) outliers start: 10 outliers final: 9 residues processed: 114 average time/residue: 0.0900 time to fit residues: 13.6758 Evaluate side-chains 114 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 107 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 2 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 52 optimal weight: 0.0870 chunk 26 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 0.0050 chunk 23 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.3772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 HIS ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.141234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.114555 restraints weight = 12471.967| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.84 r_work: 0.3407 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7018 Z= 0.104 Angle : 0.525 6.431 9447 Z= 0.279 Chirality : 0.041 0.135 1010 Planarity : 0.004 0.054 1221 Dihedral : 6.008 75.893 942 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 1.95 % Allowed : 12.27 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.29), residues: 839 helix: -0.36 (0.28), residues: 355 sheet: -2.33 (0.47), residues: 120 loop : -2.56 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 149 TYR 0.016 0.001 TYR A 37 PHE 0.008 0.001 PHE A 247 TRP 0.014 0.001 TRP B 261 HIS 0.005 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 ( 7017) covalent geometry : angle 0.52450 / 0.28 ( 9447) hydrogen bonds : bond 0.02922 / 1.74 ( 227) hydrogen bonds : angle 4.49038 / 3.16 ( 654) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 206 TRP cc_start: 0.4462 (OUTLIER) cc_final: 0.3950 (m100) REVERT: A 228 ASP cc_start: 0.8204 (p0) cc_final: 0.7958 (p0) REVERT: A 229 LYS cc_start: 0.8916 (mmmt) cc_final: 0.8606 (pttm) REVERT: C 89 ASN cc_start: 0.8159 (p0) cc_final: 0.7875 (p0) REVERT: C 233 MET cc_start: 0.7730 (mmp) cc_final: 0.7461 (mmm) REVERT: D 140 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7202 (mm-30) outliers start: 14 outliers final: 10 residues processed: 117 average time/residue: 0.0775 time to fit residues: 12.2436 Evaluate side-chains 118 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain D residue 89 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 HIS ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.136637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.110154 restraints weight = 12687.765| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.87 r_work: 0.3331 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7018 Z= 0.196 Angle : 0.591 5.390 9447 Z= 0.311 Chirality : 0.043 0.133 1010 Planarity : 0.005 0.055 1221 Dihedral : 6.271 75.217 942 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 2.51 % Allowed : 14.23 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.29), residues: 839 helix: -0.62 (0.28), residues: 362 sheet: -2.47 (0.46), residues: 122 loop : -2.44 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 149 TYR 0.022 0.002 TYR A 37 PHE 0.030 0.002 PHE A 247 TRP 0.019 0.001 TRP B 261 HIS 0.006 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 ( 7017) covalent geometry : angle 0.59131 / 0.31 ( 9447) hydrogen bonds : bond 0.03460 / 2.17 ( 227) hydrogen bonds : angle 4.79728 / 3.42 ( 654) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.8309 (p0) cc_final: 0.8047 (p0) REVERT: A 229 LYS cc_start: 0.9023 (mmmt) cc_final: 0.8664 (pttt) REVERT: A 261 GLN cc_start: 0.6400 (tm-30) cc_final: 0.5996 (tm-30) REVERT: C 89 ASN cc_start: 0.8110 (p0) cc_final: 0.7837 (p0) REVERT: C 107 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8215 (p0) REVERT: C 233 MET cc_start: 0.7843 (mmp) cc_final: 0.7608 (mmm) REVERT: C 262 ILE cc_start: 0.8085 (mp) cc_final: 0.7783 (mm) REVERT: D 140 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7279 (mm-30) outliers start: 18 outliers final: 16 residues processed: 116 average time/residue: 0.0736 time to fit residues: 11.8236 Evaluate side-chains 123 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain D residue 89 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.136339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.110926 restraints weight = 12680.500| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.79 r_work: 0.3338 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7018 Z= 0.191 Angle : 0.600 7.903 9447 Z= 0.315 Chirality : 0.043 0.133 1010 Planarity : 0.005 0.056 1221 Dihedral : 6.288 74.180 942 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 2.65 % Allowed : 15.34 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.29), residues: 839 helix: -0.60 (0.28), residues: 363 sheet: -2.49 (0.46), residues: 122 loop : -2.43 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 149 TYR 0.022 0.002 TYR A 37 PHE 0.011 0.001 PHE A 78 TRP 0.016 0.001 TRP B 261 HIS 0.013 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 ( 7017) covalent geometry : angle 0.59962 / 0.31 ( 9447) hydrogen bonds : bond 0.03343 / 2.09 ( 227) hydrogen bonds : angle 4.76954 / 3.40 ( 654) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.8277 (p0) cc_final: 0.8036 (p0) REVERT: A 229 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8685 (pttm) REVERT: A 261 GLN cc_start: 0.6393 (tm-30) cc_final: 0.5924 (tm-30) REVERT: C 89 ASN cc_start: 0.8106 (p0) cc_final: 0.7842 (p0) REVERT: C 107 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8198 (p0) REVERT: C 233 MET cc_start: 0.7823 (mmp) cc_final: 0.7603 (mmm) outliers start: 19 outliers final: 16 residues processed: 117 average time/residue: 0.0724 time to fit residues: 11.7503 Evaluate side-chains 122 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 118 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 36 optimal weight: 0.0870 chunk 62 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 HIS ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.138491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.111250 restraints weight = 12383.288| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.91 r_work: 0.3370 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7018 Z= 0.130 Angle : 0.553 6.683 9447 Z= 0.293 Chirality : 0.041 0.137 1010 Planarity : 0.004 0.056 1221 Dihedral : 6.025 70.209 942 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.51 % Allowed : 15.76 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.29), residues: 839 helix: -0.50 (0.28), residues: 374 sheet: -2.32 (0.47), residues: 122 loop : -2.45 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 106 TYR 0.018 0.001 TYR A 37 PHE 0.039 0.001 PHE A 247 TRP 0.012 0.001 TRP B 261 HIS 0.005 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 7017) covalent geometry : angle 0.55349 / 0.29 ( 9447) hydrogen bonds : bond 0.02978 / 1.83 ( 227) hydrogen bonds : angle 4.53627 / 3.23 ( 654) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.7679 (mmt) cc_final: 0.7451 (mmt) REVERT: A 228 ASP cc_start: 0.8180 (p0) cc_final: 0.7934 (p0) REVERT: A 229 LYS cc_start: 0.8995 (mmmt) cc_final: 0.8687 (pttt) REVERT: A 261 GLN cc_start: 0.6381 (tm-30) cc_final: 0.5977 (tm-30) REVERT: B 302 TYR cc_start: 0.7757 (t80) cc_final: 0.7330 (t80) REVERT: C 76 GLU cc_start: 0.8135 (pm20) cc_final: 0.7841 (pm20) REVERT: C 89 ASN cc_start: 0.8148 (p0) cc_final: 0.7889 (p0) REVERT: C 107 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8194 (p0) REVERT: D 110 THR cc_start: 0.6969 (p) cc_final: 0.6700 (p) outliers start: 18 outliers final: 13 residues processed: 117 average time/residue: 0.0815 time to fit residues: 12.8590 Evaluate side-chains 118 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain D residue 89 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 67 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.138518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.110745 restraints weight = 12666.666| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.05 r_work: 0.3363 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7018 Z= 0.128 Angle : 0.564 9.354 9447 Z= 0.297 Chirality : 0.041 0.134 1010 Planarity : 0.004 0.055 1221 Dihedral : 5.903 67.236 942 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.23 % Allowed : 16.88 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.29), residues: 839 helix: -0.43 (0.28), residues: 374 sheet: -2.20 (0.48), residues: 122 loop : -2.40 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 106 TYR 0.017 0.001 TYR A 37 PHE 0.029 0.001 PHE A 247 TRP 0.012 0.001 TRP B 261 HIS 0.004 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 7017) covalent geometry : angle 0.56397 / 0.30 ( 9447) hydrogen bonds : bond 0.02920 / 1.80 ( 227) hydrogen bonds : angle 4.47074 / 3.19 ( 654) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.8225 (p0) cc_final: 0.7991 (p0) REVERT: A 229 LYS cc_start: 0.9001 (mmmt) cc_final: 0.8681 (pttt) REVERT: A 261 GLN cc_start: 0.6464 (tm-30) cc_final: 0.6066 (tm-30) REVERT: B 173 LYS cc_start: 0.6417 (mttt) cc_final: 0.5123 (mmtt) REVERT: B 302 TYR cc_start: 0.7802 (t80) cc_final: 0.7377 (t80) REVERT: C 89 ASN cc_start: 0.8141 (p0) cc_final: 0.7869 (p0) REVERT: C 107 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8336 (p0) REVERT: C 233 MET cc_start: 0.7838 (mmp) cc_final: 0.7573 (mmm) REVERT: D 110 THR cc_start: 0.6916 (p) cc_final: 0.6680 (p) outliers start: 16 outliers final: 14 residues processed: 115 average time/residue: 0.0840 time to fit residues: 12.9588 Evaluate side-chains 120 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain D residue 141 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 78 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 40 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.137259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.109728 restraints weight = 12230.672| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.88 r_work: 0.3363 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7018 Z= 0.144 Angle : 0.591 11.930 9447 Z= 0.309 Chirality : 0.042 0.141 1010 Planarity : 0.004 0.056 1221 Dihedral : 5.917 66.307 942 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 2.23 % Allowed : 17.29 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.29), residues: 839 helix: -0.49 (0.28), residues: 374 sheet: -2.17 (0.48), residues: 122 loop : -2.37 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 106 TYR 0.018 0.001 TYR A 37 PHE 0.025 0.001 PHE A 247 TRP 0.012 0.001 TRP B 261 HIS 0.005 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 ( 7017) covalent geometry : angle 0.59054 / 0.31 ( 9447) hydrogen bonds : bond 0.03162 / 1.92 ( 227) hydrogen bonds : angle 4.48187 / 3.20 ( 654) Misc. bond : bond 0.00026 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LYS cc_start: 0.9005 (mmmt) cc_final: 0.8447 (pttt) REVERT: A 261 GLN cc_start: 0.6438 (tm-30) cc_final: 0.6079 (tm-30) REVERT: B 173 LYS cc_start: 0.6418 (mttt) cc_final: 0.5112 (mmtt) REVERT: B 302 TYR cc_start: 0.7857 (t80) cc_final: 0.7408 (t80) REVERT: B 467 HIS cc_start: 0.8746 (OUTLIER) cc_final: 0.8464 (m-70) REVERT: C 89 ASN cc_start: 0.8111 (p0) cc_final: 0.7852 (p0) REVERT: C 107 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8319 (p0) REVERT: C 233 MET cc_start: 0.7801 (mmp) cc_final: 0.7529 (mmm) REVERT: D 110 THR cc_start: 0.6920 (p) cc_final: 0.6682 (p) outliers start: 16 outliers final: 14 residues processed: 115 average time/residue: 0.0841 time to fit residues: 13.2532 Evaluate side-chains 121 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain D residue 141 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 44 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.136874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.110095 restraints weight = 12549.662| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.81 r_work: 0.3351 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7018 Z= 0.173 Angle : 0.617 12.493 9447 Z= 0.322 Chirality : 0.042 0.139 1010 Planarity : 0.005 0.056 1221 Dihedral : 6.036 67.384 942 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 2.65 % Allowed : 17.43 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.29), residues: 839 helix: -0.55 (0.27), residues: 375 sheet: -2.21 (0.48), residues: 122 loop : -2.37 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 106 TYR 0.020 0.002 TYR A 37 PHE 0.023 0.001 PHE A 247 TRP 0.013 0.001 TRP B 261 HIS 0.005 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 7017) covalent geometry : angle 0.61663 / 0.32 ( 9447) hydrogen bonds : bond 0.03330 / 2.04 ( 227) hydrogen bonds : angle 4.58624 / 3.28 ( 654) Misc. bond : bond 0.00016 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LYS cc_start: 0.8880 (mmmt) cc_final: 0.8514 (pttt) REVERT: B 302 TYR cc_start: 0.7853 (t80) cc_final: 0.7411 (t80) REVERT: B 467 HIS cc_start: 0.8803 (OUTLIER) cc_final: 0.8461 (m-70) REVERT: C 89 ASN cc_start: 0.8060 (p0) cc_final: 0.7800 (p0) REVERT: C 107 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8331 (p0) REVERT: C 271 LYS cc_start: 0.8175 (mttt) cc_final: 0.7962 (mttm) REVERT: D 110 THR cc_start: 0.6905 (p) cc_final: 0.6659 (p) outliers start: 19 outliers final: 16 residues processed: 113 average time/residue: 0.0749 time to fit residues: 11.5215 Evaluate side-chains 119 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain D residue 141 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 70 optimal weight: 0.9990 chunk 31 optimal weight: 0.0040 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 0.0870 chunk 50 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 overall best weight: 0.3570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 GLN B 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.139718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.113525 restraints weight = 12466.382| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.76 r_work: 0.3397 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7018 Z= 0.110 Angle : 0.574 12.712 9447 Z= 0.300 Chirality : 0.041 0.137 1010 Planarity : 0.004 0.057 1221 Dihedral : 5.687 61.338 942 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 1.81 % Allowed : 18.55 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.29), residues: 839 helix: -0.36 (0.28), residues: 375 sheet: -2.03 (0.50), residues: 122 loop : -2.36 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 106 TYR 0.014 0.001 TYR A 37 PHE 0.022 0.001 PHE A 247 TRP 0.011 0.001 TRP A 214 HIS 0.004 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 7017) covalent geometry : angle 0.57377 / 0.30 ( 9447) hydrogen bonds : bond 0.02873 / 1.72 ( 227) hydrogen bonds : angle 4.30387 / 3.07 ( 654) Misc. bond : bond 0.00017 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1433.14 seconds wall clock time: 25 minutes 26.16 seconds (1526.16 seconds total)