Starting phenix.real_space_refine on Sun Jul 5 03:24:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bvq_16268/07_2026/8bvq_16268.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bvq_16268/07_2026/8bvq_16268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bvq_16268/07_2026/8bvq_16268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bvq_16268/07_2026/8bvq_16268.map" model { file = "/net/cci-nas-00/data/ceres_data/8bvq_16268/07_2026/8bvq_16268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bvq_16268/07_2026/8bvq_16268.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8bvq_16268/07_2026/8bvq_16268.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bvq_16268/07_2026/8bvq_16268.cif" } resolution = 3.3 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2650 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 7486 2.51 5 N 2029 2.21 5 O 2328 1.98 5 H 11258 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s 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: 23133 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 12092 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 29, 'TRANS': 755} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 5337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 5337 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 11, 'TRANS': 352} Chain: "C" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 793 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 6, 'TRANS': 51} Chain: "D" Number of atoms: 3478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3478 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 12, 'TRANS': 206} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1294 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 139 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'NH2NOTPRO': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'UX8:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 4.01, per 1000 atoms: 0.17 Number of scatterers: 23133 At special positions: 0 Unit cell: (122.84, 106.24, 134.46, 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 32 16.00 O 2328 8.00 N 2029 7.00 C 7486 6.00 H 11258 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 653.2 milliseconds 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2774 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 18 sheets defined 22.5% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.542A pdb=" N MET A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.802A pdb=" N LEU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 144 removed outlier: 3.768A pdb=" N ASP A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 216 through 233 removed outlier: 3.828A pdb=" N ARG A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.558A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.858A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 4.061A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'C' and resid 33 through 38 Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 47 through 62 removed outlier: 3.619A pdb=" N ALA D 51 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 121 removed outlier: 3.569A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 209 through 225 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 228 through 241 Processing helix chain 'E' and resid 41 through 46 Processing helix chain 'E' and resid 51 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 80 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 4.749A pdb=" N ILE A 94 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU A 165 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER A 96 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU A 167 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR A 98 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE A 169 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER A 100 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 5.667A pdb=" N ILE A 254 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN A 179 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 260 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 193 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295 removed outlier: 4.378A pdb=" N GLU A 294 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL A 335 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY A 270 " --> pdb=" O VAL A 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 375 through 376 removed outlier: 3.905A pdb=" N ALA A 375 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 2 through 5 removed outlier: 3.636A pdb=" N UX8 G 3 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 426 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR A 617 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 519 " --> pdb=" O ASN A 523 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.547A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 50 removed outlier: 4.204A pdb=" N TRP B 48 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.026A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 100 through 101 removed outlier: 3.725A pdb=" N SER B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 122 through 124 removed outlier: 7.173A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.367A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.462A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.537A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.657A pdb=" N ALA B 307 " --> pdb=" O TRP B 317 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.730A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=AB9, first strand: chain 'E' and resid 64 through 65 removed outlier: 4.559A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE E 74 " --> pdb=" O MET E 64 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR E 94 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN E 103 " --> pdb=" O THR E 94 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1479 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.60 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 11252 1.02 - 1.22: 5 1.22 - 1.42: 5149 1.42 - 1.61: 6924 1.61 - 1.81: 64 Bond restraints: 23394 Sorted by residual: bond pdb=" CB UX8 G 3 " pdb=" HB2 UX8 G 3 " ideal model delta sigma weight residual 0.970 1.243 -0.273 2.00e-02 2.50e+03 1.87e+02 bond pdb=" CZ3 UX8 G 3 " pdb=" HZ3 UX8 G 3 " ideal model delta sigma weight residual 0.930 1.132 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" CE3 UX8 G 3 " pdb=" HE3 UX8 G 3 " ideal model delta sigma weight residual 0.930 1.118 -0.188 2.00e-02 2.50e+03 8.84e+01 bond pdb=" CA UX8 G 3 " pdb=" C UX8 G 3 " ideal model delta sigma weight residual 1.525 1.334 0.191 2.10e-02 2.27e+03 8.24e+01 bond pdb=" CA UX8 G 3 " pdb=" CB UX8 G 3 " ideal model delta sigma weight residual 1.530 1.711 -0.181 2.00e-02 2.50e+03 8.21e+01 ... (remaining 23389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.95: 41981 7.95 - 15.90: 7 15.90 - 23.85: 2 23.85 - 31.79: 0 31.79 - 39.74: 3 Bond angle restraints: 41993 Sorted by residual: angle pdb=" CA UX8 G 3 " pdb=" C UX8 G 3 " pdb=" O UX8 G 3 " ideal model delta sigma weight residual 120.80 143.43 -22.63 1.70e+00 3.46e-01 1.77e+02 angle pdb=" C PRO A 684 " pdb=" CA PRO A 684 " pdb=" HA PRO A 684 " ideal model delta sigma weight residual 109.00 69.26 39.74 3.00e+00 1.11e-01 1.75e+02 angle pdb=" N PRO A 684 " pdb=" CA PRO A 684 " pdb=" HA PRO A 684 " ideal model delta sigma weight residual 110.00 74.86 35.14 3.00e+00 1.11e-01 1.37e+02 angle pdb=" CB PRO A 684 " pdb=" CA PRO A 684 " pdb=" HA PRO A 684 " ideal model delta sigma weight residual 109.00 76.06 32.94 3.00e+00 1.11e-01 1.21e+02 angle pdb=" CA UX8 G 3 " pdb=" C UX8 G 3 " pdb=" N THR G 4 " ideal model delta sigma weight residual 116.20 103.08 13.12 2.00e+00 2.50e-01 4.30e+01 ... (remaining 41988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 9775 17.75 - 35.50: 964 35.50 - 53.25: 289 53.25 - 71.00: 78 71.00 - 88.74: 11 Dihedral angle restraints: 11117 sinusoidal: 5960 harmonic: 5157 Sorted by residual: dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual 93.00 151.79 -58.79 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CA ASP A 614 " pdb=" CB ASP A 614 " pdb=" CG ASP A 614 " pdb=" OD1 ASP A 614 " ideal model delta sinusoidal sigma weight residual -30.00 -84.40 54.40 1 2.00e+01 2.50e-03 1.00e+01 dihedral pdb=" CA ARG C 33 " pdb=" CB ARG C 33 " pdb=" CG ARG C 33 " pdb=" CD ARG C 33 " ideal model delta sinusoidal sigma weight residual 180.00 120.59 59.41 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 11114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1649 0.082 - 0.164: 145 0.164 - 0.246: 1 0.246 - 0.328: 0 0.328 - 0.409: 2 Chirality restraints: 1797 Sorted by residual: chirality pdb=" CB UX8 G 3 " pdb=" CA UX8 G 3 " pdb=" CG UX8 G 3 " pdb=" O9 UX8 G 3 " both_signs ideal model delta sigma weight residual False -2.38 -2.79 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CA PRO A 684 " pdb=" N PRO A 684 " pdb=" C PRO A 684 " pdb=" CB PRO A 684 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA UX8 G 3 " pdb=" N UX8 G 3 " pdb=" C UX8 G 3 " pdb=" CB UX8 G 3 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.93e-01 ... (remaining 1794 not shown) Planarity restraints: 3599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 35 " -0.027 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO B 36 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 185 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C ASN A 185 " 0.026 2.00e-02 2.50e+03 pdb=" O ASN A 185 " -0.010 2.00e-02 2.50e+03 pdb=" N HIS A 186 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 31 " 0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO D 32 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO D 32 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 32 " 0.018 5.00e-02 4.00e+02 ... (remaining 3596 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 514 2.12 - 2.74: 40715 2.74 - 3.36: 63818 3.36 - 3.98: 81734 3.98 - 4.60: 127390 Nonbonded interactions: 314171 Sorted by model distance: nonbonded pdb=" O HIS A 677 " pdb=" H THR A 692 " model vdw 1.503 2.450 nonbonded pdb=" OE1 GLU A 435 " pdb=" H GLU A 435 " model vdw 1.618 2.450 nonbonded pdb=" OG1 THR B 309 " pdb=" H VAL B 314 " model vdw 1.626 2.450 nonbonded pdb=" O LEU A 66 " pdb=" HG1 THR A 69 " model vdw 1.631 2.450 nonbonded pdb=" OD2 ASP A 362 " pdb="HH21 ARG A 366 " model vdw 1.635 2.450 ... (remaining 314166 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: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.140 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 23.900 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 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 : 0.004 0.191 12139 Z= 0.203 Angle : 0.551 22.631 16499 Z= 0.290 Chirality : 0.044 0.409 1797 Planarity : 0.003 0.040 2173 Dihedral : 16.055 88.745 4390 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.31 % Allowed : 23.46 % Favored : 76.22 % 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: -0.42 (0.22), residues: 1503 helix: 2.48 (0.30), residues: 316 sheet: -0.90 (0.24), residues: 471 loop : -1.07 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 273 TYR 0.013 0.001 TYR D 184 PHE 0.015 0.001 PHE A 738 TRP 0.014 0.001 TRP B 317 HIS 0.003 0.001 HIS A 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 (12136) covalent geometry : angle 0.55109 / 0.29 (16497) SS BOND : bond 0.00062 / 0.03 ( 1) SS BOND : angle 0.45105 / 0.25 ( 2) hydrogen bonds : bond 0.11265 / 8.15 ( 531) hydrogen bonds : angle 5.80752 / 4.04 ( 1479) Misc. bond : bond 0.00072 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 170 time to evaluate : 0.619 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: D 183 GLU cc_start: 0.8235 (tp30) cc_final: 0.7579 (tt0) outliers start: 4 outliers final: 3 residues processed: 173 average time/residue: 0.1965 time to fit residues: 51.4051 Evaluate side-chains 165 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 162 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 808 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 GLN ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.194057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.139265 restraints weight = 43706.360| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.30 r_work: 0.3304 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.0672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 12139 Z= 0.234 Angle : 0.554 6.913 16499 Z= 0.300 Chirality : 0.045 0.364 1797 Planarity : 0.004 0.053 2173 Dihedral : 4.545 58.772 1673 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.99 % Allowed : 21.42 % Favored : 75.59 % 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: -0.88 (0.21), residues: 1503 helix: 1.84 (0.29), residues: 324 sheet: -0.98 (0.24), residues: 470 loop : -1.44 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 91 TYR 0.019 0.001 TYR D 184 PHE 0.014 0.001 PHE A 426 TRP 0.009 0.001 TRP A 376 HIS 0.006 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (12136) covalent geometry : angle 0.55433 / 0.30 (16497) SS BOND : bond 0.00003 / 0.00 ( 1) SS BOND : angle 0.32168 / 0.17 ( 2) hydrogen bonds : bond 0.04206 / 2.95 ( 531) hydrogen bonds : angle 5.44961 / 3.79 ( 1479) Misc. bond : bond 0.00131 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.647 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 178 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8671 (tt0) REVERT: A 243 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8613 (p) REVERT: B 230 GLN cc_start: 0.7209 (tp-100) cc_final: 0.6815 (tp40) REVERT: B 306 MET cc_start: 0.7238 (ptp) cc_final: 0.6969 (ptp) REVERT: B 323 LEU cc_start: 0.8153 (tp) cc_final: 0.7882 (mt) REVERT: C 57 ILE cc_start: 0.8116 (pt) cc_final: 0.7834 (tp) REVERT: C 78 LYS cc_start: 0.8300 (ttmt) cc_final: 0.8058 (mtpt) outliers start: 38 outliers final: 27 residues processed: 207 average time/residue: 0.2020 time to fit residues: 63.1738 Evaluate side-chains 192 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 49 optimal weight: 0.0470 chunk 69 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.194026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.138577 restraints weight = 43274.431| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.25 r_work: 0.3323 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12139 Z= 0.147 Angle : 0.508 6.262 16499 Z= 0.273 Chirality : 0.043 0.366 1797 Planarity : 0.004 0.042 2173 Dihedral : 4.490 59.723 1673 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.44 % Allowed : 22.05 % Favored : 75.51 % 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: -0.75 (0.22), residues: 1503 helix: 2.01 (0.29), residues: 325 sheet: -0.94 (0.24), residues: 475 loop : -1.36 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 91 TYR 0.016 0.001 TYR D 184 PHE 0.011 0.001 PHE A 426 TRP 0.008 0.001 TRP A 376 HIS 0.004 0.001 HIS A 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (12136) covalent geometry : angle 0.50805 / 0.27 (16497) SS BOND : bond 0.00096 / 0.05 ( 1) SS BOND : angle 0.37662 / 0.21 ( 2) hydrogen bonds : bond 0.03870 / 2.72 ( 531) hydrogen bonds : angle 5.25625 / 3.66 ( 1479) Misc. bond : bond 0.00093 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.465 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 243 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8596 (p) REVERT: B 230 GLN cc_start: 0.7221 (tp-100) cc_final: 0.6862 (tp40) REVERT: B 306 MET cc_start: 0.7261 (ptp) cc_final: 0.6988 (ptp) REVERT: B 323 LEU cc_start: 0.8144 (tp) cc_final: 0.7879 (mt) REVERT: C 57 ILE cc_start: 0.8117 (pt) cc_final: 0.7860 (tp) REVERT: C 78 LYS cc_start: 0.8168 (ttmt) cc_final: 0.7942 (mtpt) outliers start: 31 outliers final: 23 residues processed: 196 average time/residue: 0.1851 time to fit residues: 55.4337 Evaluate side-chains 184 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 86 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 119 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 81 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** 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 = 0.4173 r_free = 0.4173 target = 0.195460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.140220 restraints weight = 44041.114| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.56 r_work: 0.3335 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12139 Z= 0.096 Angle : 0.476 6.226 16499 Z= 0.254 Chirality : 0.043 0.367 1797 Planarity : 0.003 0.045 2173 Dihedral : 4.332 59.543 1673 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.05 % Allowed : 22.68 % Favored : 75.28 % 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: -0.57 (0.22), residues: 1503 helix: 2.26 (0.29), residues: 326 sheet: -0.83 (0.24), residues: 469 loop : -1.31 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 91 TYR 0.015 0.001 TYR D 184 PHE 0.009 0.001 PHE A 426 TRP 0.008 0.001 TRP A 376 HIS 0.004 0.001 HIS A 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (12136) covalent geometry : angle 0.47585 / 0.25 (16497) SS BOND : bond 0.00181 / 0.10 ( 1) SS BOND : angle 0.40305 / 0.23 ( 2) hydrogen bonds : bond 0.03314 / 2.31 ( 531) hydrogen bonds : angle 5.01804 / 3.51 ( 1479) Misc. bond : bond 0.00128 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.553 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 243 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8590 (p) REVERT: B 230 GLN cc_start: 0.7199 (tp-100) cc_final: 0.6841 (tp40) REVERT: B 259 PHE cc_start: 0.8162 (m-80) cc_final: 0.7852 (m-80) REVERT: B 306 MET cc_start: 0.7222 (ptp) cc_final: 0.7015 (ptp) REVERT: B 323 LEU cc_start: 0.8195 (tp) cc_final: 0.7940 (mt) REVERT: C 57 ILE cc_start: 0.8226 (pt) cc_final: 0.8005 (tp) REVERT: D 183 GLU cc_start: 0.8504 (tp30) cc_final: 0.8209 (tt0) outliers start: 26 outliers final: 19 residues processed: 190 average time/residue: 0.1888 time to fit residues: 55.2638 Evaluate side-chains 183 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 3 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** 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 = 0.4145 r_free = 0.4145 target = 0.192510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.137690 restraints weight = 43142.187| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.20 r_work: 0.3329 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12139 Z= 0.143 Angle : 0.491 6.384 16499 Z= 0.262 Chirality : 0.043 0.366 1797 Planarity : 0.003 0.049 2173 Dihedral : 4.364 58.678 1673 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.68 % Allowed : 22.20 % Favored : 75.12 % 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: -0.64 (0.21), residues: 1503 helix: 2.16 (0.29), residues: 327 sheet: -0.86 (0.24), residues: 470 loop : -1.34 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 91 TYR 0.016 0.001 TYR D 184 PHE 0.011 0.001 PHE A 426 TRP 0.007 0.001 TRP A 205 HIS 0.002 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (12136) covalent geometry : angle 0.49142 / 0.26 (16497) SS BOND : bond 0.00100 / 0.05 ( 1) SS BOND : angle 0.44670 / 0.24 ( 2) hydrogen bonds : bond 0.03519 / 2.45 ( 531) hydrogen bonds : angle 5.02497 / 3.52 ( 1479) Misc. bond : bond 0.00104 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.616 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 243 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8595 (p) REVERT: B 230 GLN cc_start: 0.7182 (tp-100) cc_final: 0.6795 (tp40) REVERT: B 259 PHE cc_start: 0.8173 (m-80) cc_final: 0.7871 (m-80) REVERT: B 306 MET cc_start: 0.7282 (ptp) cc_final: 0.7013 (ptp) REVERT: B 323 LEU cc_start: 0.8159 (tp) cc_final: 0.7925 (mt) REVERT: C 57 ILE cc_start: 0.8185 (pt) cc_final: 0.7952 (tp) outliers start: 34 outliers final: 28 residues processed: 189 average time/residue: 0.1904 time to fit residues: 55.6474 Evaluate side-chains 188 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 34 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** 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 = 0.4179 r_free = 0.4179 target = 0.195932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.141579 restraints weight = 43563.341| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.29 r_work: 0.3332 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12139 Z= 0.118 Angle : 0.480 6.298 16499 Z= 0.256 Chirality : 0.043 0.367 1797 Planarity : 0.003 0.053 2173 Dihedral : 4.317 58.911 1673 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.44 % Allowed : 22.20 % Favored : 75.35 % 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: -0.58 (0.21), residues: 1503 helix: 2.25 (0.29), residues: 326 sheet: -0.83 (0.24), residues: 469 loop : -1.32 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 91 TYR 0.017 0.001 TYR D 80 PHE 0.010 0.001 PHE A 426 TRP 0.007 0.001 TRP A 376 HIS 0.002 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (12136) covalent geometry : angle 0.48046 / 0.26 (16497) SS BOND : bond 0.00117 / 0.06 ( 1) SS BOND : angle 0.43497 / 0.24 ( 2) hydrogen bonds : bond 0.03363 / 2.35 ( 531) hydrogen bonds : angle 4.93929 / 3.47 ( 1479) Misc. bond : bond 0.00099 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.565 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 243 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8611 (p) REVERT: B 230 GLN cc_start: 0.7267 (tp-100) cc_final: 0.6861 (tp40) REVERT: B 259 PHE cc_start: 0.8184 (m-80) cc_final: 0.7875 (m-80) REVERT: B 306 MET cc_start: 0.7295 (ptp) cc_final: 0.7020 (ptp) REVERT: B 323 LEU cc_start: 0.8149 (tp) cc_final: 0.7935 (mt) REVERT: C 57 ILE cc_start: 0.8203 (pt) cc_final: 0.7977 (tp) REVERT: D 183 GLU cc_start: 0.8637 (tp30) cc_final: 0.8304 (tt0) outliers start: 31 outliers final: 27 residues processed: 191 average time/residue: 0.1818 time to fit residues: 53.9375 Evaluate side-chains 186 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 31 optimal weight: 3.9990 chunk 89 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** 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 = 0.4176 r_free = 0.4176 target = 0.195520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.141575 restraints weight = 43333.291| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.13 r_work: 0.3343 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12139 Z= 0.114 Angle : 0.478 6.659 16499 Z= 0.254 Chirality : 0.043 0.366 1797 Planarity : 0.003 0.053 2173 Dihedral : 4.280 58.659 1673 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.86 % Favored : 95.08 % Rotamer: Outliers : 2.52 % Allowed : 22.36 % Favored : 75.12 % 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: -0.53 (0.22), residues: 1503 helix: 2.32 (0.29), residues: 326 sheet: -0.82 (0.24), residues: 469 loop : -1.28 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 91 TYR 0.015 0.001 TYR D 184 PHE 0.010 0.001 PHE A 426 TRP 0.007 0.001 TRP A 376 HIS 0.002 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (12136) covalent geometry : angle 0.47850 / 0.25 (16497) SS BOND : bond 0.00107 / 0.06 ( 1) SS BOND : angle 0.42136 / 0.23 ( 2) hydrogen bonds : bond 0.03283 / 2.29 ( 531) hydrogen bonds : angle 4.88483 / 3.44 ( 1479) Misc. bond : bond 0.00106 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.626 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 243 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8605 (p) REVERT: B 230 GLN cc_start: 0.7314 (tp-100) cc_final: 0.6944 (tp40) REVERT: B 306 MET cc_start: 0.7267 (ptp) cc_final: 0.6990 (ptp) REVERT: C 57 ILE cc_start: 0.8212 (pt) cc_final: 0.7996 (tp) REVERT: D 183 GLU cc_start: 0.8576 (tp30) cc_final: 0.8249 (tt0) outliers start: 32 outliers final: 28 residues processed: 193 average time/residue: 0.1903 time to fit residues: 56.2377 Evaluate side-chains 187 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 36 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 118 optimal weight: 0.1980 chunk 115 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.195381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.139589 restraints weight = 43738.267| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.50 r_work: 0.3360 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 12139 Z= 0.099 Angle : 0.473 6.757 16499 Z= 0.250 Chirality : 0.043 0.367 1797 Planarity : 0.003 0.053 2173 Dihedral : 4.219 58.615 1673 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.39 % Favored : 95.54 % Rotamer: Outliers : 2.52 % Allowed : 21.89 % Favored : 75.59 % 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: -0.43 (0.22), residues: 1503 helix: 2.43 (0.29), residues: 327 sheet: -0.79 (0.24), residues: 475 loop : -1.22 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 91 TYR 0.017 0.001 TYR D 80 PHE 0.009 0.001 PHE A 426 TRP 0.008 0.001 TRP A 376 HIS 0.002 0.001 HIS D 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (12136) covalent geometry : angle 0.47287 / 0.25 (16497) SS BOND : bond 0.00122 / 0.06 ( 1) SS BOND : angle 0.42108 / 0.23 ( 2) hydrogen bonds : bond 0.03140 / 2.19 ( 531) hydrogen bonds : angle 4.78668 / 3.37 ( 1479) Misc. bond : bond 0.00111 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.610 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 243 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8648 (p) REVERT: B 230 GLN cc_start: 0.7460 (tp-100) cc_final: 0.7088 (tp40) REVERT: B 259 PHE cc_start: 0.8323 (m-80) cc_final: 0.8039 (m-80) REVERT: B 306 MET cc_start: 0.7331 (ptp) cc_final: 0.7129 (ptp) REVERT: C 57 ILE cc_start: 0.8327 (pt) cc_final: 0.8117 (tp) REVERT: D 82 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8579 (t0) REVERT: D 183 GLU cc_start: 0.8790 (tp30) cc_final: 0.8505 (tt0) outliers start: 32 outliers final: 27 residues processed: 192 average time/residue: 0.1921 time to fit residues: 56.9391 Evaluate side-chains 188 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 82 ASN Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 69 optimal weight: 0.4980 chunk 111 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 117 optimal weight: 0.3980 chunk 94 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 347 HIS ** 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 = 0.4187 r_free = 0.4187 target = 0.196826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.141753 restraints weight = 43418.422| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.24 r_work: 0.3358 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 12139 Z= 0.098 Angle : 0.472 6.675 16499 Z= 0.250 Chirality : 0.043 0.367 1797 Planarity : 0.003 0.053 2173 Dihedral : 4.226 58.391 1673 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.79 % Favored : 95.14 % Rotamer: Outliers : 2.44 % Allowed : 21.81 % Favored : 75.75 % 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: -0.38 (0.22), residues: 1503 helix: 2.47 (0.29), residues: 328 sheet: -0.76 (0.24), residues: 475 loop : -1.20 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 91 TYR 0.016 0.001 TYR D 80 PHE 0.009 0.001 PHE A 426 TRP 0.007 0.001 TRP A 376 HIS 0.002 0.001 HIS D 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (12136) covalent geometry : angle 0.47215 / 0.25 (16497) SS BOND : bond 0.00117 / 0.06 ( 1) SS BOND : angle 0.40754 / 0.23 ( 2) hydrogen bonds : bond 0.03115 / 2.17 ( 531) hydrogen bonds : angle 4.75781 / 3.35 ( 1479) Misc. bond : bond 0.00114 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.607 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 259 PHE cc_start: 0.8209 (m-80) cc_final: 0.7907 (m-80) REVERT: B 306 MET cc_start: 0.7224 (ptp) cc_final: 0.6945 (ptp) REVERT: C 57 ILE cc_start: 0.8222 (pt) cc_final: 0.8012 (tp) REVERT: D 183 GLU cc_start: 0.8589 (tp30) cc_final: 0.7860 (tt0) outliers start: 31 outliers final: 28 residues processed: 188 average time/residue: 0.1895 time to fit residues: 54.6973 Evaluate side-chains 188 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 94 optimal weight: 0.0970 chunk 79 optimal weight: 0.9990 chunk 116 optimal weight: 0.0970 chunk 101 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 65 optimal weight: 0.0970 chunk 146 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 347 HIS ** 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 = 0.4182 r_free = 0.4182 target = 0.195903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.137985 restraints weight = 43049.056| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.71 r_work: 0.3376 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 12139 Z= 0.087 Angle : 0.466 6.634 16499 Z= 0.246 Chirality : 0.043 0.367 1797 Planarity : 0.003 0.053 2173 Dihedral : 4.125 57.921 1673 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.46 % Favored : 95.48 % Rotamer: Outliers : 1.97 % Allowed : 22.20 % Favored : 75.83 % 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: -0.28 (0.22), residues: 1503 helix: 2.53 (0.29), residues: 334 sheet: -0.73 (0.24), residues: 470 loop : -1.13 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 91 TYR 0.014 0.001 TYR D 184 PHE 0.008 0.001 PHE A 426 TRP 0.009 0.001 TRP A 376 HIS 0.002 0.001 HIS D 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (12136) covalent geometry : angle 0.46564 / 0.25 (16497) SS BOND : bond 0.00143 / 0.08 ( 1) SS BOND : angle 0.40239 / 0.22 ( 2) hydrogen bonds : bond 0.02934 / 2.04 ( 531) hydrogen bonds : angle 4.65905 / 3.28 ( 1479) Misc. bond : bond 0.00125 / 0.06 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.615 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 259 PHE cc_start: 0.8179 (m-80) cc_final: 0.7868 (m-80) REVERT: B 306 MET cc_start: 0.7221 (ptp) cc_final: 0.6943 (ptp) REVERT: C 57 ILE cc_start: 0.8233 (pt) cc_final: 0.8029 (tp) REVERT: D 183 GLU cc_start: 0.8465 (tp30) cc_final: 0.7756 (tt0) outliers start: 25 outliers final: 23 residues processed: 189 average time/residue: 0.1919 time to fit residues: 54.8848 Evaluate side-chains 186 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 127 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 3 optimal weight: 50.0000 chunk 7 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 347 HIS ** 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 = 0.4157 r_free = 0.4157 target = 0.193355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.134523 restraints weight = 43273.601| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.70 r_work: 0.3328 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12139 Z= 0.188 Angle : 0.512 6.687 16499 Z= 0.274 Chirality : 0.044 0.364 1797 Planarity : 0.004 0.055 2173 Dihedral : 4.328 58.428 1673 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.20 % Allowed : 22.20 % Favored : 75.59 % 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: -0.52 (0.22), residues: 1503 helix: 2.32 (0.29), residues: 326 sheet: -0.82 (0.24), residues: 475 loop : -1.28 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 132 TYR 0.015 0.001 TYR D 184 PHE 0.013 0.001 PHE A 791 TRP 0.009 0.001 TRP A 205 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (12136) covalent geometry : angle 0.51249 / 0.27 (16497) SS BOND : bond 0.00044 / 0.02 ( 1) SS BOND : angle 0.47240 / 0.26 ( 2) hydrogen bonds : bond 0.03582 / 2.49 ( 531) hydrogen bonds : angle 4.88496 / 3.43 ( 1479) Misc. bond : bond 0.00078 / 0.04 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6265.11 seconds wall clock time: 106 minutes 52.69 seconds (6412.69 seconds total)