Starting phenix.real_space_refine on Mon Aug 25 04:24:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bvq_16268/08_2025/8bvq_16268.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bvq_16268/08_2025/8bvq_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 { model { file = "/net/cci-nas-00/data/ceres_data/8bvq_16268/08_2025/8bvq_16268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bvq_16268/08_2025/8bvq_16268.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bvq_16268/08_2025/8bvq_16268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bvq_16268/08_2025/8bvq_16268.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.75, per 1000 atoms: 0.16 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: 2.15 Conformation dependent library (CDL) restraints added in 523.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.52 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: 5.34 Time building geometry restraints manager: 3.00 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: 9778 17.75 - 35.50: 964 35.50 - 53.25: 289 53.25 - 71.00: 78 71.00 - 88.74: 11 Dihedral angle restraints: 11120 sinusoidal: 5963 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 11117 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.120 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 20.650 Find NCS groups from input model: 0.070 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 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 aren 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 covalent geometry : bond 0.00421 (12136) covalent geometry : angle 0.55109 (16497) SS BOND : bond 0.00062 ( 1) SS BOND : angle 0.45105 ( 2) hydrogen bonds : bond 0.11265 ( 531) hydrogen bonds : angle 5.80752 ( 1479) Misc. bond : bond 0.00072 ( 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 : 0.666 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: 0.1887 time to fit residues: 48.6580 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 : 0.599 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4162 r_free = 0.4162 target = 0.194200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.139823 restraints weight = 43614.111| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.24 r_work: 0.3313 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.0605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 12139 Z= 0.231 Angle : 0.549 6.978 16499 Z= 0.297 Chirality : 0.045 0.364 1797 Planarity : 0.004 0.051 2173 Dihedral : 4.489 58.901 1673 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.68 % Allowed : 21.73 % 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 aren not related in a simple way. whole: -0.84 (0.21), residues: 1503 helix: 1.89 (0.29), residues: 324 sheet: -0.96 (0.24), residues: 470 loop : -1.41 (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 0.016 0.001 PHE A 426 TRP 0.010 0.001 TRP A 376 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00532 (12136) covalent geometry : angle 0.54944 (16497) SS BOND : bond 0.00015 ( 1) SS BOND : angle 0.35875 ( 2) hydrogen bonds : bond 0.04250 ( 531) hydrogen bonds : angle 5.45183 ( 1479) Misc. bond : bond 0.00144 ( 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 207 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.637 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: 0.8907 (OUTLIER) cc_final: 0.8668 (tt0) REVERT: A 243 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8615 (p) REVERT: A 501 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7549 (tt) REVERT: B 230 GLN cc_start: 0.7210 (tp-100) cc_final: 0.6719 (tp-100) REVERT: B 306 MET cc_start: 0.7251 (ptp) cc_final: 0.6988 (ptp) REVERT: B 323 LEU cc_start: 0.8162 (tp) cc_final: 0.7892 (mt) REVERT: C 57 ILE cc_start: 0.8116 (pt) cc_final: 0.7837 (tp) REVERT: C 78 LYS cc_start: 0.8255 (ttmt) cc_final: 0.7997 (mtpt) outliers start: 34 outliers final: 24 residues processed: 202 average time/residue: 0.1872 time to fit residues: 57.2730 Evaluate side-chains 193 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 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 501 LEU 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 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 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: 2.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 84 optimal weight: 0.0060 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4176 r_free = 0.4176 target = 0.195692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.140171 restraints weight = 43998.801| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.49 r_work: 0.3411 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12139 Z= 0.158 Angle : 0.512 6.119 16499 Z= 0.275 Chirality : 0.044 0.366 1797 Planarity : 0.004 0.043 2173 Dihedral : 4.491 59.492 1673 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % 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 aren not related in a simple way. whole: -0.72 (0.21), residues: 1503 helix: 1.99 (0.29), residues: 325 sheet: -0.87 (0.24), residues: 464 loop : -1.36 (0.22), residues: 714 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 covalent geometry : bond 0.00364 (12136) covalent geometry : angle 0.51218 (16497) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.44324 ( 2) hydrogen bonds : bond 0.03896 ( 531) hydrogen bonds : angle 5.26128 ( 1479) Misc. bond : bond 0.00096 ( 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 205 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 0.502 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: 0.8933 (OUTLIER) cc_final: 0.8647 (p) REVERT: B 230 GLN cc_start: 0.7352 (tp-100) cc_final: 0.7032 (tp40) REVERT: B 323 LEU cc_start: 0.8291 (tp) cc_final: 0.8016 (mt) REVERT: C 57 ILE cc_start: 0.8249 (pt) cc_final: 0.8007 (tp) REVERT: C 78 LYS cc_start: 0.8115 (ttmt) cc_final: 0.7889 (mtpt) outliers start: 32 outliers final: 25 residues processed: 198 average time/residue: 0.1694 time to fit residues: 50.9387 Evaluate side-chains 187 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 501 LEU 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 690 CYS 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: 2.9990 chunk 13 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 119 optimal weight: 0.0270 chunk 54 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4175 r_free = 0.4175 target = 0.195625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.141647 restraints weight = 44080.676| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.19 r_work: 0.3357 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12139 Z= 0.097 Angle : 0.478 6.013 16499 Z= 0.254 Chirality : 0.043 0.367 1797 Planarity : 0.003 0.045 2173 Dihedral : 4.327 59.603 1673 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.20 % Allowed : 22.60 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.22), residues: 1503 helix: 2.25 (0.29), residues: 326 sheet: -0.82 (0.24), residues: 475 loop : -1.29 (0.22), residues: 702 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 0.009 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 covalent geometry : bond 0.00223 (12136) covalent geometry : angle 0.47796 (16497) SS BOND : bond 0.00087 ( 1) SS BOND : angle 0.33514 ( 2) hydrogen bonds : bond 0.03324 ( 531) hydrogen bonds : angle 5.01564 ( 1479) Misc. bond : bond 0.00137 ( 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 197 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.456 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: 0.8796 (OUTLIER) cc_final: 0.8586 (p) REVERT: A 741 MET cc_start: 0.6623 (tmm) cc_final: 0.6416 (tmm) REVERT: B 230 GLN cc_start: 0.7165 (tp-100) cc_final: 0.6787 (tp40) REVERT: B 259 PHE cc_start: 0.8148 (m-80) cc_final: 0.7850 (m-80) REVERT: B 323 LEU cc_start: 0.8152 (tp) cc_final: 0.7895 (mt) REVERT: C 57 ILE cc_start: 0.8137 (pt) cc_final: 0.7896 (tp) REVERT: D 183 GLU cc_start: 0.8607 (tp30) cc_final: 0.8280 (tt0) outliers start: 28 outliers final: 21 residues processed: 193 average time/residue: 0.1753 time to fit residues: 51.7730 Evaluate side-chains 183 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 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 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 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: 10.0000 chunk 96 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 75 optimal weight: 0.0970 chunk 114 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 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 = 0.4149 r_free = 0.4149 target = 0.192931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.137254 restraints weight = 43069.593| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.45 r_work: 0.3322 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.0984 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= 0.132 Angle : 0.487 6.549 16499 Z= 0.259 Chirality : 0.043 0.366 1797 Planarity : 0.003 0.050 2173 Dihedral : 4.338 58.694 1673 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.60 % Allowed : 22.36 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.22), residues: 1503 helix: 2.19 (0.29), residues: 327 sheet: -0.83 (0.24), residues: 475 loop : -1.30 (0.22), residues: 701 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 749 HIS 0.002 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00303 (12136) covalent geometry : angle 0.48726 (16497) SS BOND : bond 0.00078 ( 1) SS BOND : angle 0.39068 ( 2) hydrogen bonds : bond 0.03442 ( 531) hydrogen bonds : angle 4.99326 ( 1479) Misc. bond : bond 0.00112 ( 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 199 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.607 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: 0.8819 (OUTLIER) cc_final: 0.8603 (p) REVERT: A 741 MET cc_start: 0.6678 (tmm) cc_final: 0.6476 (tmm) REVERT: B 230 GLN cc_start: 0.7283 (tp-100) cc_final: 0.6900 (tp40) REVERT: B 259 PHE cc_start: 0.8177 (m-80) cc_final: 0.7868 (m-80) REVERT: B 323 LEU cc_start: 0.8189 (tp) cc_final: 0.7970 (mt) REVERT: C 57 ILE cc_start: 0.8189 (pt) cc_final: 0.7948 (tp) REVERT: D 183 GLU cc_start: 0.8674 (tp30) cc_final: 0.8341 (tt0) outliers start: 33 outliers final: 26 residues processed: 191 average time/residue: 0.1777 time to fit residues: 52.4875 Evaluate side-chains 188 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 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 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 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: 0.6980 chunk 86 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 32 optimal weight: 0.0980 chunk 43 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.195813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.140696 restraints weight = 44141.115| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.50 r_work: 0.3343 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12139 Z= 0.094 Angle : 0.469 6.511 16499 Z= 0.249 Chirality : 0.043 0.368 1797 Planarity : 0.003 0.053 2173 Dihedral : 4.227 58.929 1673 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.13 % Allowed : 22.60 % 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 aren not related in a simple way. whole: -0.46 (0.22), residues: 1503 helix: 2.37 (0.29), residues: 327 sheet: -0.77 (0.24), residues: 469 loop : -1.25 (0.22), residues: 707 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 0.009 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 covalent geometry : bond 0.00217 (12136) covalent geometry : angle 0.46856 (16497) SS BOND : bond 0.00121 ( 1) SS BOND : angle 0.38201 ( 2) hydrogen bonds : bond 0.03138 ( 531) hydrogen bonds : angle 4.84185 ( 1479) Misc. bond : bond 0.00120 ( 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 193 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.554 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: 0.8848 (OUTLIER) cc_final: 0.8643 (p) REVERT: B 230 GLN cc_start: 0.7417 (tp-100) cc_final: 0.7031 (tp40) REVERT: B 259 PHE cc_start: 0.8259 (m-80) cc_final: 0.7960 (m-80) REVERT: B 323 LEU cc_start: 0.8223 (tp) cc_final: 0.8005 (mt) REVERT: C 57 ILE cc_start: 0.8226 (pt) cc_final: 0.8003 (tp) REVERT: D 183 GLU cc_start: 0.8739 (tp30) cc_final: 0.8448 (tt0) outliers start: 27 outliers final: 23 residues processed: 188 average time/residue: 0.1853 time to fit residues: 53.4722 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 : 0.633 ------------------------------------------------------------------------------- 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 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 628 VAL Chi-restraints excluded: chain A residue 645 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 31 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 90 optimal weight: 0.0470 chunk 142 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 38 optimal weight: 0.0470 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.195307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.139429 restraints weight = 43259.899| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.33 r_work: 0.3370 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 12139 Z= 0.092 Angle : 0.465 6.579 16499 Z= 0.246 Chirality : 0.042 0.367 1797 Planarity : 0.003 0.053 2173 Dihedral : 4.168 58.409 1673 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.41 % Rotamer: Outliers : 2.20 % Allowed : 22.52 % 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 aren not related in a simple way. whole: -0.43 (0.22), residues: 1503 helix: 2.38 (0.29), residues: 333 sheet: -0.78 (0.24), residues: 470 loop : -1.24 (0.22), residues: 700 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 0.007 0.001 TRP A 376 HIS 0.002 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00214 (12136) covalent geometry : angle 0.46511 (16497) SS BOND : bond 0.00107 ( 1) SS BOND : angle 0.38442 ( 2) hydrogen bonds : bond 0.03072 ( 531) hydrogen bonds : angle 4.76624 ( 1479) Misc. bond : bond 0.00123 ( 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 196 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.537 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: A 243 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8649 (p) REVERT: B 259 PHE cc_start: 0.8297 (m-80) cc_final: 0.8015 (m-80) REVERT: B 323 LEU cc_start: 0.8231 (tp) cc_final: 0.8015 (mt) REVERT: C 57 ILE cc_start: 0.8292 (pt) cc_final: 0.8079 (tp) REVERT: D 82 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8535 (t0) REVERT: D 183 GLU cc_start: 0.8693 (tp30) cc_final: 0.8420 (tt0) REVERT: D 225 MET cc_start: 0.8368 (mtp) cc_final: 0.8068 (mtp) outliers start: 28 outliers final: 22 residues processed: 190 average time/residue: 0.1587 time to fit residues: 46.3167 Evaluate side-chains 185 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 195 SER Chi-restraints excluded: chain A residue 243 THR 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 628 VAL Chi-restraints excluded: chain A residue 645 GLU 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 82 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 118 optimal weight: 0.5980 chunk 115 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.196698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141801 restraints weight = 43177.472| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 3.20 r_work: 0.3450 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12139 Z= 0.115 Angle : 0.474 6.542 16499 Z= 0.251 Chirality : 0.043 0.367 1797 Planarity : 0.003 0.053 2173 Dihedral : 4.220 58.271 1673 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.66 % Favored : 95.28 % Rotamer: Outliers : 2.44 % Allowed : 22.13 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.22), residues: 1503 helix: 2.33 (0.29), residues: 334 sheet: -0.77 (0.24), residues: 469 loop : -1.26 (0.22), residues: 700 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 0.006 0.001 TRP A 776 HIS 0.002 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00267 (12136) covalent geometry : angle 0.47414 (16497) SS BOND : bond 0.00085 ( 1) SS BOND : angle 0.41542 ( 2) hydrogen bonds : bond 0.03168 ( 531) hydrogen bonds : angle 4.76911 ( 1479) Misc. bond : bond 0.00108 ( 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 194 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.454 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 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: 0.8875 (OUTLIER) cc_final: 0.8648 (p) REVERT: B 259 PHE cc_start: 0.8304 (m-80) cc_final: 0.8027 (m-80) REVERT: B 323 LEU cc_start: 0.8245 (tp) cc_final: 0.8021 (mt) REVERT: D 183 GLU cc_start: 0.8688 (tp30) cc_final: 0.8416 (tt0) outliers start: 31 outliers final: 27 residues processed: 188 average time/residue: 0.1966 time to fit residues: 56.1075 Evaluate side-chains 191 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 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 176 GLU 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 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 645 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 69 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4161 r_free = 0.4161 target = 0.193954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.138694 restraints weight = 43702.945| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 3.25 r_work: 0.3406 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12139 Z= 0.194 Angle : 0.532 6.807 16499 Z= 0.286 Chirality : 0.044 0.363 1797 Planarity : 0.004 0.055 2173 Dihedral : 4.461 58.457 1673 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.60 % Allowed : 21.97 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.21), residues: 1503 helix: 2.15 (0.29), residues: 326 sheet: -0.91 (0.24), residues: 468 loop : -1.39 (0.21), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 6 TYR 0.016 0.001 TYR D 184 PHE 0.015 0.001 PHE G 7 TRP 0.010 0.001 TRP A 205 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00448 (12136) covalent geometry : angle 0.53159 (16497) SS BOND : bond 0.00022 ( 1) SS BOND : angle 0.54279 ( 2) hydrogen bonds : bond 0.03819 ( 531) hydrogen bonds : angle 5.01532 ( 1479) Misc. bond : bond 0.00086 ( 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 200 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.639 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: 0.8908 (OUTLIER) cc_final: 0.8639 (p) REVERT: B 259 PHE cc_start: 0.8305 (m-80) cc_final: 0.8032 (m-80) REVERT: B 323 LEU cc_start: 0.8223 (tp) cc_final: 0.8016 (mt) outliers start: 33 outliers final: 29 residues processed: 195 average time/residue: 0.1999 time to fit residues: 58.1989 Evaluate side-chains 188 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 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 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 645 GLU 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 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: 0.9990 chunk 2 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 116 optimal weight: 0.3980 chunk 101 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4166 r_free = 0.4166 target = 0.194169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.135546 restraints weight = 43303.998| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.71 r_work: 0.3339 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12139 Z= 0.119 Angle : 0.488 5.915 16499 Z= 0.260 Chirality : 0.043 0.365 1797 Planarity : 0.003 0.055 2173 Dihedral : 4.350 59.078 1673 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.20 % Allowed : 22.05 % 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 aren not related in a simple way. whole: -0.56 (0.22), residues: 1503 helix: 2.33 (0.29), residues: 326 sheet: -0.85 (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 0.015 0.001 TYR D 184 PHE 0.011 0.001 PHE A 426 TRP 0.008 0.001 TRP A 376 HIS 0.002 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00273 (12136) covalent geometry : angle 0.48774 (16497) SS BOND : bond 0.00140 ( 1) SS BOND : angle 0.45459 ( 2) hydrogen bonds : bond 0.03377 ( 531) hydrogen bonds : angle 4.86611 ( 1479) Misc. bond : bond 0.00093 ( 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 190 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.518 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 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: 0.8809 (OUTLIER) cc_final: 0.8589 (p) REVERT: B 259 PHE cc_start: 0.8201 (m-80) cc_final: 0.7909 (m-80) REVERT: B 323 LEU cc_start: 0.8143 (tp) cc_final: 0.7939 (mt) outliers start: 28 outliers final: 25 residues processed: 184 average time/residue: 0.1770 time to fit residues: 49.5032 Evaluate side-chains 187 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 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 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 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 127 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 22 optimal weight: 0.0980 chunk 30 optimal weight: 0.0030 chunk 48 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 50.0000 chunk 7 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4158 r_free = 0.4158 target = 0.193322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.140405 restraints weight = 43256.785| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 3.32 r_work: 0.3319 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12139 Z= 0.150 Angle : 0.497 5.875 16499 Z= 0.266 Chirality : 0.043 0.365 1797 Planarity : 0.004 0.056 2173 Dihedral : 4.375 58.294 1673 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % 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 aren not related in a simple way. whole: -0.62 (0.22), residues: 1503 helix: 2.26 (0.29), residues: 326 sheet: -0.88 (0.24), residues: 469 loop : -1.34 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 6 TYR 0.015 0.001 TYR D 184 PHE 0.010 0.001 PHE A 426 TRP 0.008 0.001 TRP A 205 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00346 (12136) covalent geometry : angle 0.49749 (16497) SS BOND : bond 0.00077 ( 1) SS BOND : angle 0.49097 ( 2) hydrogen bonds : bond 0.03493 ( 531) hydrogen bonds : angle 4.90109 ( 1479) Misc. bond : bond 0.00092 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5953.64 seconds wall clock time: 101 minutes 22.84 seconds (6082.84 seconds total)