Starting phenix.real_space_refine on Sat Jun 21 21:19:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bvq_16268/06_2025/8bvq_16268.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bvq_16268/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8bvq_16268/06_2025/8bvq_16268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bvq_16268/06_2025/8bvq_16268.map" model { file = "/net/cci-nas-00/data/ceres_data/8bvq_16268/06_2025/8bvq_16268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bvq_16268/06_2025/8bvq_16268.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.12, per 1000 atoms: 0.44 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: 6.21 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.22 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: 8.80 Time building geometry restraints manager: 7.53 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.390 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 49.510 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.020 ------------------------------------------------------------------------------- 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 : 7.55 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (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 TRP 0.014 0.001 TRP B 317 HIS 0.003 0.001 HIS A 677 PHE 0.015 0.001 PHE A 738 TYR 0.013 0.001 TYR D 184 ARG 0.005 0.000 ARG B 273 Details of bonding type rmsd hydrogen bonds : bond 0.11265 ( 531) hydrogen bonds : angle 5.80752 ( 1479) SS BOND : bond 0.00062 ( 1) SS BOND : angle 0.45105 ( 2) covalent geometry : bond 0.00421 (12136) covalent geometry : angle 0.55109 (16497) 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 : 1.718 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: 0.4773 time to fit residues: 123.7375 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 : 2.016 ------------------------------------------------------------------------------- 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 124 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 0.0270 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- 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** ** 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 = 0.4194 r_free = 0.4194 target = 0.197518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.142895 restraints weight = 44068.322| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.41 r_work: 0.3353 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.0457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12139 Z= 0.132 Angle : 0.499 5.949 16499 Z= 0.267 Chirality : 0.043 0.366 1797 Planarity : 0.004 0.052 2173 Dihedral : 4.302 59.750 1673 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.73 % Allowed : 21.81 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.22), residues: 1503 helix: 2.21 (0.29), residues: 325 sheet: -0.84 (0.24), residues: 470 loop : -1.27 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 376 HIS 0.004 0.001 HIS A 280 PHE 0.010 0.001 PHE A 426 TYR 0.017 0.001 TYR D 184 ARG 0.005 0.000 ARG A 91 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 531) hydrogen bonds : angle 5.25785 ( 1479) SS BOND : bond 0.00032 ( 1) SS BOND : angle 0.27022 ( 2) covalent geometry : bond 0.00301 (12136) covalent geometry : angle 0.49942 (16497) Misc. bond : bond 0.00091 ( 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 196 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 1.613 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 178 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8634 (tt0) REVERT: A 243 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8604 (p) REVERT: A 501 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7392 (tt) REVERT: B 230 GLN cc_start: 0.7209 (tp-100) cc_final: 0.6810 (tp40) REVERT: B 306 MET cc_start: 0.7296 (ptp) cc_final: 0.7059 (ptp) REVERT: B 323 LEU cc_start: 0.8156 (tp) cc_final: 0.7882 (mt) REVERT: C 57 ILE cc_start: 0.8073 (pt) cc_final: 0.7794 (tp) REVERT: C 78 LYS cc_start: 0.8214 (ttmt) cc_final: 0.7964 (mtpt) REVERT: D 183 GLU cc_start: 0.8634 (tp30) cc_final: 0.8305 (tt0) outliers start: 22 outliers final: 16 residues processed: 193 average time/residue: 0.5028 time to fit residues: 148.6651 Evaluate side-chains 184 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 3.079 ------------------------------------------------------------------------------- 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 243 THR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 573 ASN 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 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 91 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.192226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.132920 restraints weight = 43153.743| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.72 r_work: 0.3336 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 12139 Z= 0.176 Angle : 0.513 6.236 16499 Z= 0.275 Chirality : 0.043 0.365 1797 Planarity : 0.004 0.042 2173 Dihedral : 4.445 59.478 1673 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.68 % Allowed : 21.42 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.22), residues: 1503 helix: 2.09 (0.29), residues: 325 sheet: -0.89 (0.24), residues: 474 loop : -1.34 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 376 HIS 0.004 0.001 HIS A 677 PHE 0.012 0.001 PHE A 426 TYR 0.016 0.001 TYR D 184 ARG 0.004 0.000 ARG A 91 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 531) hydrogen bonds : angle 5.23368 ( 1479) SS BOND : bond 0.00876 ( 1) SS BOND : angle 0.47068 ( 2) covalent geometry : bond 0.00401 (12136) covalent geometry : angle 0.51290 (16497) Misc. bond : bond 0.00115 ( 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 206 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 2.500 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: A 243 THR cc_start: 0.8847 (OUTLIER) cc_final: 0.8599 (p) REVERT: B 230 GLN cc_start: 0.7190 (tp-100) cc_final: 0.6848 (tp40) REVERT: B 306 MET cc_start: 0.7266 (ptp) cc_final: 0.6989 (ptp) REVERT: B 323 LEU cc_start: 0.8140 (tp) cc_final: 0.7869 (mt) REVERT: C 57 ILE cc_start: 0.8142 (pt) cc_final: 0.7890 (tp) REVERT: C 78 LYS cc_start: 0.8165 (ttmt) cc_final: 0.7940 (mtpt) outliers start: 34 outliers final: 24 residues processed: 199 average time/residue: 0.4674 time to fit residues: 140.7958 Evaluate side-chains 188 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 1.963 ------------------------------------------------------------------------------- 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 250 ASP 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 511 THR 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 B residue 300 ASP 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 100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 8 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 21 optimal weight: 0.0060 chunk 56 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 overall best weight: 1.3202 ------------------------------------------------------------------------------- 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 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.192659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.133258 restraints weight = 43362.490| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.77 r_work: 0.3342 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12139 Z= 0.137 Angle : 0.493 6.208 16499 Z= 0.263 Chirality : 0.043 0.366 1797 Planarity : 0.003 0.047 2173 Dihedral : 4.405 59.543 1673 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.60 % Allowed : 22.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.22), residues: 1503 helix: 2.13 (0.29), residues: 326 sheet: -0.87 (0.24), residues: 475 loop : -1.32 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 376 HIS 0.004 0.001 HIS A 677 PHE 0.011 0.001 PHE A 426 TYR 0.016 0.001 TYR D 184 ARG 0.003 0.000 ARG A 91 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 531) hydrogen bonds : angle 5.09309 ( 1479) SS BOND : bond 0.00343 ( 1) SS BOND : angle 0.36045 ( 2) covalent geometry : bond 0.00313 (12136) covalent geometry : angle 0.49317 (16497) Misc. bond : bond 0.00104 ( 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 204 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 1.813 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: A 243 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8593 (p) REVERT: B 230 GLN cc_start: 0.7164 (tp-100) cc_final: 0.6788 (tp40) REVERT: B 259 PHE cc_start: 0.8161 (m-80) cc_final: 0.7864 (m-80) REVERT: B 306 MET cc_start: 0.7278 (ptp) cc_final: 0.7009 (ptp) REVERT: B 323 LEU cc_start: 0.8139 (tp) cc_final: 0.7873 (mt) REVERT: C 57 ILE cc_start: 0.8164 (pt) cc_final: 0.7923 (tp) REVERT: E 71 ASN cc_start: 0.7650 (m-40) cc_final: 0.7276 (t0) outliers start: 33 outliers final: 23 residues processed: 198 average time/residue: 0.4722 time to fit residues: 142.8196 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 : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 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 511 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR 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 285 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 115 optimal weight: 0.4980 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4159 r_free = 0.4159 target = 0.193905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.137625 restraints weight = 44089.207| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.45 r_work: 0.3332 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12139 Z= 0.120 Angle : 0.482 6.487 16499 Z= 0.257 Chirality : 0.043 0.366 1797 Planarity : 0.003 0.049 2173 Dihedral : 4.338 58.863 1673 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.68 % Allowed : 22.20 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.22), residues: 1503 helix: 2.22 (0.29), residues: 326 sheet: -0.84 (0.24), residues: 476 loop : -1.29 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 376 HIS 0.002 0.001 HIS A 533 PHE 0.010 0.001 PHE A 426 TYR 0.016 0.001 TYR D 80 ARG 0.003 0.000 ARG A 91 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 531) hydrogen bonds : angle 4.98626 ( 1479) SS BOND : bond 0.00151 ( 1) SS BOND : angle 0.39626 ( 2) covalent geometry : bond 0.00276 (12136) covalent geometry : angle 0.48206 (16497) 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: 34 poor density : 165 time to evaluate : 3.096 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: 0.8827 (OUTLIER) cc_final: 0.8600 (p) REVERT: B 230 GLN cc_start: 0.7268 (tp-100) cc_final: 0.6900 (tp40) REVERT: B 259 PHE cc_start: 0.8152 (m-80) cc_final: 0.7852 (m-80) REVERT: B 306 MET cc_start: 0.7221 (ptp) cc_final: 0.7001 (ptp) REVERT: B 323 LEU cc_start: 0.8176 (tp) cc_final: 0.7947 (mt) REVERT: C 57 ILE cc_start: 0.8277 (pt) cc_final: 0.8068 (tp) REVERT: D 183 GLU cc_start: 0.8510 (tp30) cc_final: 0.8201 (tt0) outliers start: 34 outliers final: 29 residues processed: 190 average time/residue: 0.5436 time to fit residues: 161.0712 Evaluate side-chains 191 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 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 736 SER 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 300 ASP Chi-restraints excluded: chain D residue 96 ILE 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 0 optimal weight: 60.0000 chunk 102 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4167 r_free = 0.4167 target = 0.194703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.135422 restraints weight = 43456.355| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.74 r_work: 0.3334 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12139 Z= 0.159 Angle : 0.502 6.608 16499 Z= 0.268 Chirality : 0.043 0.365 1797 Planarity : 0.004 0.054 2173 Dihedral : 4.423 58.228 1673 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.31 % Allowed : 21.73 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.21), residues: 1503 helix: 2.13 (0.29), residues: 326 sheet: -0.89 (0.24), residues: 469 loop : -1.38 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 205 HIS 0.003 0.001 HIS A 533 PHE 0.011 0.001 PHE A 426 TYR 0.017 0.001 TYR D 80 ARG 0.004 0.000 ARG A 91 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 531) hydrogen bonds : angle 5.03482 ( 1479) SS BOND : bond 0.00063 ( 1) SS BOND : angle 0.42467 ( 2) covalent geometry : bond 0.00367 (12136) covalent geometry : angle 0.50152 (16497) Misc. bond : bond 0.00094 ( 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 207 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 1.791 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: 0.8823 (OUTLIER) cc_final: 0.8600 (p) REVERT: B 230 GLN cc_start: 0.7365 (tp-100) cc_final: 0.6974 (tp40) REVERT: B 259 PHE cc_start: 0.8195 (m-80) cc_final: 0.7890 (m-80) REVERT: B 306 MET cc_start: 0.7262 (ptp) cc_final: 0.7002 (ptp) REVERT: B 323 LEU cc_start: 0.8102 (tp) cc_final: 0.7897 (mt) REVERT: C 57 ILE cc_start: 0.8242 (pt) cc_final: 0.8019 (tp) outliers start: 42 outliers final: 37 residues processed: 197 average time/residue: 0.4205 time to fit residues: 127.5289 Evaluate side-chains 197 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 573 ASN 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 677 HIS 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 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 96 ILE Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 123 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4174 r_free = 0.4174 target = 0.195428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.141045 restraints weight = 43443.611| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.32 r_work: 0.3332 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12139 Z= 0.127 Angle : 0.486 6.581 16499 Z= 0.259 Chirality : 0.043 0.366 1797 Planarity : 0.003 0.053 2173 Dihedral : 4.359 58.602 1673 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.07 % Allowed : 22.20 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1503 helix: 2.24 (0.29), residues: 326 sheet: -0.87 (0.24), residues: 470 loop : -1.31 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 376 HIS 0.002 0.001 HIS A 533 PHE 0.010 0.001 PHE A 426 TYR 0.018 0.001 TYR D 80 ARG 0.003 0.000 ARG A 91 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 531) hydrogen bonds : angle 4.94373 ( 1479) SS BOND : bond 0.00134 ( 1) SS BOND : angle 0.41901 ( 2) covalent geometry : bond 0.00293 (12136) covalent geometry : angle 0.48613 (16497) Misc. bond : bond 0.00102 ( 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 205 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 1.626 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: 0.8812 (OUTLIER) cc_final: 0.8600 (p) REVERT: A 560 ASP cc_start: 0.7093 (t0) cc_final: 0.6879 (t0) REVERT: B 259 PHE cc_start: 0.8197 (m-80) cc_final: 0.7880 (m-80) REVERT: B 306 MET cc_start: 0.7246 (ptp) cc_final: 0.6988 (ptp) REVERT: C 57 ILE cc_start: 0.8235 (pt) cc_final: 0.8031 (tp) outliers start: 39 outliers final: 30 residues processed: 197 average time/residue: 0.4607 time to fit residues: 137.7968 Evaluate side-chains 192 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 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 677 HIS Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 60 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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** A 748 ASN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4154 r_free = 0.4154 target = 0.193303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138314 restraints weight = 43663.110| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.35 r_work: 0.3299 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12139 Z= 0.196 Angle : 0.525 6.444 16499 Z= 0.282 Chirality : 0.044 0.364 1797 Planarity : 0.004 0.055 2173 Dihedral : 4.520 57.358 1673 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.78 % Allowed : 21.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.21), residues: 1503 helix: 1.96 (0.28), residues: 326 sheet: -0.98 (0.24), residues: 469 loop : -1.43 (0.21), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 205 HIS 0.004 0.001 HIS A 533 PHE 0.014 0.001 PHE A 791 TYR 0.016 0.001 TYR D 184 ARG 0.004 0.000 ARG G 6 Details of bonding type rmsd hydrogen bonds : bond 0.03871 ( 531) hydrogen bonds : angle 5.09591 ( 1479) SS BOND : bond 0.00046 ( 1) SS BOND : angle 0.48936 ( 2) covalent geometry : bond 0.00453 (12136) covalent geometry : angle 0.52529 (16497) Misc. bond : bond 0.00092 ( 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 213 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 165 time to evaluate : 2.596 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: A 243 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8612 (p) REVERT: A 560 ASP cc_start: 0.7123 (t0) cc_final: 0.6922 (t0) REVERT: B 259 PHE cc_start: 0.8163 (m-80) cc_final: 0.7849 (m-80) REVERT: C 57 ILE cc_start: 0.8255 (pt) cc_final: 0.8042 (tp) outliers start: 48 outliers final: 39 residues processed: 204 average time/residue: 0.4960 time to fit residues: 153.2747 Evaluate side-chains 199 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 599 VAL 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 677 HIS Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 90 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 5 optimal weight: 30.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4151 r_free = 0.4151 target = 0.193018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.138165 restraints weight = 43196.591| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.33 r_work: 0.3307 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1428 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= 0.150 Angle : 0.509 6.533 16499 Z= 0.273 Chirality : 0.043 0.364 1797 Planarity : 0.004 0.054 2173 Dihedral : 4.510 58.011 1673 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.66 % Favored : 94.28 % Rotamer: Outliers : 2.91 % Allowed : 21.73 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.21), residues: 1503 helix: 2.04 (0.28), residues: 326 sheet: -0.94 (0.24), residues: 470 loop : -1.39 (0.21), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 749 HIS 0.002 0.001 HIS A 533 PHE 0.011 0.001 PHE G 7 TYR 0.018 0.001 TYR D 80 ARG 0.003 0.000 ARG A 91 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 531) hydrogen bonds : angle 5.02393 ( 1479) SS BOND : bond 0.00105 ( 1) SS BOND : angle 0.42256 ( 2) covalent geometry : bond 0.00344 (12136) covalent geometry : angle 0.50872 (16497) Misc. bond : bond 0.00091 ( 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 202 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 1.836 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 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: 0.8837 (OUTLIER) cc_final: 0.8607 (p) REVERT: A 560 ASP cc_start: 0.7161 (t0) cc_final: 0.6953 (t0) REVERT: B 259 PHE cc_start: 0.8171 (m-80) cc_final: 0.7856 (m-80) REVERT: C 57 ILE cc_start: 0.8259 (pt) cc_final: 0.8050 (tp) outliers start: 37 outliers final: 35 residues processed: 196 average time/residue: 0.5414 time to fit residues: 162.5767 Evaluate side-chains 199 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 599 VAL 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 677 HIS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 91 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 30.0000 chunk 77 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4153 r_free = 0.4153 target = 0.192836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.138714 restraints weight = 43578.097| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.29 r_work: 0.3314 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.004 0.061 12139 Z= 0.154 Angle : 0.507 6.662 16499 Z= 0.272 Chirality : 0.043 0.365 1797 Planarity : 0.004 0.054 2173 Dihedral : 4.492 57.977 1673 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.92 % Favored : 94.01 % Rotamer: Outliers : 2.91 % Allowed : 21.97 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.21), residues: 1503 helix: 2.06 (0.28), residues: 326 sheet: -0.94 (0.24), residues: 470 loop : -1.39 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 749 HIS 0.003 0.001 HIS A 533 PHE 0.011 0.001 PHE A 426 TYR 0.018 0.001 TYR D 80 ARG 0.003 0.000 ARG A 91 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 531) hydrogen bonds : angle 5.00613 ( 1479) SS BOND : bond 0.00104 ( 1) SS BOND : angle 0.41229 ( 2) covalent geometry : bond 0.00356 (12136) covalent geometry : angle 0.50748 (16497) Misc. bond : bond 0.00091 ( 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 203 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 1.917 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 revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. REVERT: A 243 THR cc_start: 0.8832 (OUTLIER) cc_final: 0.8594 (p) REVERT: A 560 ASP cc_start: 0.7160 (t0) cc_final: 0.6950 (t0) REVERT: A 748 ASN cc_start: 0.9081 (t0) cc_final: 0.8634 (t0) REVERT: B 259 PHE cc_start: 0.8173 (m-80) cc_final: 0.7868 (m-80) REVERT: C 57 ILE cc_start: 0.8257 (pt) cc_final: 0.8048 (tp) outliers start: 37 outliers final: 34 residues processed: 197 average time/residue: 0.4640 time to fit residues: 138.9710 Evaluate side-chains 197 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 599 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 42 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4157 r_free = 0.4157 target = 0.193228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.134533 restraints weight = 43439.512| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.70 r_work: 0.3328 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1531 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= 0.139 Angle : 0.496 5.904 16499 Z= 0.266 Chirality : 0.043 0.366 1797 Planarity : 0.004 0.054 2173 Dihedral : 4.451 57.903 1673 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.66 % Favored : 94.28 % Rotamer: Outliers : 2.99 % Allowed : 22.05 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.21), residues: 1503 helix: 2.14 (0.29), residues: 326 sheet: -0.92 (0.24), residues: 470 loop : -1.35 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 749 HIS 0.002 0.001 HIS A 533 PHE 0.011 0.001 PHE A 426 TYR 0.016 0.001 TYR D 184 ARG 0.003 0.000 ARG A 91 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 531) hydrogen bonds : angle 4.95504 ( 1479) SS BOND : bond 0.00117 ( 1) SS BOND : angle 0.39206 ( 2) covalent geometry : bond 0.00320 (12136) covalent geometry : angle 0.49607 (16497) Misc. bond : bond 0.00096 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14643.81 seconds wall clock time: 257 minutes 40.63 seconds (15460.63 seconds total)