Starting phenix.real_space_refine on Fri Sep 11 13:14:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xwn_10632/09_2026/6xwn_10632.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xwn_10632/09_2026/6xwn_10632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xwn_10632/09_2026/6xwn_10632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xwn_10632/09_2026/6xwn_10632.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6xwn_10632/09_2026/6xwn_10632.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xwn_10632/09_2026/6xwn_10632.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xwn_10632/09_2026/6xwn_10632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xwn_10632/09_2026/6xwn_10632.map" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6298 2.51 5 N 1539 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9547 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3184 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 18, 'TRANS': 408} Chain: "B" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Chain: "C" Number of atoms: 3151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3151 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'TB1': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'TB1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.30, per 1000 atoms: 0.24 Number of scatterers: 9547 At special positions: 0 Unit cell: (82.984, 107.272, 108.284, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1662 8.00 N 1539 7.00 C 6298 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 373.5 milliseconds 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2282 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 0 sheets defined 78.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 Processing helix chain 'A' and resid 13 through 35 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.884A pdb=" N GLY A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 76 removed outlier: 4.198A pdb=" N LEU A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 110 removed outlier: 3.868A pdb=" N VAL A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 137 Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 153 through 172 Processing helix chain 'A' and resid 176 through 222 Proline residue: A 208 - end of helix Processing helix chain 'A' and resid 227 through 255 Processing helix chain 'A' and resid 259 through 278 removed outlier: 5.415A pdb=" N ASP A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ALA A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 298 through 312 removed outlier: 4.084A pdb=" N LEU A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Proline residue: A 307 - end of helix Processing helix chain 'A' and resid 315 through 333 removed outlier: 4.253A pdb=" N LEU A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 353 removed outlier: 3.581A pdb=" N ILE A 353 " --> pdb=" O VAL A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 361 Processing helix chain 'A' and resid 362 through 373 removed outlier: 3.695A pdb=" N VAL A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 392 removed outlier: 3.529A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 419 removed outlier: 3.749A pdb=" N LEU A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N MET A 403 " --> pdb=" O MET A 399 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.910A pdb=" N LYS A 427 " --> pdb=" O ASP A 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 11 removed outlier: 3.684A pdb=" N LEU B 10 " --> pdb=" O LEU B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 33 removed outlier: 3.547A pdb=" N ILE B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU B 19 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N TRP B 20 " --> pdb=" O TRP B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 45 Processing helix chain 'B' and resid 45 through 58 removed outlier: 3.880A pdb=" N GLY B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 73 Processing helix chain 'B' and resid 76 through 110 Processing helix chain 'B' and resid 131 through 139 Processing helix chain 'B' and resid 143 through 149 Processing helix chain 'B' and resid 153 through 172 Processing helix chain 'B' and resid 175 through 222 Proline residue: B 208 - end of helix Processing helix chain 'B' and resid 228 through 256 removed outlier: 4.153A pdb=" N TYR B 249 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N PHE B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 278 removed outlier: 5.396A pdb=" N ASP B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ALA B 270 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE B 272 " --> pdb=" O LYS B 268 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL B 276 " --> pdb=" O ILE B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 301 through 310 Proline residue: B 307 - end of helix Processing helix chain 'B' and resid 314 through 332 removed outlier: 3.750A pdb=" N LEU B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 355 removed outlier: 3.744A pdb=" N ILE B 353 " --> pdb=" O VAL B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 372 Processing helix chain 'B' and resid 381 through 420 removed outlier: 3.874A pdb=" N ILE B 393 " --> pdb=" O MET B 389 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALA B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ILE B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLY B 400 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 35 removed outlier: 4.078A pdb=" N TRP C 20 " --> pdb=" O TRP C 16 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 24 " --> pdb=" O TRP C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 45 Processing helix chain 'C' and resid 45 through 58 removed outlier: 3.721A pdb=" N GLY C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 73 Processing helix chain 'C' and resid 76 through 110 Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 143 through 149 Processing helix chain 'C' and resid 153 through 171 Processing helix chain 'C' and resid 183 through 204 Processing helix chain 'C' and resid 206 through 222 Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 230 through 256 removed outlier: 4.274A pdb=" N VAL C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 235 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE C 250 " --> pdb=" O VAL C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 268 Processing helix chain 'C' and resid 283 through 295 Processing helix chain 'C' and resid 304 through 313 removed outlier: 3.932A pdb=" N LEU C 308 " --> pdb=" O PHE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 332 removed outlier: 3.674A pdb=" N ILE C 332 " --> pdb=" O VAL C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 354 Processing helix chain 'C' and resid 364 through 372 Processing helix chain 'C' and resid 381 through 391 removed outlier: 3.779A pdb=" N ALA C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET C 389 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE C 390 " --> pdb=" O ALA C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 420 removed outlier: 4.714A pdb=" N GLY C 400 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP C 409 " --> pdb=" O ASN C 405 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 2094 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: 1.59 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2963 1.34 - 1.46: 1423 1.46 - 1.57: 5242 1.57 - 1.69: 0 1.69 - 1.80: 96 Bond restraints: 9724 Sorted by residual: bond pdb=" C10 TB1 C 501 " pdb=" C7 TB1 C 501 " ideal model delta sigma weight residual 1.548 1.523 0.025 2.00e-02 2.50e+03 1.54e+00 bond pdb=" C1 TB1 B 501 " pdb=" C4 TB1 B 501 " ideal model delta sigma weight residual 1.503 1.526 -0.023 2.00e-02 2.50e+03 1.37e+00 bond pdb=" C10 TB1 B 501 " pdb=" C7 TB1 B 501 " ideal model delta sigma weight residual 1.548 1.525 0.023 2.00e-02 2.50e+03 1.34e+00 bond pdb=" C11 TB1 C 501 " pdb=" C9 TB1 C 501 " ideal model delta sigma weight residual 1.545 1.524 0.021 2.00e-02 2.50e+03 1.11e+00 bond pdb=" C1 TB1 C 501 " pdb=" C4 TB1 C 501 " ideal model delta sigma weight residual 1.503 1.523 -0.020 2.00e-02 2.50e+03 1.03e+00 ... (remaining 9719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 13017 1.94 - 3.88: 176 3.88 - 5.82: 33 5.82 - 7.76: 7 7.76 - 9.70: 1 Bond angle restraints: 13234 Sorted by residual: angle pdb=" N ALA A 124 " pdb=" CA ALA A 124 " pdb=" C ALA A 124 " ideal model delta sigma weight residual 114.56 109.66 4.90 1.27e+00 6.20e-01 1.49e+01 angle pdb=" N VAL C 276 " pdb=" CA VAL C 276 " pdb=" C VAL C 276 " ideal model delta sigma weight residual 113.53 110.25 3.28 9.80e-01 1.04e+00 1.12e+01 angle pdb=" N ALA A 207 " pdb=" CA ALA A 207 " pdb=" C ALA A 207 " ideal model delta sigma weight residual 109.81 116.00 -6.19 2.21e+00 2.05e-01 7.84e+00 angle pdb=" CA LEU B 15 " pdb=" CB LEU B 15 " pdb=" CG LEU B 15 " ideal model delta sigma weight residual 116.30 126.00 -9.70 3.50e+00 8.16e-02 7.68e+00 angle pdb=" C VAL A 115 " pdb=" N ASN A 116 " pdb=" CA ASN A 116 " ideal model delta sigma weight residual 121.54 126.76 -5.22 1.91e+00 2.74e-01 7.47e+00 ... (remaining 13229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 4909 16.69 - 33.39: 625 33.39 - 50.08: 141 50.08 - 66.77: 31 66.77 - 83.46: 6 Dihedral angle restraints: 5712 sinusoidal: 2115 harmonic: 3597 Sorted by residual: dihedral pdb=" CA TRP C 16 " pdb=" C TRP C 16 " pdb=" N LYS C 17 " pdb=" CA LYS C 17 " ideal model delta harmonic sigma weight residual 180.00 162.49 17.51 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA GLN A 340 " pdb=" C GLN A 340 " pdb=" N GLN A 341 " pdb=" CA GLN A 341 " ideal model delta harmonic sigma weight residual 180.00 164.12 15.88 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ASN B 330 " pdb=" CB ASN B 330 " pdb=" CG ASN B 330 " pdb=" OD1 ASN B 330 " ideal model delta sinusoidal sigma weight residual 120.00 -174.56 -65.44 2 2.00e+01 2.50e-03 9.93e+00 ... (remaining 5709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1153 0.038 - 0.076: 396 0.076 - 0.113: 87 0.113 - 0.151: 9 0.151 - 0.189: 2 Chirality restraints: 1647 Sorted by residual: chirality pdb=" C7 TB1 B 501 " pdb=" N TB1 B 501 " pdb=" C10 TB1 B 501 " pdb=" C11 TB1 B 501 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.92e-01 chirality pdb=" C7 TB1 C 501 " pdb=" N TB1 C 501 " pdb=" C10 TB1 C 501 " pdb=" C11 TB1 C 501 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA ASN A 116 " pdb=" N ASN A 116 " pdb=" C ASN A 116 " pdb=" CB ASN A 116 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 1644 not shown) Planarity restraints: 1626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 245 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.82e+00 pdb=" C ILE C 245 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE C 245 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL C 246 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 46 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO C 47 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 47 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 47 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 207 " -0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO B 208 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 208 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 208 " -0.029 5.00e-02 4.00e+02 ... (remaining 1623 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 124 2.68 - 3.23: 9912 3.23 - 3.79: 15430 3.79 - 4.34: 20166 4.34 - 4.90: 33983 Nonbonded interactions: 79615 Sorted by model distance: nonbonded pdb=" O LYS C 299 " pdb=" OG SER C 303 " model vdw 2.121 3.040 nonbonded pdb=" OG SER C 67 " pdb=" OH TYR C 197 " model vdw 2.140 3.040 nonbonded pdb=" O MET C 368 " pdb=" OG SER C 372 " model vdw 2.193 3.040 nonbonded pdb=" O THR C 378 " pdb=" OG SER C 381 " model vdw 2.198 3.040 nonbonded pdb=" O ILE B 63 " pdb=" OG SER B 67 " model vdw 2.218 3.040 ... (remaining 79610 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 8 through 430) selection = (chain 'B' and resid 8 through 430) selection = (chain 'C' and resid 8 through 430) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.630 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 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 0.035 9724 Z= 0.177 Angle : 0.614 9.699 13234 Z= 0.332 Chirality : 0.039 0.189 1647 Planarity : 0.005 0.052 1626 Dihedral : 15.635 83.463 3430 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 8.00 % Allowed : 18.10 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.20), residues: 1270 helix: -1.39 (0.14), residues: 988 sheet: None (None), residues: 0 loop : -3.05 (0.32), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 179 TYR 0.010 0.001 TYR A 9 PHE 0.013 0.001 PHE B 302 TRP 0.008 0.001 TRP A 16 HIS 0.004 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 ( 9724) covalent geometry : angle 0.61418 / 0.33 (13234) hydrogen bonds : bond 0.10265 / 7.00 ( 700) hydrogen bonds : angle 5.84250 / 4.12 ( 2094) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 119 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.6773 (m-10) REVERT: A 365 MET cc_start: 0.6575 (ttm) cc_final: 0.6191 (ttm) REVERT: B 109 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6539 (m-10) outliers start: 80 outliers final: 44 residues processed: 193 average time/residue: 0.0696 time to fit residues: 20.9888 Evaluate side-chains 130 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 84 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 413 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.0670 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.0270 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.9178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 GLN B 128 GLN B 134 GLN B 330 ASN B 340 GLN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.060828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.051301 restraints weight = 40446.921| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.49 r_work: 0.2810 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9724 Z= 0.125 Angle : 0.584 9.012 13234 Z= 0.293 Chirality : 0.040 0.180 1647 Planarity : 0.005 0.058 1626 Dihedral : 6.627 58.106 1429 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.00 % Allowed : 21.80 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.23), residues: 1270 helix: 0.13 (0.16), residues: 1003 sheet: None (None), residues: 0 loop : -2.49 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 179 TYR 0.010 0.001 TYR B 217 PHE 0.013 0.001 PHE B 275 TRP 0.007 0.001 TRP C 20 HIS 0.004 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 9724) covalent geometry : angle 0.58422 / 0.29 (13234) hydrogen bonds : bond 0.03777 / 2.44 ( 700) hydrogen bonds : angle 4.48344 / 3.19 ( 2094) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.8203 (m-10) REVERT: A 321 GLN cc_start: 0.8652 (mt0) cc_final: 0.8346 (mt0) REVERT: A 365 MET cc_start: 0.8450 (ttm) cc_final: 0.7889 (ttm) REVERT: A 389 MET cc_start: 0.9311 (mtm) cc_final: 0.9094 (mtm) REVERT: B 109 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.7591 (m-10) REVERT: B 219 MET cc_start: 0.9227 (mmm) cc_final: 0.9017 (mmt) REVERT: B 239 THR cc_start: 0.9450 (m) cc_final: 0.9061 (p) REVERT: B 314 MET cc_start: 0.9003 (mpp) cc_final: 0.8669 (mpp) REVERT: C 314 MET cc_start: 0.9042 (mmt) cc_final: 0.8752 (mmm) REVERT: C 365 MET cc_start: 0.9186 (mtm) cc_final: 0.8684 (mtt) outliers start: 30 outliers final: 14 residues processed: 120 average time/residue: 0.0731 time to fit residues: 13.9164 Evaluate side-chains 100 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 373 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 23 optimal weight: 0.5980 chunk 73 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 GLN B 128 GLN C 321 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.059821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.049936 restraints weight = 40512.056| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.52 r_work: 0.2799 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9724 Z= 0.130 Angle : 0.560 8.643 13234 Z= 0.279 Chirality : 0.039 0.152 1647 Planarity : 0.004 0.058 1626 Dihedral : 5.354 57.549 1376 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.50 % Allowed : 22.40 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.24), residues: 1270 helix: 0.81 (0.17), residues: 1000 sheet: None (None), residues: 0 loop : -2.14 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 225 TYR 0.010 0.001 TYR C 217 PHE 0.010 0.001 PHE B 302 TRP 0.008 0.001 TRP A 16 HIS 0.004 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 9724) covalent geometry : angle 0.55994 / 0.28 (13234) hydrogen bonds : bond 0.03646 / 2.35 ( 700) hydrogen bonds : angle 4.28826 / 3.06 ( 2094) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.9266 (OUTLIER) cc_final: 0.8936 (tmm160) REVERT: A 35 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8148 (m-10) REVERT: A 295 MET cc_start: 0.9083 (mmt) cc_final: 0.8551 (mmm) REVERT: A 365 MET cc_start: 0.8711 (ttm) cc_final: 0.8007 (ttm) REVERT: B 101 PHE cc_start: 0.9235 (OUTLIER) cc_final: 0.8789 (m-10) REVERT: B 109 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.7675 (m-10) REVERT: B 219 MET cc_start: 0.9189 (mmm) cc_final: 0.8960 (mmm) REVERT: B 239 THR cc_start: 0.9462 (m) cc_final: 0.9079 (p) REVERT: B 314 MET cc_start: 0.9018 (mpp) cc_final: 0.8697 (mpp) REVERT: C 314 MET cc_start: 0.9026 (mmt) cc_final: 0.8601 (mmm) REVERT: C 365 MET cc_start: 0.9094 (mtm) cc_final: 0.8626 (mtt) outliers start: 35 outliers final: 17 residues processed: 122 average time/residue: 0.0771 time to fit residues: 14.6975 Evaluate side-chains 98 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 424 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 38 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 12 optimal weight: 0.0060 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 GLN B 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.059273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.049562 restraints weight = 40768.403| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 3.50 r_work: 0.2799 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9724 Z= 0.131 Angle : 0.554 8.463 13234 Z= 0.278 Chirality : 0.039 0.156 1647 Planarity : 0.004 0.059 1626 Dihedral : 4.939 56.074 1374 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.60 % Allowed : 23.10 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.24), residues: 1270 helix: 1.16 (0.17), residues: 1007 sheet: None (None), residues: 0 loop : -2.05 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 401 TYR 0.009 0.001 TYR A 90 PHE 0.014 0.001 PHE A 100 TRP 0.007 0.001 TRP C 20 HIS 0.004 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 9724) covalent geometry : angle 0.55366 / 0.28 (13234) hydrogen bonds : bond 0.03586 / 2.30 ( 700) hydrogen bonds : angle 4.21029 / 2.99 ( 2094) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 88 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.8940 (tmm160) REVERT: A 30 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8860 (mm) REVERT: A 35 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.8184 (m-10) REVERT: A 288 MET cc_start: 0.9610 (mpp) cc_final: 0.9338 (mpp) REVERT: A 302 PHE cc_start: 0.9413 (OUTLIER) cc_final: 0.9106 (p90) REVERT: A 365 MET cc_start: 0.8609 (ttm) cc_final: 0.7978 (ttt) REVERT: B 101 PHE cc_start: 0.9227 (OUTLIER) cc_final: 0.8825 (m-10) REVERT: B 109 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.7721 (m-10) REVERT: B 239 THR cc_start: 0.9475 (m) cc_final: 0.9112 (p) REVERT: B 314 MET cc_start: 0.8996 (mpp) cc_final: 0.8681 (mpp) REVERT: C 314 MET cc_start: 0.9031 (mmt) cc_final: 0.8585 (mmm) REVERT: C 365 MET cc_start: 0.9236 (mtm) cc_final: 0.8665 (mtt) outliers start: 36 outliers final: 20 residues processed: 120 average time/residue: 0.0738 time to fit residues: 13.9750 Evaluate side-chains 106 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 302 PHE Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 404 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 35 optimal weight: 0.0020 chunk 52 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.059597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.050033 restraints weight = 40818.715| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.55 r_work: 0.2818 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9724 Z= 0.118 Angle : 0.549 8.065 13234 Z= 0.273 Chirality : 0.039 0.157 1647 Planarity : 0.004 0.058 1626 Dihedral : 4.816 54.518 1374 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.10 % Allowed : 23.50 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.24), residues: 1270 helix: 1.34 (0.17), residues: 1010 sheet: None (None), residues: 0 loop : -1.88 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 401 TYR 0.008 0.001 TYR A 90 PHE 0.012 0.001 PHE B 302 TRP 0.005 0.001 TRP C 20 HIS 0.003 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 9724) covalent geometry : angle 0.54912 / 0.27 (13234) hydrogen bonds : bond 0.03462 / 2.23 ( 700) hydrogen bonds : angle 4.13849 / 2.94 ( 2094) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 87 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8889 (tmm160) REVERT: A 30 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8738 (mt) REVERT: A 35 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8231 (m-10) REVERT: A 288 MET cc_start: 0.9607 (OUTLIER) cc_final: 0.9400 (mpp) REVERT: A 302 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.8997 (p90) REVERT: B 101 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8884 (m-10) REVERT: B 109 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.7701 (m-10) REVERT: B 128 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8720 (mm-40) REVERT: B 239 THR cc_start: 0.9460 (m) cc_final: 0.9098 (p) REVERT: B 314 MET cc_start: 0.8993 (mpp) cc_final: 0.8699 (mpp) REVERT: C 87 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9190 (tp) REVERT: C 128 GLN cc_start: 0.9206 (tp40) cc_final: 0.8706 (mp10) REVERT: C 365 MET cc_start: 0.9208 (mtm) cc_final: 0.8675 (mtt) REVERT: C 390 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8960 (tt) outliers start: 41 outliers final: 19 residues processed: 123 average time/residue: 0.0785 time to fit residues: 15.0711 Evaluate side-chains 112 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 302 PHE Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 404 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 35 optimal weight: 0.0000 chunk 76 optimal weight: 3.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 ASN A 222 GLN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.061254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.051724 restraints weight = 40667.380| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.44 r_work: 0.2859 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9724 Z= 0.106 Angle : 0.539 7.080 13234 Z= 0.268 Chirality : 0.039 0.158 1647 Planarity : 0.004 0.059 1626 Dihedral : 4.563 53.675 1371 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.50 % Allowed : 23.80 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.24), residues: 1270 helix: 1.48 (0.17), residues: 1009 sheet: None (None), residues: 0 loop : -1.77 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 401 TYR 0.008 0.001 TYR A 90 PHE 0.013 0.001 PHE B 302 TRP 0.004 0.001 TRP A 428 HIS 0.003 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 9724) covalent geometry : angle 0.53917 / 0.27 (13234) hydrogen bonds : bond 0.03322 / 2.15 ( 700) hydrogen bonds : angle 4.05816 / 2.88 ( 2094) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8856 (tmm160) REVERT: A 35 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.8287 (m-10) REVERT: A 110 ASN cc_start: 0.9058 (t0) cc_final: 0.8856 (t0) REVERT: A 204 MET cc_start: 0.9461 (mmm) cc_final: 0.9231 (mtt) REVERT: A 302 PHE cc_start: 0.9341 (OUTLIER) cc_final: 0.8935 (p90) REVERT: B 101 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8865 (m-10) REVERT: B 109 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.7778 (m-10) REVERT: B 239 THR cc_start: 0.9450 (m) cc_final: 0.9090 (p) REVERT: B 314 MET cc_start: 0.8932 (mpp) cc_final: 0.8653 (mpp) REVERT: B 321 GLN cc_start: 0.9171 (mt0) cc_final: 0.8941 (mt0) REVERT: C 110 ASN cc_start: 0.9459 (t0) cc_final: 0.9082 (t0) REVERT: C 128 GLN cc_start: 0.9189 (tp40) cc_final: 0.8745 (mp10) REVERT: C 365 MET cc_start: 0.9227 (mtm) cc_final: 0.8715 (mtt) outliers start: 25 outliers final: 12 residues processed: 112 average time/residue: 0.0779 time to fit residues: 13.7795 Evaluate side-chains 104 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 302 PHE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 404 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 116 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 78 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.061164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.051488 restraints weight = 40909.217| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.53 r_work: 0.2847 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9724 Z= 0.113 Angle : 0.574 10.653 13234 Z= 0.279 Chirality : 0.040 0.210 1647 Planarity : 0.004 0.059 1626 Dihedral : 3.869 53.439 1365 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.60 % Allowed : 24.20 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.24), residues: 1270 helix: 1.59 (0.17), residues: 1007 sheet: None (None), residues: 0 loop : -1.72 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 401 TYR 0.007 0.001 TYR A 90 PHE 0.013 0.001 PHE B 302 TRP 0.004 0.001 TRP A 428 HIS 0.003 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 9724) covalent geometry : angle 0.57399 / 0.28 (13234) hydrogen bonds : bond 0.03340 / 2.17 ( 700) hydrogen bonds : angle 4.02531 / 2.86 ( 2094) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8856 (tmm160) REVERT: A 35 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.8252 (m-10) REVERT: A 302 PHE cc_start: 0.9321 (OUTLIER) cc_final: 0.8997 (p90) REVERT: B 109 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.7733 (m-10) REVERT: B 205 GLN cc_start: 0.9319 (tp40) cc_final: 0.9056 (tp-100) REVERT: B 239 THR cc_start: 0.9411 (m) cc_final: 0.9067 (p) REVERT: B 314 MET cc_start: 0.8887 (mpp) cc_final: 0.8628 (mpp) REVERT: B 321 GLN cc_start: 0.9184 (mt0) cc_final: 0.8964 (mt0) REVERT: B 409 ASP cc_start: 0.8830 (m-30) cc_final: 0.8621 (m-30) REVERT: C 110 ASN cc_start: 0.9441 (t0) cc_final: 0.9041 (t0) REVERT: C 128 GLN cc_start: 0.9178 (tp40) cc_final: 0.8776 (mp10) REVERT: C 365 MET cc_start: 0.9219 (mtm) cc_final: 0.8701 (mtt) outliers start: 26 outliers final: 17 residues processed: 120 average time/residue: 0.0745 time to fit residues: 14.1582 Evaluate side-chains 111 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 302 PHE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 414 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 56 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.059194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.049571 restraints weight = 41336.248| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.49 r_work: 0.2777 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9724 Z= 0.199 Angle : 0.625 9.090 13234 Z= 0.312 Chirality : 0.042 0.236 1647 Planarity : 0.004 0.058 1626 Dihedral : 4.011 52.954 1365 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.40 % Allowed : 23.70 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.24), residues: 1270 helix: 1.57 (0.17), residues: 1010 sheet: None (None), residues: 0 loop : -1.59 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 8 TYR 0.010 0.001 TYR B 238 PHE 0.013 0.001 PHE B 302 TRP 0.012 0.001 TRP C 20 HIS 0.003 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 ( 9724) covalent geometry : angle 0.62526 / 0.31 (13234) hydrogen bonds : bond 0.03868 / 2.52 ( 700) hydrogen bonds : angle 4.23802 / 3.03 ( 2094) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8842 (tmm160) REVERT: A 35 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8436 (m-10) REVERT: A 302 PHE cc_start: 0.9363 (OUTLIER) cc_final: 0.9115 (p90) REVERT: B 109 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.7798 (m-10) REVERT: B 116 ASN cc_start: 0.8266 (m-40) cc_final: 0.7979 (m110) REVERT: B 128 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8594 (mm-40) REVERT: B 239 THR cc_start: 0.9481 (m) cc_final: 0.9115 (p) REVERT: B 312 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.9013 (mm) REVERT: B 314 MET cc_start: 0.8897 (mpp) cc_final: 0.8633 (mpp) REVERT: B 321 GLN cc_start: 0.9213 (mt0) cc_final: 0.8993 (mp10) REVERT: C 128 GLN cc_start: 0.9209 (tp40) cc_final: 0.8761 (mp10) REVERT: C 365 MET cc_start: 0.9245 (mtm) cc_final: 0.8622 (mtt) outliers start: 34 outliers final: 23 residues processed: 116 average time/residue: 0.0720 time to fit residues: 13.2455 Evaluate side-chains 114 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 302 PHE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 414 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 69 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 37 optimal weight: 0.0970 chunk 77 optimal weight: 0.0770 chunk 123 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.060793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.051284 restraints weight = 40374.329| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.56 r_work: 0.2851 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9724 Z= 0.114 Angle : 0.597 11.590 13234 Z= 0.291 Chirality : 0.040 0.239 1647 Planarity : 0.004 0.059 1626 Dihedral : 3.939 52.571 1365 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.20 % Allowed : 25.30 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.24), residues: 1270 helix: 1.69 (0.17), residues: 1010 sheet: None (None), residues: 0 loop : -1.56 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 401 TYR 0.008 0.001 TYR A 238 PHE 0.013 0.001 PHE B 302 TRP 0.003 0.000 TRP C 16 HIS 0.004 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 9724) covalent geometry : angle 0.59696 / 0.29 (13234) hydrogen bonds : bond 0.03363 / 2.17 ( 700) hydrogen bonds : angle 4.06636 / 2.91 ( 2094) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8811 (tmm160) REVERT: A 35 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8426 (m-10) REVERT: A 302 PHE cc_start: 0.9278 (OUTLIER) cc_final: 0.8980 (p90) REVERT: A 365 MET cc_start: 0.8226 (tpt) cc_final: 0.7709 (tpp) REVERT: B 109 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.7766 (m-10) REVERT: B 239 THR cc_start: 0.9422 (m) cc_final: 0.9078 (p) REVERT: B 314 MET cc_start: 0.8844 (mpp) cc_final: 0.8634 (mpp) REVERT: B 409 ASP cc_start: 0.8852 (m-30) cc_final: 0.8643 (m-30) REVERT: C 20 TRP cc_start: 0.7983 (m100) cc_final: 0.7748 (m-10) REVERT: C 110 ASN cc_start: 0.9420 (t0) cc_final: 0.9029 (t0) REVERT: C 128 GLN cc_start: 0.9176 (tp40) cc_final: 0.8727 (mp10) REVERT: C 365 MET cc_start: 0.9217 (mtm) cc_final: 0.8734 (mtt) outliers start: 22 outliers final: 13 residues processed: 114 average time/residue: 0.0730 time to fit residues: 13.1693 Evaluate side-chains 105 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 302 PHE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 100 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.060656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.051393 restraints weight = 40896.978| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.37 r_work: 0.2823 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9724 Z= 0.138 Angle : 0.602 10.604 13234 Z= 0.299 Chirality : 0.041 0.240 1647 Planarity : 0.004 0.058 1626 Dihedral : 3.921 53.164 1365 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.80 % Allowed : 25.70 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.24), residues: 1270 helix: 1.76 (0.17), residues: 1007 sheet: None (None), residues: 0 loop : -1.45 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 401 TYR 0.007 0.001 TYR A 90 PHE 0.013 0.001 PHE B 302 TRP 0.006 0.001 TRP A 428 HIS 0.003 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 9724) covalent geometry : angle 0.60163 / 0.30 (13234) hydrogen bonds : bond 0.03503 / 2.28 ( 700) hydrogen bonds : angle 4.14456 / 2.97 ( 2094) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8822 (tmm160) REVERT: A 35 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8443 (m-10) REVERT: A 271 MET cc_start: 0.9072 (mtm) cc_final: 0.7980 (mpp) REVERT: A 302 PHE cc_start: 0.9281 (OUTLIER) cc_final: 0.8992 (p90) REVERT: B 109 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.7832 (m-10) REVERT: B 239 THR cc_start: 0.9425 (m) cc_final: 0.9079 (p) REVERT: B 288 MET cc_start: 0.9327 (ttm) cc_final: 0.8962 (mtm) REVERT: B 365 MET cc_start: 0.8860 (mmt) cc_final: 0.8411 (mmm) REVERT: C 110 ASN cc_start: 0.9416 (t0) cc_final: 0.9025 (t0) REVERT: C 128 GLN cc_start: 0.9158 (tp40) cc_final: 0.8730 (mp10) REVERT: C 365 MET cc_start: 0.9212 (mtm) cc_final: 0.8600 (mtt) outliers start: 18 outliers final: 13 residues processed: 101 average time/residue: 0.0737 time to fit residues: 11.7360 Evaluate side-chains 98 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 302 PHE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 55 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 120 optimal weight: 0.0770 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.060813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.051044 restraints weight = 40250.583| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.47 r_work: 0.2853 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9724 Z= 0.116 Angle : 0.607 11.039 13234 Z= 0.299 Chirality : 0.040 0.242 1647 Planarity : 0.004 0.059 1626 Dihedral : 3.915 53.097 1365 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.30 % Allowed : 25.50 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.24), residues: 1270 helix: 1.74 (0.17), residues: 1010 sheet: None (None), residues: 0 loop : -1.44 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 401 TYR 0.009 0.001 TYR A 320 PHE 0.013 0.001 PHE B 302 TRP 0.004 0.000 TRP A 428 HIS 0.003 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 9724) covalent geometry : angle 0.60708 / 0.30 (13234) hydrogen bonds : bond 0.03367 / 2.19 ( 700) hydrogen bonds : angle 4.12263 / 2.96 ( 2094) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1843.01 seconds wall clock time: 32 minutes 31.89 seconds (1951.89 seconds total)