Starting phenix.real_space_refine on Thu Feb 13 23:45:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xwn_10632/02_2025/6xwn_10632.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xwn_10632/02_2025/6xwn_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6xwn_10632/02_2025/6xwn_10632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xwn_10632/02_2025/6xwn_10632.map" model { file = "/net/cci-nas-00/data/ceres_data/6xwn_10632/02_2025/6xwn_10632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xwn_10632/02_2025/6xwn_10632.cif" } resolution = 3.47 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= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.85, per 1000 atoms: 0.61 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: 2.82 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.82 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: 2.82 Time building geometry restraints manager: 3.05 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: 4910 16.69 - 33.39: 640 33.39 - 50.08: 154 50.08 - 66.77: 32 66.77 - 83.46: 6 Dihedral angle restraints: 5742 sinusoidal: 2145 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 5739 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: 1.090 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.120 Process input model: 24.440 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 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= 0.264 Angle : 0.614 9.699 13234 Z= 0.332 Chirality : 0.039 0.189 1647 Planarity : 0.005 0.052 1626 Dihedral : 15.889 83.463 3460 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 (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: -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 TRP 0.008 0.001 TRP A 16 HIS 0.004 0.001 HIS A 334 PHE 0.013 0.001 PHE B 302 TYR 0.010 0.001 TYR A 9 ARG 0.002 0.000 ARG B 179 *********************** 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 : 1.010 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: 0.1715 time to fit residues: 50.1500 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 : 1.106 ------------------------------------------------------------------------------- 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 106 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN B 128 GLN B 134 GLN B 205 GLN B 330 ASN B 340 GLN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.059936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.050350 restraints weight = 40097.217| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.49 r_work: 0.2808 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1556 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= 0.187 Angle : 0.583 8.922 13234 Z= 0.293 Chirality : 0.040 0.143 1647 Planarity : 0.005 0.057 1626 Dihedral : 7.765 58.407 1459 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.10 % Allowed : 21.80 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.73 (0.23), residues: 1270 helix: 0.12 (0.16), residues: 1003 sheet: None (None), residues: 0 loop : -2.51 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 20 HIS 0.004 0.001 HIS A 334 PHE 0.012 0.001 PHE B 275 TYR 0.011 0.001 TYR C 217 ARG 0.005 0.000 ARG C 179 *********************** 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: 31 poor density : 93 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8224 (m-10) REVERT: A 321 GLN cc_start: 0.8657 (mt0) cc_final: 0.8329 (mt0) REVERT: A 365 MET cc_start: 0.8468 (ttm) cc_final: 0.7901 (ttm) REVERT: A 389 MET cc_start: 0.9328 (mtm) cc_final: 0.9111 (mtm) REVERT: B 109 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.7587 (m-10) REVERT: B 219 MET cc_start: 0.9238 (mmm) cc_final: 0.9033 (mmt) REVERT: B 239 THR cc_start: 0.9450 (m) cc_final: 0.9060 (p) REVERT: B 314 MET cc_start: 0.9015 (mpp) cc_final: 0.8703 (mpp) REVERT: C 314 MET cc_start: 0.9035 (mmt) cc_final: 0.8754 (mmm) REVERT: C 365 MET cc_start: 0.9184 (mtm) cc_final: 0.8679 (mtt) outliers start: 31 outliers final: 13 residues processed: 119 average time/residue: 0.1695 time to fit residues: 31.0161 Evaluate side-chains 100 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 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 38 optimal weight: 0.9980 chunk 119 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN B 128 GLN B 205 GLN C 321 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.059538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.050060 restraints weight = 40841.509| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.44 r_work: 0.2804 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1935 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= 0.196 Angle : 0.563 8.668 13234 Z= 0.281 Chirality : 0.039 0.152 1647 Planarity : 0.004 0.057 1626 Dihedral : 6.650 57.798 1406 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.40 % Allowed : 22.70 % 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 (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: 0.19 (0.24), residues: 1270 helix: 0.77 (0.17), residues: 1001 sheet: None (None), residues: 0 loop : -2.16 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 16 HIS 0.004 0.001 HIS A 334 PHE 0.010 0.001 PHE A 302 TYR 0.010 0.001 TYR C 217 ARG 0.002 0.000 ARG C 401 *********************** 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 122 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 88 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8939 (tmm160) REVERT: A 35 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.8160 (m-10) REVERT: A 295 MET cc_start: 0.9079 (mmt) cc_final: 0.8555 (mmm) REVERT: A 321 GLN cc_start: 0.8690 (mt0) cc_final: 0.8469 (mt0) REVERT: A 365 MET cc_start: 0.8713 (ttm) cc_final: 0.8029 (ttm) REVERT: B 109 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.7663 (m-10) REVERT: B 219 MET cc_start: 0.9209 (mmm) cc_final: 0.8976 (mmm) REVERT: B 239 THR cc_start: 0.9459 (m) cc_final: 0.9078 (p) REVERT: B 314 MET cc_start: 0.8996 (mpp) cc_final: 0.8672 (mpp) REVERT: C 365 MET cc_start: 0.9099 (mtm) cc_final: 0.8639 (mtt) outliers start: 34 outliers final: 17 residues processed: 118 average time/residue: 0.1646 time to fit residues: 29.9304 Evaluate side-chains 96 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 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 45 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN B 128 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.060079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.050615 restraints weight = 40532.636| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 3.45 r_work: 0.2797 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2250 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= 0.188 Angle : 0.552 8.397 13234 Z= 0.276 Chirality : 0.039 0.156 1647 Planarity : 0.004 0.059 1626 Dihedral : 6.219 56.010 1404 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.70 % Allowed : 22.80 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.72 (0.24), residues: 1270 helix: 1.15 (0.17), residues: 1007 sheet: None (None), residues: 0 loop : -2.06 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 20 HIS 0.004 0.001 HIS A 334 PHE 0.013 0.001 PHE A 100 TYR 0.009 0.001 TYR A 90 ARG 0.002 0.000 ARG C 401 *********************** 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 128 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.8940 (tmm160) REVERT: A 35 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.8240 (m-10) REVERT: A 288 MET cc_start: 0.9625 (mpp) cc_final: 0.9340 (mpp) REVERT: A 302 PHE cc_start: 0.9396 (OUTLIER) cc_final: 0.8987 (p90) REVERT: A 321 GLN cc_start: 0.8680 (mt0) cc_final: 0.8444 (mt0) REVERT: A 365 MET cc_start: 0.8523 (ttm) cc_final: 0.7597 (ttt) REVERT: B 101 PHE cc_start: 0.9248 (OUTLIER) cc_final: 0.8852 (m-10) REVERT: B 109 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.7723 (m-10) REVERT: B 239 THR cc_start: 0.9475 (m) cc_final: 0.9115 (p) REVERT: B 314 MET cc_start: 0.8983 (mpp) cc_final: 0.8692 (mpp) REVERT: C 365 MET cc_start: 0.9238 (mtm) cc_final: 0.8665 (mtt) outliers start: 37 outliers final: 21 residues processed: 123 average time/residue: 0.1746 time to fit residues: 32.0750 Evaluate side-chains 107 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 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 230 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 224 VAL 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 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 101 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 118 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3160 r_free = 0.3160 target = 0.058353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.048764 restraints weight = 40834.539| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.40 r_work: 0.2783 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9724 Z= 0.218 Angle : 0.564 7.961 13234 Z= 0.283 Chirality : 0.040 0.155 1647 Planarity : 0.004 0.058 1626 Dihedral : 6.168 55.192 1404 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.60 % Allowed : 22.40 % Favored : 73.00 % 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: 1.01 (0.24), residues: 1270 helix: 1.33 (0.17), residues: 1010 sheet: None (None), residues: 0 loop : -1.91 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 20 HIS 0.004 0.001 HIS A 334 PHE 0.012 0.001 PHE B 302 TYR 0.008 0.001 TYR C 217 ARG 0.001 0.000 ARG C 401 *********************** 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 131 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 85 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8896 (tmm160) REVERT: A 35 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8282 (m-10) REVERT: A 204 MET cc_start: 0.9403 (mmm) cc_final: 0.9171 (mtm) REVERT: A 288 MET cc_start: 0.9591 (OUTLIER) cc_final: 0.9389 (mpp) REVERT: A 302 PHE cc_start: 0.9387 (OUTLIER) cc_final: 0.9031 (p90) REVERT: B 101 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8865 (m-10) REVERT: B 109 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.7753 (m-10) REVERT: B 239 THR cc_start: 0.9465 (m) cc_final: 0.9104 (p) REVERT: B 312 ILE cc_start: 0.9506 (OUTLIER) cc_final: 0.9002 (mm) REVERT: B 314 MET cc_start: 0.8992 (mpp) cc_final: 0.8699 (mpp) REVERT: C 87 ILE cc_start: 0.9429 (OUTLIER) cc_final: 0.9225 (tp) REVERT: C 128 GLN cc_start: 0.9202 (tp40) cc_final: 0.8748 (mp10) REVERT: C 365 MET cc_start: 0.9235 (mtm) cc_final: 0.8694 (mtt) outliers start: 46 outliers final: 24 residues processed: 127 average time/residue: 0.1650 time to fit residues: 32.6097 Evaluate side-chains 114 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 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 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 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 87 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 226 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 26 optimal weight: 9.9990 chunk 24 optimal weight: 0.6980 chunk 53 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 71 optimal weight: 0.0370 overall best weight: 1.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.059793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.050330 restraints weight = 41125.488| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.45 r_work: 0.2797 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9724 Z= 0.219 Angle : 0.567 7.632 13234 Z= 0.284 Chirality : 0.040 0.163 1647 Planarity : 0.004 0.059 1626 Dihedral : 6.124 54.224 1404 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.10 % Allowed : 22.40 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.15 (0.24), residues: 1270 helix: 1.41 (0.17), residues: 1010 sheet: None (None), residues: 0 loop : -1.76 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 20 HIS 0.004 0.001 HIS A 334 PHE 0.013 0.001 PHE B 302 TYR 0.008 0.001 TYR C 217 ARG 0.001 0.000 ARG C 401 *********************** 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 129 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 88 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8862 (tmm160) REVERT: A 35 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8338 (m-10) REVERT: A 100 PHE cc_start: 0.8951 (t80) cc_final: 0.8646 (t80) REVERT: A 302 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.9005 (p90) REVERT: B 101 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8865 (m-10) REVERT: B 109 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.7749 (m-10) REVERT: B 128 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8565 (mm-40) REVERT: B 239 THR cc_start: 0.9465 (m) cc_final: 0.9107 (p) REVERT: B 312 ILE cc_start: 0.9509 (OUTLIER) cc_final: 0.9035 (mm) REVERT: B 314 MET cc_start: 0.8930 (mpp) cc_final: 0.8669 (mpp) REVERT: B 321 GLN cc_start: 0.9187 (mt0) cc_final: 0.8955 (mt0) REVERT: C 128 GLN cc_start: 0.9209 (tp40) cc_final: 0.8760 (mp10) REVERT: C 269 ASP cc_start: 0.9197 (t0) cc_final: 0.8957 (t0) REVERT: C 365 MET cc_start: 0.9249 (mtm) cc_final: 0.8743 (mtt) outliers start: 41 outliers final: 26 residues processed: 125 average time/residue: 0.1684 time to fit residues: 33.1058 Evaluate side-chains 116 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 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 A residue 406 VAL Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 80 LEU 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 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 174 ASN Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 233 VAL 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 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 98 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN B 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.060580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.051077 restraints weight = 41214.342| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.47 r_work: 0.2805 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9724 Z= 0.177 Angle : 0.572 9.484 13234 Z= 0.282 Chirality : 0.040 0.202 1647 Planarity : 0.004 0.059 1626 Dihedral : 5.961 53.420 1401 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.10 % Allowed : 23.90 % Favored : 73.00 % 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: 1.27 (0.24), residues: 1270 helix: 1.49 (0.17), residues: 1009 sheet: None (None), residues: 0 loop : -1.69 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 20 HIS 0.003 0.001 HIS A 334 PHE 0.013 0.001 PHE B 302 TYR 0.008 0.001 TYR A 320 ARG 0.001 0.000 ARG C 401 *********************** 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 120 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.9255 (OUTLIER) cc_final: 0.8870 (tmm160) REVERT: A 35 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8416 (m-10) REVERT: A 204 MET cc_start: 0.9456 (mmm) cc_final: 0.9214 (mtm) REVERT: A 302 PHE cc_start: 0.9358 (OUTLIER) cc_final: 0.9084 (p90) REVERT: A 368 MET cc_start: 0.9104 (mtp) cc_final: 0.8677 (mpp) REVERT: B 101 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8858 (m-10) REVERT: B 109 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.7814 (m-10) REVERT: B 128 GLN cc_start: 0.8931 (mm110) cc_final: 0.8719 (mm-40) REVERT: B 239 THR cc_start: 0.9457 (m) cc_final: 0.9097 (p) REVERT: B 314 MET cc_start: 0.8912 (mpp) cc_final: 0.8655 (mpp) REVERT: B 321 GLN cc_start: 0.9178 (mt0) cc_final: 0.8953 (mt0) REVERT: C 128 GLN cc_start: 0.9254 (tp40) cc_final: 0.8759 (mp10) REVERT: C 269 ASP cc_start: 0.9201 (t0) cc_final: 0.8972 (t0) REVERT: C 365 MET cc_start: 0.9235 (mtm) cc_final: 0.8703 (mtt) outliers start: 31 outliers final: 22 residues processed: 116 average time/residue: 0.1700 time to fit residues: 30.3145 Evaluate side-chains 111 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 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 A residue 406 VAL Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 80 LEU 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 174 ASN Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 404 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 56 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.060355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.050677 restraints weight = 40926.289| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.48 r_work: 0.2853 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9724 Z= 0.158 Angle : 0.577 10.782 13234 Z= 0.282 Chirality : 0.040 0.211 1647 Planarity : 0.004 0.059 1626 Dihedral : 5.850 53.049 1401 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.50 % Allowed : 24.20 % 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 (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: 1.45 (0.24), residues: 1270 helix: 1.59 (0.17), residues: 1009 sheet: None (None), residues: 0 loop : -1.53 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 428 HIS 0.003 0.001 HIS A 334 PHE 0.013 0.001 PHE B 302 TYR 0.009 0.001 TYR A 320 ARG 0.002 0.000 ARG C 401 *********************** 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 117 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8846 (tmm160) REVERT: A 35 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8438 (m-10) REVERT: A 302 PHE cc_start: 0.9314 (OUTLIER) cc_final: 0.9027 (p90) REVERT: A 365 MET cc_start: 0.8323 (tpp) cc_final: 0.7870 (tpp) REVERT: A 368 MET cc_start: 0.9108 (mtp) cc_final: 0.8800 (mtp) REVERT: B 101 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8890 (m-10) REVERT: B 109 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.7747 (m-10) REVERT: B 239 THR cc_start: 0.9421 (m) cc_final: 0.9077 (p) REVERT: B 314 MET cc_start: 0.8845 (mpp) cc_final: 0.8634 (mpp) REVERT: C 128 GLN cc_start: 0.9193 (tp40) cc_final: 0.8723 (mp10) REVERT: C 269 ASP cc_start: 0.9091 (t0) cc_final: 0.8718 (t0) REVERT: C 365 MET cc_start: 0.9236 (mtm) cc_final: 0.8726 (mtt) outliers start: 25 outliers final: 15 residues processed: 112 average time/residue: 0.1749 time to fit residues: 30.3374 Evaluate side-chains 105 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 58 MET 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 227 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 404 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 78 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3230 r_free = 0.3230 target = 0.061084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.051606 restraints weight = 40727.787| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.49 r_work: 0.2823 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3177 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= 0.171 Angle : 0.583 9.600 13234 Z= 0.289 Chirality : 0.040 0.229 1647 Planarity : 0.004 0.059 1626 Dihedral : 5.375 53.282 1395 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.40 % Allowed : 24.50 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.50 (0.24), residues: 1270 helix: 1.62 (0.17), residues: 1010 sheet: None (None), residues: 0 loop : -1.49 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 428 HIS 0.003 0.001 HIS A 334 PHE 0.013 0.001 PHE B 302 TYR 0.010 0.001 TYR A 320 ARG 0.002 0.000 ARG C 401 *********************** 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 115 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8853 (tmm160) REVERT: A 35 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.8430 (m-10) REVERT: A 302 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.9013 (p90) REVERT: B 101 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8856 (m-10) REVERT: B 109 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.7722 (m-10) REVERT: B 239 THR cc_start: 0.9428 (m) cc_final: 0.9085 (p) REVERT: B 288 MET cc_start: 0.9306 (ttm) cc_final: 0.8935 (mtm) REVERT: B 365 MET cc_start: 0.8848 (mmt) cc_final: 0.8269 (mmm) REVERT: B 409 ASP cc_start: 0.8832 (m-30) cc_final: 0.8629 (m-30) REVERT: C 110 ASN cc_start: 0.9420 (t0) cc_final: 0.9020 (t0) REVERT: C 128 GLN cc_start: 0.9168 (tp40) cc_final: 0.8723 (mp10) REVERT: C 269 ASP cc_start: 0.9056 (t0) cc_final: 0.8700 (t0) REVERT: C 365 MET cc_start: 0.9227 (mtm) cc_final: 0.8629 (mtt) outliers start: 24 outliers final: 15 residues processed: 109 average time/residue: 0.1756 time to fit residues: 29.5094 Evaluate side-chains 108 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 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 321 GLN Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 20 TRP 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 378 THR 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 35 optimal weight: 0.0000 chunk 98 optimal weight: 0.7980 chunk 84 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 2 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3241 r_free = 0.3241 target = 0.061400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.051935 restraints weight = 41495.425| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.44 r_work: 0.2864 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 9724 Z= 0.171 Angle : 0.609 10.669 13234 Z= 0.299 Chirality : 0.041 0.298 1647 Planarity : 0.004 0.059 1626 Dihedral : 5.376 52.897 1395 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % 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 (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: 1.58 (0.24), residues: 1270 helix: 1.69 (0.17), residues: 1009 sheet: None (None), residues: 0 loop : -1.50 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 428 HIS 0.003 0.001 HIS A 334 PHE 0.013 0.001 PHE B 302 TYR 0.010 0.001 TYR A 320 ARG 0.002 0.000 ARG C 401 ********************** 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 112 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8805 (tmm160) REVERT: A 35 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8424 (m-10) REVERT: A 302 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8976 (p90) REVERT: A 365 MET cc_start: 0.8316 (tpp) cc_final: 0.8031 (tpp) REVERT: B 109 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.7777 (m-10) REVERT: B 239 THR cc_start: 0.9422 (m) cc_final: 0.9081 (p) REVERT: C 110 ASN cc_start: 0.9401 (t0) cc_final: 0.9020 (t0) REVERT: C 128 GLN cc_start: 0.9165 (tp40) cc_final: 0.8739 (mp10) REVERT: C 269 ASP cc_start: 0.9071 (t0) cc_final: 0.8726 (t0) REVERT: C 365 MET cc_start: 0.9236 (mtm) cc_final: 0.8750 (mtt) outliers start: 23 outliers final: 15 residues processed: 107 average time/residue: 0.1731 time to fit residues: 28.5985 Evaluate side-chains 103 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 20 TRP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 74 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.058917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.049534 restraints weight = 41716.655| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.41 r_work: 0.2796 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 9724 Z= 0.312 Angle : 0.663 10.117 13234 Z= 0.332 Chirality : 0.043 0.276 1647 Planarity : 0.004 0.058 1626 Dihedral : 5.504 52.775 1395 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.60 % Allowed : 25.10 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.52 (0.24), residues: 1270 helix: 1.64 (0.17), residues: 1008 sheet: None (None), residues: 0 loop : -1.47 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 428 HIS 0.003 0.001 HIS A 334 PHE 0.014 0.001 PHE B 302 TYR 0.010 0.001 TYR B 238 ARG 0.002 0.000 ARG B 7 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3378.22 seconds wall clock time: 61 minutes 13.02 seconds (3673.02 seconds total)