Starting phenix.real_space_refine on Thu Jul 2 19:19:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m7w_63695/07_2026/9m7w_63695.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m7w_63695/07_2026/9m7w_63695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m7w_63695/07_2026/9m7w_63695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m7w_63695/07_2026/9m7w_63695.map" model { file = "/net/cci-nas-00/data/ceres_data/9m7w_63695/07_2026/9m7w_63695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m7w_63695/07_2026/9m7w_63695.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.074 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: 5 Type Number sf(0) Gaussians P 74 5.49 5 S 68 5.16 5 C 6147 2.51 5 N 1559 2.21 5 O 1848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9696 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2861 Classifications: {'peptide': 356} Link IDs: {'PTRANS': 21, 'TRANS': 334} Chain breaks: 1 Chain: "B" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2621 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 15, 'TRANS': 313} Chain: "C" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2621 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 15, 'TRANS': 313} Chain: "G" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1593 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 9, 'rna3p_pur': 28, 'rna3p_pyr': 30} Link IDs: {'rna2p': 16, 'rna3p': 58} Time building chain proxies: 1.71, per 1000 atoms: 0.18 Number of scatterers: 9696 At special positions: 0 Unit cell: (95.04, 103.68, 104.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 74 15.00 O 1848 8.00 N 1559 7.00 C 6147 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: 0.66 Conformation dependent library (CDL) restraints added in 226.0 milliseconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1944 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 0 sheets defined 77.6% alpha, 0.0% beta 22 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 222 through 230 removed outlier: 3.713A pdb=" N TYR A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 264 through 282 removed outlier: 3.575A pdb=" N TRP A 276 " --> pdb=" O GLN A 272 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 280 " --> pdb=" O TRP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 320 removed outlier: 3.750A pdb=" N GLN A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 329 removed outlier: 3.841A pdb=" N VAL A 324 " --> pdb=" O PHE A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 removed outlier: 4.292A pdb=" N ASN A 335 " --> pdb=" O PRO A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 346 removed outlier: 3.684A pdb=" N LEU A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 383 removed outlier: 4.169A pdb=" N TRP A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR A 365 " --> pdb=" O HIS A 361 " (cutoff:3.500A) Proline residue: A 370 - end of helix removed outlier: 3.812A pdb=" N LYS A 377 " --> pdb=" O CYS A 373 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET A 383 " --> pdb=" O TYR A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' Processing helix chain 'A' and resid 398 through 416 removed outlier: 4.197A pdb=" N VAL A 402 " --> pdb=" O ASN A 398 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 439 removed outlier: 3.891A pdb=" N ILE A 422 " --> pdb=" O ARG A 418 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 424 " --> pdb=" O GLY A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 460 Processing helix chain 'A' and resid 461 through 476 removed outlier: 4.021A pdb=" N MET A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 498 removed outlier: 3.643A pdb=" N VAL A 498 " --> pdb=" O PHE A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 533 removed outlier: 3.676A pdb=" N THR A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 523 " --> pdb=" O MET A 519 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 524 " --> pdb=" O THR A 520 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 563 removed outlier: 3.607A pdb=" N ALA A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR A 550 " --> pdb=" O CYS A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 removed outlier: 3.685A pdb=" N ALA A 578 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 574 through 579' Processing helix chain 'B' and resid 32 through 41 removed outlier: 4.004A pdb=" N ARG B 39 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER B 40 " --> pdb=" O SER B 36 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 64 removed outlier: 4.424A pdb=" N SER B 49 " --> pdb=" O TYR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 73 removed outlier: 4.165A pdb=" N HIS B 72 " --> pdb=" O PRO B 68 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 68 through 73' Processing helix chain 'B' and resid 76 through 107 removed outlier: 3.768A pdb=" N MET B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 117 removed outlier: 3.691A pdb=" N VAL B 111 " --> pdb=" O PHE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 124 Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'B' and resid 131 through 137 removed outlier: 3.810A pdb=" N LEU B 135 " --> pdb=" O TRP B 131 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 168 removed outlier: 3.550A pdb=" N GLN B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Proline residue: B 158 - end of helix Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 183 through 186 Processing helix chain 'B' and resid 187 through 203 removed outlier: 3.586A pdb=" N MET B 203 " --> pdb=" O GLY B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 230 Processing helix chain 'B' and resid 246 through 264 Proline residue: B 252 - end of helix Processing helix chain 'B' and resid 267 through 286 Processing helix chain 'B' and resid 293 through 297 removed outlier: 3.861A pdb=" N ARG B 297 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 305 through 316 removed outlier: 4.175A pdb=" N LEU B 309 " --> pdb=" O TYR B 305 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 353 removed outlier: 3.872A pdb=" N VAL B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 358 removed outlier: 3.825A pdb=" N LEU B 358 " --> pdb=" O SER B 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 40 removed outlier: 3.549A pdb=" N SER C 40 " --> pdb=" O SER C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 63 Processing helix chain 'C' and resid 68 through 73 Processing helix chain 'C' and resid 76 through 107 Processing helix chain 'C' and resid 107 through 116 removed outlier: 3.534A pdb=" N VAL C 111 " --> pdb=" O PHE C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 123 Processing helix chain 'C' and resid 124 through 133 removed outlier: 4.662A pdb=" N SER C 128 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 166 removed outlier: 3.931A pdb=" N GLN C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Proline residue: C 158 - end of helix Processing helix chain 'C' and resid 179 through 186 Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'C' and resid 192 through 204 Processing helix chain 'C' and resid 207 through 229 removed outlier: 3.849A pdb=" N MET C 212 " --> pdb=" O CYS C 208 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 215 " --> pdb=" O CYS C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 251 Processing helix chain 'C' and resid 253 through 264 removed outlier: 4.119A pdb=" N LEU C 257 " --> pdb=" O ALA C 253 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 286 Processing helix chain 'C' and resid 291 through 296 removed outlier: 3.788A pdb=" N LYS C 296 " --> pdb=" O LYS C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 304 Processing helix chain 'C' and resid 305 through 324 removed outlier: 3.811A pdb=" N LEU C 309 " --> pdb=" O TYR C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 345 removed outlier: 4.452A pdb=" N LEU C 331 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET C 332 " --> pdb=" O GLY C 328 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU C 333 " --> pdb=" O SER C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 353 removed outlier: 4.028A pdb=" N ALA C 351 " --> pdb=" O MET C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 358 487 hydrogen bonds defined for protein. 1407 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1889 1.33 - 1.45: 2891 1.45 - 1.57: 5086 1.57 - 1.69: 148 1.69 - 1.81: 117 Bond restraints: 10131 Sorted by residual: bond pdb=" C PHE A 517 " pdb=" N PRO A 518 " ideal model delta sigma weight residual 1.335 1.384 -0.049 1.28e-02 6.10e+03 1.49e+01 bond pdb=" CA ARG B 287 " pdb=" C ARG B 287 " ideal model delta sigma weight residual 1.525 1.566 -0.040 1.12e-02 7.97e+03 1.30e+01 bond pdb=" C ARG B 287 " pdb=" N PRO B 288 " ideal model delta sigma weight residual 1.336 1.368 -0.032 1.08e-02 8.57e+03 8.91e+00 bond pdb=" C HIS A 330 " pdb=" N PRO A 331 " ideal model delta sigma weight residual 1.335 1.370 -0.034 1.36e-02 5.41e+03 6.33e+00 bond pdb=" CA ASN A 395 " pdb=" C ASN A 395 " ideal model delta sigma weight residual 1.528 1.555 -0.027 1.26e-02 6.30e+03 4.52e+00 ... (remaining 10126 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 13928 2.38 - 4.76: 181 4.76 - 7.14: 20 7.14 - 9.52: 7 9.52 - 11.90: 1 Bond angle restraints: 14137 Sorted by residual: angle pdb=" N ILE B 244 " pdb=" CA ILE B 244 " pdb=" C ILE B 244 " ideal model delta sigma weight residual 113.47 105.31 8.16 1.01e+00 9.80e-01 6.53e+01 angle pdb=" N LEU C 124 " pdb=" CA LEU C 124 " pdb=" C LEU C 124 " ideal model delta sigma weight residual 112.89 104.36 8.53 1.24e+00 6.50e-01 4.74e+01 angle pdb=" N ARG A 333 " pdb=" CA ARG A 333 " pdb=" C ARG A 333 " ideal model delta sigma weight residual 112.89 118.36 -5.47 1.24e+00 6.50e-01 1.94e+01 angle pdb=" N VAL B 317 " pdb=" CA VAL B 317 " pdb=" C VAL B 317 " ideal model delta sigma weight residual 113.16 106.79 6.37 1.49e+00 4.50e-01 1.83e+01 angle pdb=" N TRP A 382 " pdb=" CA TRP A 382 " pdb=" C TRP A 382 " ideal model delta sigma weight residual 111.14 106.56 4.58 1.08e+00 8.57e-01 1.80e+01 ... (remaining 14132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.91: 5759 34.91 - 69.82: 262 69.82 - 104.73: 30 104.73 - 139.65: 1 139.65 - 174.56: 3 Dihedral angle restraints: 6055 sinusoidal: 3061 harmonic: 2994 Sorted by residual: dihedral pdb=" O4' C G 74 " pdb=" C1' C G 74 " pdb=" N1 C G 74 " pdb=" C2 C G 74 " ideal model delta sinusoidal sigma weight residual -128.00 46.56 -174.56 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" C4' G G 72 " pdb=" C3' G G 72 " pdb=" O3' G G 72 " pdb=" P C G 73 " ideal model delta sinusoidal sigma weight residual -140.00 30.41 -170.41 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' A G 57 " pdb=" C3' A G 57 " pdb=" O3' A G 57 " pdb=" P U G 58 " ideal model delta sinusoidal sigma weight residual -140.00 29.13 -169.13 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 6052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1584 0.077 - 0.154: 82 0.154 - 0.232: 3 0.232 - 0.309: 1 0.309 - 0.386: 1 Chirality restraints: 1671 Sorted by residual: chirality pdb=" CA PHE C 115 " pdb=" N PHE C 115 " pdb=" C PHE C 115 " pdb=" CB PHE C 115 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CA ARG A 333 " pdb=" N ARG A 333 " pdb=" C ARG A 333 " pdb=" CB ARG A 333 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA SER C 179 " pdb=" N SER C 179 " pdb=" C SER C 179 " pdb=" CB SER C 179 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.42e-01 ... (remaining 1668 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 325 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO B 326 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 326 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 326 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 420 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO A 421 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 421 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 421 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 252 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO A 253 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.031 5.00e-02 4.00e+02 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 613 2.73 - 3.27: 9983 3.27 - 3.81: 17188 3.81 - 4.36: 21702 4.36 - 4.90: 34419 Nonbonded interactions: 83905 Sorted by model distance: nonbonded pdb=" OD1 ASN B 122 " pdb=" OH TYR B 167 " model vdw 2.182 3.040 nonbonded pdb=" O4 U G 13 " pdb=" O6 G G 22 " model vdw 2.204 2.432 nonbonded pdb=" O2' G G 15 " pdb=" OP1 U G 16 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR A 529 " pdb=" OE1 GLU C 207 " model vdw 2.227 3.040 nonbonded pdb=" O ILE C 61 " pdb=" OG SER C 67 " model vdw 2.262 3.040 ... (remaining 83900 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 'B' selection = chain 'C' } 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: 1.190 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.850 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 0.049 10131 Z= 0.195 Angle : 0.688 11.902 14137 Z= 0.430 Chirality : 0.039 0.386 1671 Planarity : 0.006 0.071 1448 Dihedral : 18.671 174.558 4111 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: -0.27 (0.27), residues: 1006 helix: 0.01 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -0.28 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 287 TYR 0.015 0.002 TYR A 432 PHE 0.020 0.002 PHE A 517 TRP 0.031 0.001 TRP B 170 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.20 (10131) covalent geometry : angle 0.68848 / 0.43 (14137) hydrogen bonds : bond 0.17439 / 10.95 ( 545) hydrogen bonds : angle 6.99188 / 4.86 ( 1507) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.8254 (mmm) cc_final: 0.7588 (mmp) REVERT: C 123 TYR cc_start: 0.8339 (m-80) cc_final: 0.7978 (m-80) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.0988 time to fit residues: 32.1302 Evaluate side-chains 170 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.3980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 40.0000 chunk 38 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 HIS A 405 ASN B 193 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.214043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.145008 restraints weight = 10659.876| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.04 r_work: 0.3579 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10131 Z= 0.146 Angle : 0.586 6.827 14137 Z= 0.306 Chirality : 0.038 0.152 1671 Planarity : 0.006 0.072 1448 Dihedral : 20.020 173.792 2279 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.83 % Allowed : 7.66 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.27), residues: 1006 helix: 0.48 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -0.22 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG C 356 TYR 0.015 0.002 TYR B 100 PHE 0.021 0.002 PHE B 98 TRP 0.014 0.001 TRP C 153 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (10131) covalent geometry : angle 0.58617 / 0.31 (14137) hydrogen bonds : bond 0.04637 / 2.98 ( 545) hydrogen bonds : angle 4.51526 / 3.24 ( 1507) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 258 TYR cc_start: 0.8321 (t80) cc_final: 0.7762 (t80) REVERT: B 217 MET cc_start: 0.8831 (mmm) cc_final: 0.8055 (mmp) REVERT: B 230 ARG cc_start: 0.7622 (ptt90) cc_final: 0.7373 (ppt170) REVERT: B 309 LEU cc_start: 0.8841 (mp) cc_final: 0.8597 (mp) REVERT: B 348 VAL cc_start: 0.8777 (p) cc_final: 0.8541 (m) REVERT: C 51 SER cc_start: 0.8208 (t) cc_final: 0.7745 (p) REVERT: C 212 MET cc_start: 0.8144 (mpp) cc_final: 0.7787 (mtt) REVERT: C 240 LYS cc_start: 0.6778 (pttm) cc_final: 0.6274 (ptpt) REVERT: C 333 LEU cc_start: 0.8017 (mp) cc_final: 0.7738 (tt) outliers start: 16 outliers final: 13 residues processed: 191 average time/residue: 0.0851 time to fit residues: 23.9297 Evaluate side-chains 177 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 306 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 0.0370 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 84 optimal weight: 0.0270 chunk 8 optimal weight: 0.9990 chunk 102 optimal weight: 40.0000 chunk 11 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 ASN B 72 HIS C 321 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.211862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.143055 restraints weight = 10618.566| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.02 r_work: 0.3565 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10131 Z= 0.132 Angle : 0.529 6.827 14137 Z= 0.276 Chirality : 0.037 0.163 1671 Planarity : 0.006 0.071 1448 Dihedral : 19.898 173.904 2279 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.94 % Allowed : 11.54 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.27), residues: 1006 helix: 0.77 (0.20), residues: 699 sheet: None (None), residues: 0 loop : -0.11 (0.38), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 225 TYR 0.016 0.002 TYR C 123 PHE 0.019 0.002 PHE A 517 TRP 0.011 0.001 TRP C 153 HIS 0.007 0.001 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (10131) covalent geometry : angle 0.52895 / 0.28 (14137) hydrogen bonds : bond 0.04221 / 2.68 ( 545) hydrogen bonds : angle 4.15774 / 2.97 ( 1507) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.335 Fit side-chains REVERT: B 217 MET cc_start: 0.8890 (mmm) cc_final: 0.8112 (mmp) REVERT: B 230 ARG cc_start: 0.7528 (ptt90) cc_final: 0.7277 (ppt170) REVERT: B 348 VAL cc_start: 0.8827 (p) cc_final: 0.8579 (m) REVERT: C 212 MET cc_start: 0.8164 (mpp) cc_final: 0.7958 (mtt) REVERT: C 333 LEU cc_start: 0.8097 (mp) cc_final: 0.7743 (tt) outliers start: 17 outliers final: 12 residues processed: 180 average time/residue: 0.0825 time to fit residues: 22.0836 Evaluate side-chains 177 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 344 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 62 optimal weight: 0.9980 chunk 99 optimal weight: 50.0000 chunk 67 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 87 optimal weight: 0.0570 chunk 88 optimal weight: 0.4980 chunk 25 optimal weight: 0.0670 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.214667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.143005 restraints weight = 10748.805| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.18 r_work: 0.3640 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10131 Z= 0.119 Angle : 0.509 6.768 14137 Z= 0.264 Chirality : 0.036 0.177 1671 Planarity : 0.005 0.069 1448 Dihedral : 19.811 174.107 2279 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.51 % Allowed : 12.34 % Favored : 85.14 % 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: 0.99 (0.27), residues: 1006 helix: 1.00 (0.20), residues: 698 sheet: None (None), residues: 0 loop : 0.10 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 225 TYR 0.018 0.001 TYR C 123 PHE 0.021 0.001 PHE B 335 TRP 0.011 0.001 TRP C 153 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (10131) covalent geometry : angle 0.50892 / 0.26 (14137) hydrogen bonds : bond 0.03943 / 2.50 ( 545) hydrogen bonds : angle 3.98380 / 2.84 ( 1507) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.329 Fit side-chains REVERT: B 217 MET cc_start: 0.8876 (mmm) cc_final: 0.8026 (mmm) REVERT: B 230 ARG cc_start: 0.7395 (ptt90) cc_final: 0.7099 (ppt170) outliers start: 22 outliers final: 16 residues processed: 183 average time/residue: 0.0857 time to fit residues: 23.3635 Evaluate side-chains 177 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 344 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 74 optimal weight: 0.8980 chunk 93 optimal weight: 0.0870 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 0.0020 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 overall best weight: 0.4766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 ASN C 193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.213825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.142394 restraints weight = 10793.944| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.15 r_work: 0.3525 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10131 Z= 0.114 Angle : 0.498 8.437 14137 Z= 0.256 Chirality : 0.036 0.175 1671 Planarity : 0.005 0.067 1448 Dihedral : 19.749 174.437 2279 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.06 % Allowed : 14.17 % Favored : 83.77 % 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: 1.16 (0.27), residues: 1006 helix: 1.10 (0.20), residues: 700 sheet: None (None), residues: 0 loop : 0.22 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 176 TYR 0.012 0.001 TYR A 440 PHE 0.021 0.001 PHE B 115 TRP 0.011 0.001 TRP C 153 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (10131) covalent geometry : angle 0.49775 / 0.26 (14137) hydrogen bonds : bond 0.03849 / 2.44 ( 545) hydrogen bonds : angle 3.88481 / 2.76 ( 1507) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.341 Fit side-chains REVERT: B 98 PHE cc_start: 0.8000 (t80) cc_final: 0.7755 (t80) REVERT: B 217 MET cc_start: 0.8835 (mmm) cc_final: 0.8025 (mmm) REVERT: B 230 ARG cc_start: 0.7449 (ptt90) cc_final: 0.7194 (ppt170) REVERT: C 176 ARG cc_start: 0.7202 (ttm-80) cc_final: 0.6846 (mtp85) outliers start: 18 outliers final: 17 residues processed: 178 average time/residue: 0.0845 time to fit residues: 22.4839 Evaluate side-chains 184 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 344 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 321 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.209215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.138570 restraints weight = 10734.494| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.05 r_work: 0.3532 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10131 Z= 0.134 Angle : 0.513 8.460 14137 Z= 0.263 Chirality : 0.036 0.167 1671 Planarity : 0.005 0.065 1448 Dihedral : 19.682 174.498 2279 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.51 % Allowed : 14.63 % Favored : 82.86 % 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: 1.13 (0.27), residues: 1006 helix: 1.11 (0.20), residues: 704 sheet: None (None), residues: 0 loop : 0.12 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 176 TYR 0.011 0.001 TYR C 123 PHE 0.021 0.001 PHE A 517 TRP 0.013 0.001 TRP C 131 HIS 0.007 0.001 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (10131) covalent geometry : angle 0.51280 / 0.26 (14137) hydrogen bonds : bond 0.03912 / 2.49 ( 545) hydrogen bonds : angle 3.85622 / 2.73 ( 1507) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.323 Fit side-chains REVERT: B 98 PHE cc_start: 0.8081 (t80) cc_final: 0.7858 (t80) REVERT: B 165 LYS cc_start: 0.7720 (tppt) cc_final: 0.7460 (tppt) REVERT: B 217 MET cc_start: 0.8904 (mmm) cc_final: 0.8443 (mmp) REVERT: B 230 ARG cc_start: 0.7418 (ptt90) cc_final: 0.7092 (ppt170) REVERT: C 73 MET cc_start: 0.5523 (OUTLIER) cc_final: 0.5143 (mmm) REVERT: C 282 MET cc_start: 0.7833 (mmm) cc_final: 0.7611 (mmt) outliers start: 22 outliers final: 15 residues processed: 180 average time/residue: 0.0886 time to fit residues: 23.4974 Evaluate side-chains 177 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 344 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 10 optimal weight: 0.2980 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 25 optimal weight: 0.2980 chunk 62 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.211461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.140690 restraints weight = 10646.223| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.08 r_work: 0.3620 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10131 Z= 0.114 Angle : 0.523 13.517 14137 Z= 0.259 Chirality : 0.036 0.211 1671 Planarity : 0.005 0.064 1448 Dihedral : 19.628 174.704 2279 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.29 % Allowed : 15.20 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.27), residues: 1006 helix: 1.19 (0.20), residues: 704 sheet: None (None), residues: 0 loop : 0.26 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 442 TYR 0.017 0.001 TYR C 123 PHE 0.021 0.001 PHE A 517 TRP 0.011 0.001 TRP C 153 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (10131) covalent geometry : angle 0.52306 / 0.26 (14137) hydrogen bonds : bond 0.03748 / 2.39 ( 545) hydrogen bonds : angle 3.78571 / 2.67 ( 1507) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.312 Fit side-chains REVERT: A 375 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7189 (tt0) REVERT: A 532 VAL cc_start: 0.8732 (m) cc_final: 0.8488 (p) REVERT: B 98 PHE cc_start: 0.7937 (t80) cc_final: 0.7695 (t80) REVERT: B 217 MET cc_start: 0.8854 (mmm) cc_final: 0.7982 (mmm) REVERT: B 348 VAL cc_start: 0.8804 (p) cc_final: 0.8601 (m) REVERT: C 73 MET cc_start: 0.5476 (OUTLIER) cc_final: 0.5089 (mmm) REVERT: C 181 LEU cc_start: 0.7550 (mt) cc_final: 0.7349 (mt) outliers start: 20 outliers final: 15 residues processed: 177 average time/residue: 0.0862 time to fit residues: 22.6955 Evaluate side-chains 178 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 344 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 1 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 0.0770 chunk 28 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 ASN B 117 HIS B 193 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.209310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.138604 restraints weight = 10730.935| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.07 r_work: 0.3531 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10131 Z= 0.122 Angle : 0.534 11.805 14137 Z= 0.263 Chirality : 0.037 0.291 1671 Planarity : 0.005 0.064 1448 Dihedral : 19.589 174.710 2279 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.51 % Allowed : 15.89 % Favored : 81.60 % 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: 1.36 (0.27), residues: 1006 helix: 1.27 (0.20), residues: 700 sheet: None (None), residues: 0 loop : 0.24 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 442 TYR 0.016 0.001 TYR C 123 PHE 0.021 0.001 PHE A 517 TRP 0.014 0.001 TRP B 205 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (10131) covalent geometry : angle 0.53444 / 0.26 (14137) hydrogen bonds : bond 0.03743 / 2.39 ( 545) hydrogen bonds : angle 3.77608 / 2.65 ( 1507) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.313 Fit side-chains REVERT: A 469 MET cc_start: 0.8936 (mtp) cc_final: 0.8635 (mtm) REVERT: B 98 PHE cc_start: 0.8046 (t80) cc_final: 0.7807 (t80) REVERT: C 73 MET cc_start: 0.5471 (OUTLIER) cc_final: 0.5097 (mmm) REVERT: C 163 ASP cc_start: 0.8344 (m-30) cc_final: 0.8092 (m-30) REVERT: C 181 LEU cc_start: 0.7902 (mt) cc_final: 0.7682 (mt) REVERT: C 282 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7379 (mmm) REVERT: C 344 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7770 (mp) outliers start: 22 outliers final: 16 residues processed: 177 average time/residue: 0.0807 time to fit residues: 21.6875 Evaluate side-chains 184 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 344 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.0570 chunk 7 optimal weight: 0.0980 chunk 68 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 103 optimal weight: 50.0000 chunk 101 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.209777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.140313 restraints weight = 10732.074| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.03 r_work: 0.3557 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10131 Z= 0.115 Angle : 0.534 13.728 14137 Z= 0.261 Chirality : 0.037 0.440 1671 Planarity : 0.005 0.064 1448 Dihedral : 19.559 174.778 2279 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.06 % Allowed : 16.23 % Favored : 81.71 % 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: 1.40 (0.28), residues: 1006 helix: 1.30 (0.20), residues: 703 sheet: None (None), residues: 0 loop : 0.23 (0.39), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 442 TYR 0.015 0.001 TYR C 123 PHE 0.025 0.001 PHE B 115 TRP 0.013 0.001 TRP B 302 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 (10131) covalent geometry : angle 0.53357 / 0.26 (14137) hydrogen bonds : bond 0.03667 / 2.34 ( 545) hydrogen bonds : angle 3.75715 / 2.63 ( 1507) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.255 Fit side-chains REVERT: A 469 MET cc_start: 0.8936 (mtp) cc_final: 0.8669 (mtm) REVERT: A 532 VAL cc_start: 0.8738 (m) cc_final: 0.8525 (p) REVERT: B 62 MET cc_start: 0.8238 (mmm) cc_final: 0.8017 (mmm) REVERT: B 98 PHE cc_start: 0.8027 (t80) cc_final: 0.7787 (t80) REVERT: B 217 MET cc_start: 0.8858 (mmm) cc_final: 0.8646 (mmp) REVERT: C 73 MET cc_start: 0.5448 (OUTLIER) cc_final: 0.5079 (mmm) REVERT: C 163 ASP cc_start: 0.8414 (m-30) cc_final: 0.8137 (m-30) REVERT: C 181 LEU cc_start: 0.7832 (mt) cc_final: 0.7630 (mt) REVERT: C 212 MET cc_start: 0.8014 (mtm) cc_final: 0.7516 (mtt) outliers start: 18 outliers final: 15 residues processed: 173 average time/residue: 0.0807 time to fit residues: 21.1492 Evaluate side-chains 180 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 68 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 81 optimal weight: 0.0570 chunk 15 optimal weight: 0.4980 chunk 99 optimal weight: 50.0000 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 0.0060 chunk 62 optimal weight: 1.9990 chunk 102 optimal weight: 40.0000 chunk 51 optimal weight: 1.9990 overall best weight: 0.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.208849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.139625 restraints weight = 10730.084| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.01 r_work: 0.3566 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10131 Z= 0.110 Angle : 0.536 13.636 14137 Z= 0.262 Chirality : 0.037 0.384 1671 Planarity : 0.005 0.064 1448 Dihedral : 19.535 174.861 2279 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.83 % Allowed : 17.03 % Favored : 81.14 % 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: 1.48 (0.27), residues: 1006 helix: 1.37 (0.20), residues: 703 sheet: None (None), residues: 0 loop : 0.23 (0.39), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 442 TYR 0.013 0.001 TYR A 493 PHE 0.021 0.001 PHE A 517 TRP 0.011 0.001 TRP C 153 HIS 0.004 0.001 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (10131) covalent geometry : angle 0.53619 / 0.26 (14137) hydrogen bonds : bond 0.03627 / 2.31 ( 545) hydrogen bonds : angle 3.76759 / 2.63 ( 1507) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.362 Fit side-chains REVERT: A 469 MET cc_start: 0.8913 (mtp) cc_final: 0.8654 (mtm) REVERT: A 532 VAL cc_start: 0.8721 (m) cc_final: 0.8488 (p) REVERT: B 98 PHE cc_start: 0.8011 (t80) cc_final: 0.7767 (t80) REVERT: B 217 MET cc_start: 0.8827 (mmm) cc_final: 0.8598 (mmp) REVERT: B 224 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7938 (m-80) REVERT: B 321 GLN cc_start: 0.7549 (mt0) cc_final: 0.7202 (mt0) REVERT: C 73 MET cc_start: 0.5363 (OUTLIER) cc_final: 0.5004 (mmm) REVERT: C 163 ASP cc_start: 0.8416 (m-30) cc_final: 0.8150 (m-30) REVERT: C 212 MET cc_start: 0.7990 (mtm) cc_final: 0.7501 (mtt) outliers start: 16 outliers final: 12 residues processed: 172 average time/residue: 0.0799 time to fit residues: 20.8959 Evaluate side-chains 178 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 16 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 81 optimal weight: 0.0270 chunk 68 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 85 optimal weight: 0.0970 chunk 50 optimal weight: 0.2980 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.214008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.142249 restraints weight = 10664.965| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.17 r_work: 0.3640 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 10131 Z= 0.104 Angle : 0.534 13.514 14137 Z= 0.259 Chirality : 0.037 0.384 1671 Planarity : 0.005 0.064 1448 Dihedral : 19.502 174.999 2279 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.71 % Allowed : 17.60 % Favored : 80.69 % 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: 1.55 (0.27), residues: 1006 helix: 1.44 (0.20), residues: 703 sheet: None (None), residues: 0 loop : 0.21 (0.39), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 442 TYR 0.013 0.001 TYR A 493 PHE 0.021 0.001 PHE A 517 TRP 0.010 0.001 TRP C 153 HIS 0.004 0.000 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 (10131) covalent geometry : angle 0.53381 / 0.26 (14137) hydrogen bonds : bond 0.03525 / 2.25 ( 545) hydrogen bonds : angle 3.73874 / 2.61 ( 1507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3209.65 seconds wall clock time: 55 minutes 39.35 seconds (3339.35 seconds total)