Starting phenix.real_space_refine on Wed Aug 5 12:37:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m7w_63695/08_2026/9m7w_63695.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m7w_63695/08_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_63695/08_2026/9m7w_63695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m7w_63695/08_2026/9m7w_63695.map" model { file = "/net/cci-nas-00/data/ceres_data/9m7w_63695/08_2026/9m7w_63695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m7w_63695/08_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-2.2rc3-6140/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: 1.97, per 1000 atoms: 0.20 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: 1.05 Conformation dependent library (CDL) restraints added in 203.1 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: 0.75 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: 1.05 Time building geometry restraints manager: 1.26 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: 13858 2.38 - 4.76: 251 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: 1509 0.077 - 0.154: 157 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: 0.010 Normalize map: mean=0, sd=1: 1.200 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 8.860 Find NCS groups from input model: 0.060 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.360 ------------------------------------------------------------------------------- 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= 0.200 Angle : 0.743 11.902 14137 Z= 0.483 Chirality : 0.047 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 0.00366 / 0.20 (10131) covalent geometry : angle 0.74265 / 0.48 (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 : 0.188 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: 0.0821 time to fit residues: 26.8390 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 : 0.179 ------------------------------------------------------------------------------- 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 = 0.213973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.145932 restraints weight = 10646.781| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.02 r_work: 0.3594 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1855 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= 0.143 Angle : 0.586 6.841 14137 Z= 0.305 Chirality : 0.037 0.151 1671 Planarity : 0.006 0.072 1448 Dihedral : 19.958 174.721 2279 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.71 % Allowed : 7.89 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.27), residues: 1006 helix: 0.48 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -0.21 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 356 TYR 0.015 0.002 TYR B 100 PHE 0.021 0.002 PHE A 517 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 0.00320 / 0.14 (10131) covalent geometry : angle 0.58630 / 0.31 (14137) hydrogen bonds : bond 0.04846 / 3.12 ( 545) hydrogen bonds : angle 4.55607 / 3.26 ( 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 194 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 258 TYR cc_start: 0.8343 (t80) cc_final: 0.7803 (t80) REVERT: B 217 MET cc_start: 0.8841 (mmm) cc_final: 0.8047 (mmp) REVERT: B 230 ARG cc_start: 0.7592 (ptt90) cc_final: 0.7345 (ppt170) REVERT: B 309 LEU cc_start: 0.8833 (mp) cc_final: 0.8595 (mp) REVERT: B 348 VAL cc_start: 0.8771 (p) cc_final: 0.8539 (m) REVERT: C 51 SER cc_start: 0.8205 (t) cc_final: 0.7734 (p) REVERT: C 212 MET cc_start: 0.8128 (mpp) cc_final: 0.7754 (mtt) REVERT: C 240 LYS cc_start: 0.6745 (pttm) cc_final: 0.6240 (ptpt) outliers start: 15 outliers final: 13 residues processed: 188 average time/residue: 0.0680 time to fit residues: 18.7151 Evaluate side-chains 176 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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: 0.9980 chunk 27 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 84 optimal weight: 0.0060 chunk 8 optimal weight: 0.7980 chunk 102 optimal weight: 50.0000 chunk 11 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 39 optimal weight: 0.4980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 72 HIS C 321 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.211624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.142654 restraints weight = 10610.045| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.03 r_work: 0.3557 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10131 Z= 0.130 Angle : 0.534 6.753 14137 Z= 0.277 Chirality : 0.037 0.168 1671 Planarity : 0.006 0.071 1448 Dihedral : 19.814 173.599 2279 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.29 % Allowed : 10.97 % Favored : 86.74 % 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: 0.62 (0.27), residues: 1006 helix: 0.74 (0.20), residues: 701 sheet: None (None), residues: 0 loop : -0.11 (0.38), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 287 TYR 0.017 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 0.00298 / 0.13 (10131) covalent geometry : angle 0.53420 / 0.28 (14137) hydrogen bonds : bond 0.04260 / 2.70 ( 545) hydrogen bonds : angle 4.14868 / 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 194 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.324 Fit side-chains REVERT: A 375 GLU cc_start: 0.7704 (tt0) cc_final: 0.7494 (tt0) REVERT: B 217 MET cc_start: 0.8879 (mmm) cc_final: 0.8123 (mmp) REVERT: B 230 ARG cc_start: 0.7528 (ptt90) cc_final: 0.7282 (ppt170) REVERT: B 348 VAL cc_start: 0.8824 (p) cc_final: 0.8574 (m) REVERT: C 212 MET cc_start: 0.8173 (mpp) cc_final: 0.7948 (mtt) REVERT: C 333 LEU cc_start: 0.8098 (mp) cc_final: 0.7742 (tt) REVERT: C 342 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8360 (mm) outliers start: 20 outliers final: 12 residues processed: 183 average time/residue: 0.0748 time to fit residues: 20.3814 Evaluate side-chains 176 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 342 ILE 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: 0.3980 chunk 99 optimal weight: 50.0000 chunk 67 optimal weight: 8.9990 chunk 59 optimal weight: 0.5980 chunk 35 optimal weight: 9.9990 chunk 87 optimal weight: 0.0570 chunk 88 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 = 0.4413 r_free = 0.4413 target = 0.210573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.140777 restraints weight = 10734.727| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.05 r_work: 0.3554 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2539 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= 0.116 Angle : 0.505 6.824 14137 Z= 0.261 Chirality : 0.036 0.169 1671 Planarity : 0.005 0.069 1448 Dihedral : 19.749 174.411 2279 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.63 % Allowed : 12.11 % Favored : 85.26 % 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: 0.99 (0.20), residues: 699 sheet: None (None), residues: 0 loop : 0.12 (0.38), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 287 TYR 0.016 0.001 TYR C 123 PHE 0.020 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 / 0.12 (10131) covalent geometry : angle 0.50542 / 0.26 (14137) hydrogen bonds : bond 0.04004 / 2.54 ( 545) hydrogen bonds : angle 3.96173 / 2.82 ( 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 198 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.309 Fit side-chains REVERT: B 217 MET cc_start: 0.8895 (mmm) cc_final: 0.8069 (mmm) REVERT: B 230 ARG cc_start: 0.7513 (ptt90) cc_final: 0.7225 (ppt170) outliers start: 23 outliers final: 17 residues processed: 186 average time/residue: 0.0757 time to fit residues: 21.2981 Evaluate side-chains 182 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 84 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 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: 2.9990 chunk 93 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 0.0970 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4421 r_free = 0.4421 target = 0.209577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.138733 restraints weight = 10815.249| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.07 r_work: 0.3538 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10131 Z= 0.133 Angle : 0.522 8.931 14137 Z= 0.266 Chirality : 0.037 0.174 1671 Planarity : 0.005 0.067 1448 Dihedral : 19.687 174.870 2279 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.29 % Allowed : 14.29 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.27), residues: 1006 helix: 1.00 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.01 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 176 TYR 0.014 0.002 TYR A 379 PHE 0.021 0.002 PHE A 517 TRP 0.011 0.001 TRP A 513 HIS 0.007 0.001 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (10131) covalent geometry : angle 0.52171 / 0.27 (14137) hydrogen bonds : bond 0.04017 / 2.55 ( 545) hydrogen bonds : angle 3.90912 / 2.78 ( 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 189 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.309 Fit side-chains REVERT: B 98 PHE cc_start: 0.8101 (t80) cc_final: 0.7867 (t80) REVERT: B 217 MET cc_start: 0.8899 (mmm) cc_final: 0.8168 (mmp) REVERT: B 230 ARG cc_start: 0.7400 (ptt90) cc_final: 0.7117 (ppt170) REVERT: B 348 VAL cc_start: 0.8802 (p) cc_final: 0.8595 (m) REVERT: C 73 MET cc_start: 0.5514 (OUTLIER) cc_final: 0.5128 (mmm) REVERT: C 176 ARG cc_start: 0.7127 (ttm-80) cc_final: 0.6919 (mtp85) outliers start: 20 outliers final: 16 residues processed: 178 average time/residue: 0.0757 time to fit residues: 20.0854 Evaluate side-chains 181 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 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 73 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: 3.9990 chunk 47 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 35 optimal weight: 0.0570 chunk 62 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.6902 ------------------------------------------------------------------------------- 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 = 0.4426 r_free = 0.4426 target = 0.211350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.139488 restraints weight = 10794.261| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.16 r_work: 0.3531 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3041 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= 0.130 Angle : 0.514 8.797 14137 Z= 0.261 Chirality : 0.036 0.211 1671 Planarity : 0.005 0.065 1448 Dihedral : 19.642 175.235 2279 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.29 % Allowed : 14.29 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.27), residues: 1006 helix: 1.09 (0.20), residues: 709 sheet: None (None), residues: 0 loop : 0.14 (0.39), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 176 TYR 0.016 0.001 TYR C 123 PHE 0.022 0.001 PHE A 517 TRP 0.011 0.001 TRP C 153 HIS 0.006 0.001 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (10131) covalent geometry : angle 0.51448 / 0.26 (14137) hydrogen bonds : bond 0.03915 / 2.48 ( 545) hydrogen bonds : angle 3.85787 / 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 190 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.233 Fit side-chains REVERT: A 532 VAL cc_start: 0.8745 (m) cc_final: 0.8490 (p) REVERT: B 98 PHE cc_start: 0.7953 (t80) cc_final: 0.7728 (t80) REVERT: B 165 LYS cc_start: 0.7607 (tppt) cc_final: 0.7326 (tppt) REVERT: B 217 MET cc_start: 0.8854 (mmm) cc_final: 0.8430 (mmp) REVERT: B 348 VAL cc_start: 0.8837 (p) cc_final: 0.8617 (m) REVERT: C 73 MET cc_start: 0.5509 (OUTLIER) cc_final: 0.5080 (mmm) REVERT: C 282 MET cc_start: 0.7774 (mmm) cc_final: 0.7572 (mmt) outliers start: 20 outliers final: 15 residues processed: 179 average time/residue: 0.0572 time to fit residues: 15.3960 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 : 0.203 ------------------------------------------------------------------------------- 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 300 VAL 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 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: 2.9990 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 0.0270 chunk 62 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 ASN B 117 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.212127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.139862 restraints weight = 10639.513| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.16 r_work: 0.3611 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3186 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= 0.119 Angle : 0.526 14.228 14137 Z= 0.260 Chirality : 0.036 0.203 1671 Planarity : 0.005 0.065 1448 Dihedral : 19.606 175.449 2279 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.17 % Allowed : 15.31 % 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: 1.25 (0.27), residues: 1006 helix: 1.16 (0.20), residues: 704 sheet: None (None), residues: 0 loop : 0.28 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 389 TYR 0.014 0.001 TYR C 123 PHE 0.021 0.001 PHE A 517 TRP 0.013 0.001 TRP B 205 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (10131) covalent geometry : angle 0.52623 / 0.26 (14137) hydrogen bonds : bond 0.03813 / 2.42 ( 545) hydrogen bonds : angle 3.79992 / 2.68 ( 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 188 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.317 Fit side-chains REVERT: B 98 PHE cc_start: 0.7984 (t80) cc_final: 0.7745 (t80) REVERT: B 202 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7924 (mm-30) REVERT: B 348 VAL cc_start: 0.8832 (p) cc_final: 0.8599 (m) REVERT: C 73 MET cc_start: 0.5584 (OUTLIER) cc_final: 0.5158 (mmm) REVERT: C 181 LEU cc_start: 0.7583 (mt) cc_final: 0.7379 (mt) REVERT: C 282 MET cc_start: 0.7669 (mmm) cc_final: 0.7461 (mmt) outliers start: 19 outliers final: 15 residues processed: 176 average time/residue: 0.0768 time to fit residues: 20.2292 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 : 0.285 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 80 optimal weight: 0.0970 chunk 6 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 84 optimal weight: 0.0010 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 0.0060 overall best weight: 0.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 193 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.213893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.142149 restraints weight = 10677.866| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.16 r_work: 0.3622 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10131 Z= 0.103 Angle : 0.518 11.952 14137 Z= 0.255 Chirality : 0.036 0.299 1671 Planarity : 0.005 0.063 1448 Dihedral : 19.571 175.782 2279 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.06 % Allowed : 15.66 % Favored : 82.29 % 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: 1.45 (0.27), residues: 1006 helix: 1.31 (0.20), residues: 703 sheet: None (None), residues: 0 loop : 0.33 (0.39), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 356 TYR 0.015 0.001 TYR C 123 PHE 0.021 0.001 PHE A 517 TRP 0.011 0.001 TRP C 153 HIS 0.003 0.000 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (10131) covalent geometry : angle 0.51796 / 0.26 (14137) hydrogen bonds : bond 0.03685 / 2.34 ( 545) hydrogen bonds : angle 3.74344 / 2.62 ( 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 186 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.325 Fit side-chains REVERT: A 469 MET cc_start: 0.8892 (mtp) cc_final: 0.8613 (mtm) REVERT: A 532 VAL cc_start: 0.8718 (m) cc_final: 0.8460 (p) REVERT: B 62 MET cc_start: 0.8223 (mmm) cc_final: 0.8000 (mmm) REVERT: B 98 PHE cc_start: 0.7955 (t80) cc_final: 0.7704 (t80) REVERT: B 217 MET cc_start: 0.8827 (mmm) cc_final: 0.8619 (mmp) REVERT: B 302 TRP cc_start: 0.8836 (m-10) cc_final: 0.8491 (m-10) REVERT: B 348 VAL cc_start: 0.8852 (p) cc_final: 0.8623 (m) REVERT: C 73 MET cc_start: 0.5587 (OUTLIER) cc_final: 0.5186 (mmm) REVERT: C 344 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7719 (mp) outliers start: 18 outliers final: 14 residues processed: 176 average time/residue: 0.0751 time to fit residues: 19.9083 Evaluate side-chains 182 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 67 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 103 optimal weight: 50.0000 chunk 101 optimal weight: 40.0000 chunk 13 optimal weight: 0.0770 chunk 64 optimal weight: 0.0270 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.4406 r_free = 0.4406 target = 0.208671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.138417 restraints weight = 10778.316| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.03 r_work: 0.3558 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10131 Z= 0.114 Angle : 0.551 14.911 14137 Z= 0.265 Chirality : 0.037 0.391 1671 Planarity : 0.005 0.064 1448 Dihedral : 19.549 175.784 2279 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.06 % Allowed : 16.34 % 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: 1.44 (0.27), residues: 1006 helix: 1.33 (0.20), residues: 703 sheet: None (None), residues: 0 loop : 0.29 (0.38), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.012 0.001 TYR A 493 PHE 0.023 0.001 PHE B 115 TRP 0.010 0.001 TRP C 153 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (10131) covalent geometry : angle 0.55091 / 0.26 (14137) hydrogen bonds : bond 0.03712 / 2.36 ( 545) hydrogen bonds : angle 3.77887 / 2.65 ( 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 182 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.250 Fit side-chains REVERT: A 469 MET cc_start: 0.8929 (mtp) cc_final: 0.8674 (mtm) REVERT: B 98 PHE cc_start: 0.8026 (t80) cc_final: 0.7783 (t80) REVERT: B 217 MET cc_start: 0.8832 (mmm) cc_final: 0.8609 (mmp) REVERT: B 224 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7911 (m-80) REVERT: B 348 VAL cc_start: 0.8853 (p) cc_final: 0.8628 (m) REVERT: C 73 MET cc_start: 0.5415 (OUTLIER) cc_final: 0.5013 (mmm) outliers start: 18 outliers final: 14 residues processed: 173 average time/residue: 0.0813 time to fit residues: 21.1823 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 : 0.379 ------------------------------------------------------------------------------- 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 132 LEU Chi-restraints excluded: chain B residue 203 MET 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 C residue 42 HIS Chi-restraints excluded: chain C residue 52 LEU 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 187 GLN 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: 0.5980 chunk 69 optimal weight: 0.9990 chunk 81 optimal weight: 0.0470 chunk 15 optimal weight: 0.4980 chunk 99 optimal weight: 50.0000 chunk 47 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 102 optimal weight: 50.0000 chunk 51 optimal weight: 1.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- 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 = 0.4400 r_free = 0.4400 target = 0.207892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.137507 restraints weight = 10742.633| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.04 r_work: 0.3548 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10131 Z= 0.123 Angle : 0.544 13.090 14137 Z= 0.266 Chirality : 0.037 0.405 1671 Planarity : 0.005 0.063 1448 Dihedral : 19.532 175.789 2279 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.83 % Allowed : 16.91 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.27), residues: 1006 helix: 1.31 (0.20), residues: 707 sheet: None (None), residues: 0 loop : 0.23 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 287 TYR 0.012 0.001 TYR A 493 PHE 0.021 0.001 PHE A 517 TRP 0.018 0.001 TRP B 302 HIS 0.006 0.001 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (10131) covalent geometry : angle 0.54393 / 0.27 (14137) hydrogen bonds : bond 0.03731 / 2.38 ( 545) hydrogen bonds : angle 3.79329 / 2.65 ( 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 188 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.302 Fit side-chains REVERT: A 469 MET cc_start: 0.8936 (mtp) cc_final: 0.8682 (mtm) REVERT: A 532 VAL cc_start: 0.8748 (m) cc_final: 0.8516 (p) REVERT: B 98 PHE cc_start: 0.7976 (t80) cc_final: 0.7729 (t80) REVERT: B 217 MET cc_start: 0.8816 (mmm) cc_final: 0.8595 (mmp) REVERT: B 224 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.7921 (m-80) REVERT: B 302 TRP cc_start: 0.8948 (m-10) cc_final: 0.8640 (m-10) REVERT: B 321 GLN cc_start: 0.7558 (mt0) cc_final: 0.7214 (mt0) REVERT: B 348 VAL cc_start: 0.8833 (p) cc_final: 0.8611 (m) REVERT: C 73 MET cc_start: 0.5321 (OUTLIER) cc_final: 0.4922 (mmm) REVERT: C 163 ASP cc_start: 0.8423 (m-30) cc_final: 0.8153 (m-30) REVERT: C 212 MET cc_start: 0.8014 (mtm) cc_final: 0.7526 (mtt) REVERT: C 282 MET cc_start: 0.8022 (mmm) cc_final: 0.7707 (tpt) outliers start: 16 outliers final: 13 residues processed: 180 average time/residue: 0.0758 time to fit residues: 20.6080 Evaluate side-chains 184 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 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 C residue 42 HIS Chi-restraints excluded: chain C residue 52 LEU 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 187 GLN Chi-restraints excluded: chain C residue 306 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 16 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.4401 r_free = 0.4401 target = 0.208007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.138717 restraints weight = 10685.872| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.01 r_work: 0.3551 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10131 Z= 0.121 Angle : 0.553 13.882 14137 Z= 0.268 Chirality : 0.037 0.389 1671 Planarity : 0.005 0.063 1448 Dihedral : 19.519 175.818 2279 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.71 % Allowed : 17.37 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.34 (0.27), residues: 1006 helix: 1.31 (0.20), residues: 713 sheet: None (None), residues: 0 loop : 0.02 (0.38), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.013 0.001 TYR C 123 PHE 0.021 0.001 PHE A 517 TRP 0.010 0.001 TRP C 153 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (10131) covalent geometry : angle 0.55302 / 0.27 (14137) hydrogen bonds : bond 0.03700 / 2.35 ( 545) hydrogen bonds : angle 3.78866 / 2.65 ( 1507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2799.53 seconds wall clock time: 48 minutes 23.00 seconds (2903.00 seconds total)