Starting phenix.real_space_refine on Thu Jul 2 14:29:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y93_39068/07_2026/8y93_39068.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y93_39068/07_2026/8y93_39068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y93_39068/07_2026/8y93_39068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y93_39068/07_2026/8y93_39068.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y93_39068/07_2026/8y93_39068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y93_39068/07_2026/8y93_39068.map" } resolution = 3.0 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= 0.055 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: 6 Type Number sf(0) Gaussians S 40 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 6072 2.51 5 N 1413 2.21 5 O 1528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 9055 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "E" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Ad-hoc single atom residues: {' NA': 1, ' CL': 1} Unusual residues: {'TP0': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Time building chain proxies: 1.73, per 1000 atoms: 0.19 Number of scatterers: 9055 At special positions: 0 Unit cell: (97.09, 85.41, 118.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 40 16.00 Na 1 11.00 O 1528 8.00 N 1413 7.00 C 6072 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: 0.89 Conformation dependent library (CDL) restraints added in 206.0 milliseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 0 sheets defined 72.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 61 through 74 removed outlier: 3.738A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 79 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 90 through 93 removed outlier: 3.652A pdb=" N ALA A 93 " --> pdb=" O GLY A 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 93' Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 106 through 120 removed outlier: 4.085A pdb=" N GLU A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 114 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 115 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 165 removed outlier: 3.644A pdb=" N GLY A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 234 through 253 removed outlier: 3.863A pdb=" N CYS A 240 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.838A pdb=" N SER A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 282 removed outlier: 3.611A pdb=" N PHE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.889A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.505A pdb=" N THR A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 338 through 372 removed outlier: 3.699A pdb=" N ASP A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 359 " --> pdb=" O PHE A 355 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 360 " --> pdb=" O VAL A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.585A pdb=" N VAL A 387 " --> pdb=" O GLY A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 397 removed outlier: 3.863A pdb=" N THR A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.632A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 4.151A pdb=" N ARG A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 436 through 441' Processing helix chain 'A' and resid 441 through 457 removed outlier: 3.772A pdb=" N PHE A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 494 removed outlier: 4.435A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.918A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 583 through 589 Processing helix chain 'A' and resid 597 through 603 removed outlier: 3.917A pdb=" N VAL A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 602 " --> pdb=" O HIS A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 removed outlier: 3.792A pdb=" N PHE A 609 " --> pdb=" O ILE A 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 606 through 609' Processing helix chain 'A' and resid 610 through 615 removed outlier: 4.031A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 74 removed outlier: 3.792A pdb=" N PHE E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU E 66 " --> pdb=" O LYS E 62 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL E 70 " --> pdb=" O LEU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 105 Processing helix chain 'E' and resid 105 through 121 Processing helix chain 'E' and resid 131 through 134 Processing helix chain 'E' and resid 135 through 166 removed outlier: 4.071A pdb=" N TYR E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR E 151 " --> pdb=" O TYR E 147 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL E 154 " --> pdb=" O PHE E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 215 Processing helix chain 'E' and resid 234 through 253 Processing helix chain 'E' and resid 255 through 267 Processing helix chain 'E' and resid 269 through 284 removed outlier: 4.462A pdb=" N VAL E 273 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU E 274 " --> pdb=" O PRO E 270 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR E 283 " --> pdb=" O VAL E 279 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU E 284 " --> pdb=" O HIS E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 295 removed outlier: 4.048A pdb=" N ILE E 291 " --> pdb=" O ALA E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 320 removed outlier: 3.639A pdb=" N ALA E 312 " --> pdb=" O TRP E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 333 removed outlier: 3.745A pdb=" N TYR E 332 " --> pdb=" O ALA E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 372 Processing helix chain 'E' and resid 385 through 398 Proline residue: E 392 - end of helix Processing helix chain 'E' and resid 400 through 435 Processing helix chain 'E' and resid 435 through 441 Processing helix chain 'E' and resid 441 through 457 Processing helix chain 'E' and resid 464 through 494 removed outlier: 3.958A pdb=" N VAL E 468 " --> pdb=" O GLY E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 509 Processing helix chain 'E' and resid 514 through 523 Processing helix chain 'E' and resid 523 through 539 Processing helix chain 'E' and resid 551 through 567 removed outlier: 4.024A pdb=" N ASN E 555 " --> pdb=" O PRO E 551 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP E 556 " --> pdb=" O PRO E 552 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER E 565 " --> pdb=" O ILE E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 580 Processing helix chain 'E' and resid 583 through 593 Processing helix chain 'E' and resid 598 through 603 removed outlier: 3.933A pdb=" N ALA E 602 " --> pdb=" O HIS E 598 " (cutoff:3.500A) Processing helix chain 'E' and resid 610 through 616 removed outlier: 4.066A pdb=" N TRP E 614 " --> pdb=" O GLN E 610 " (cutoff:3.500A) 527 hydrogen bonds defined for protein. 1572 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1395 1.32 - 1.44: 2870 1.44 - 1.57: 5022 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 9349 Sorted by residual: bond pdb=" CA TRP E 128 " pdb=" C TRP E 128 " ideal model delta sigma weight residual 1.530 1.458 0.072 1.14e-02 7.69e+03 4.02e+01 bond pdb=" C3 TP0 A 701 " pdb=" C6 TP0 A 701 " ideal model delta sigma weight residual 1.483 1.555 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" CA VAL E 127 " pdb=" C VAL E 127 " ideal model delta sigma weight residual 1.525 1.481 0.044 1.27e-02 6.20e+03 1.18e+01 bond pdb=" CA ILE E 130 " pdb=" C ILE E 130 " ideal model delta sigma weight residual 1.520 1.470 0.050 1.54e-02 4.22e+03 1.07e+01 bond pdb=" CA LYS E 129 " pdb=" C LYS E 129 " ideal model delta sigma weight residual 1.522 1.485 0.037 1.31e-02 5.83e+03 7.81e+00 ... (remaining 9344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 12716 3.42 - 6.84: 36 6.84 - 10.26: 1 10.26 - 13.69: 3 13.69 - 17.11: 1 Bond angle restraints: 12757 Sorted by residual: angle pdb=" N LYS E 129 " pdb=" CA LYS E 129 " pdb=" C LYS E 129 " ideal model delta sigma weight residual 113.30 96.19 17.11 1.34e+00 5.57e-01 1.63e+02 angle pdb=" N VAL E 127 " pdb=" CA VAL E 127 " pdb=" C VAL E 127 " ideal model delta sigma weight residual 113.16 102.59 10.57 1.49e+00 4.50e-01 5.03e+01 angle pdb=" N ILE E 130 " pdb=" CA ILE E 130 " pdb=" C ILE E 130 " ideal model delta sigma weight residual 112.83 106.53 6.30 9.90e-01 1.02e+00 4.04e+01 angle pdb=" C14 TP0 A 701 " pdb=" N1 TP0 A 701 " pdb=" C20 TP0 A 701 " ideal model delta sigma weight residual 111.01 99.00 12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" N VAL A 137 " pdb=" CA VAL A 137 " pdb=" C VAL A 137 " ideal model delta sigma weight residual 113.00 108.42 4.58 1.30e+00 5.92e-01 1.24e+01 ... (remaining 12752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.77: 5099 28.77 - 57.55: 111 57.55 - 86.32: 8 86.32 - 115.09: 1 115.09 - 143.87: 2 Dihedral angle restraints: 5221 sinusoidal: 1957 harmonic: 3264 Sorted by residual: dihedral pdb=" C22 TP0 A 701 " pdb=" C21 TP0 A 701 " pdb=" C4 TP0 A 701 " pdb=" C6 TP0 A 701 " ideal model delta sinusoidal sigma weight residual 71.36 -72.51 143.87 1 3.00e+01 1.11e-03 1.93e+01 dihedral pdb=" C10 TP0 A 701 " pdb=" C21 TP0 A 701 " pdb=" C4 TP0 A 701 " pdb=" C22 TP0 A 701 " ideal model delta sinusoidal sigma weight residual 108.73 -108.00 -143.27 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C LYS E 129 " pdb=" N LYS E 129 " pdb=" CA LYS E 129 " pdb=" CB LYS E 129 " ideal model delta harmonic sigma weight residual -122.60 -113.18 -9.42 0 2.50e+00 1.60e-01 1.42e+01 ... (remaining 5218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1156 0.045 - 0.090: 231 0.090 - 0.134: 28 0.134 - 0.179: 1 0.179 - 0.224: 2 Chirality restraints: 1418 Sorted by residual: chirality pdb=" CB VAL E 127 " pdb=" CA VAL E 127 " pdb=" CG1 VAL E 127 " pdb=" CG2 VAL E 127 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA LYS E 129 " pdb=" N LYS E 129 " pdb=" C LYS E 129 " pdb=" CB LYS E 129 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA TRP E 128 " pdb=" N TRP E 128 " pdb=" C TRP E 128 " pdb=" CB TRP E 128 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.54e-01 ... (remaining 1415 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS E 131 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO E 132 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 132 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 132 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 391 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.29e+00 pdb=" N PRO E 392 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 392 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 392 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 127 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C VAL E 127 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL E 127 " 0.010 2.00e-02 2.50e+03 pdb=" N TRP E 128 " 0.009 2.00e-02 2.50e+03 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 122 2.68 - 3.24: 9022 3.24 - 3.79: 14631 3.79 - 4.35: 19640 4.35 - 4.90: 32766 Nonbonded interactions: 76181 Sorted by model distance: nonbonded pdb=" C20 TP0 A 701 " pdb=" C29 TP0 A 701 " model vdw 2.127 3.088 nonbonded pdb=" OG SER A 318 " pdb="CL CL A 703 " model vdw 2.227 3.270 nonbonded pdb=" N LYS E 129 " pdb=" N ILE E 130 " model vdw 2.244 2.560 nonbonded pdb=" O SER A 251 " pdb=" OG1 THR A 258 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR E 332 " pdb=" OG1 THR E 429 " model vdw 2.295 3.040 ... (remaining 76176 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 53 through 617) selection = chain 'E' } 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 7.690 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 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 : 0.003 0.072 9349 Z= 0.189 Angle : 0.603 17.108 12757 Z= 0.367 Chirality : 0.035 0.224 1418 Planarity : 0.004 0.048 1554 Dihedral : 11.793 143.867 3145 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 5.15 % Allowed : 7.14 % Favored : 87.71 % 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: -1.85 (0.23), residues: 1126 helix: -0.76 (0.18), residues: 730 sheet: None (None), residues: 0 loop : -1.94 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 216 TYR 0.007 0.001 TYR A 340 PHE 0.011 0.001 PHE A 409 TRP 0.015 0.001 TRP E 128 HIS 0.001 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.19 ( 9349) covalent geometry : angle 0.60326 / 0.37 (12757) hydrogen bonds : bond 0.14553 / 9.54 ( 527) hydrogen bonds : angle 6.59816 / 4.77 ( 1572) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 249 time to evaluate : 0.335 Fit side-chains REVERT: A 147 TYR cc_start: 0.8334 (m-10) cc_final: 0.7725 (m-10) REVERT: A 271 TYR cc_start: 0.8410 (m-80) cc_final: 0.8185 (m-80) REVERT: A 348 SER cc_start: 0.8411 (m) cc_final: 0.8208 (m) REVERT: A 439 LYS cc_start: 0.8491 (mttt) cc_final: 0.8103 (mtpm) REVERT: A 585 TRP cc_start: 0.6791 (m100) cc_final: 0.6542 (m-10) REVERT: A 611 LEU cc_start: 0.8222 (tp) cc_final: 0.7839 (tt) REVERT: E 111 TYR cc_start: 0.8222 (t80) cc_final: 0.7846 (t80) REVERT: E 120 ASN cc_start: 0.8206 (m-40) cc_final: 0.7990 (m-40) REVERT: E 133 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.6754 (m-80) REVERT: E 494 TRP cc_start: 0.7747 (m100) cc_final: 0.7422 (m100) outliers start: 49 outliers final: 9 residues processed: 279 average time/residue: 0.3474 time to fit residues: 106.7924 Evaluate side-chains 160 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 180 TRP Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 205 TYR Chi-restraints excluded: chain E residue 359 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN A 234 GLN A 236 GLN A 280 HIS A 350 ASN A 507 GLN E 120 ASN E 153 ASN E 337 ASN E 613 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.178271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.146378 restraints weight = 12447.727| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.10 r_work: 0.3711 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9349 Z= 0.155 Angle : 0.601 10.244 12757 Z= 0.303 Chirality : 0.040 0.172 1418 Planarity : 0.004 0.031 1554 Dihedral : 8.124 141.204 1242 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.73 % Allowed : 17.33 % Favored : 77.94 % 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: -0.35 (0.25), residues: 1126 helix: 0.43 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -1.45 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 604 TYR 0.017 0.001 TYR A 111 PHE 0.020 0.002 PHE A 362 TRP 0.017 0.001 TRP A 128 HIS 0.006 0.001 HIS E 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 9349) covalent geometry : angle 0.60134 / 0.30 (12757) hydrogen bonds : bond 0.04263 / 2.70 ( 527) hydrogen bonds : angle 4.52567 / 3.25 ( 1572) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 153 ASN cc_start: 0.8936 (m-40) cc_final: 0.8731 (m110) REVERT: A 271 TYR cc_start: 0.8713 (m-80) cc_final: 0.8511 (m-80) REVERT: A 297 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7987 (pt) REVERT: A 439 LYS cc_start: 0.8812 (mttt) cc_final: 0.8432 (mtpm) REVERT: A 585 TRP cc_start: 0.7193 (m100) cc_final: 0.6669 (m-10) REVERT: A 595 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: E 100 LEU cc_start: 0.8375 (tt) cc_final: 0.7272 (mm) REVERT: E 119 TYR cc_start: 0.6942 (t80) cc_final: 0.6530 (t80) REVERT: E 120 ASN cc_start: 0.8352 (m110) cc_final: 0.8079 (m-40) REVERT: E 121 ARG cc_start: 0.8129 (tpp80) cc_final: 0.7836 (mpt90) REVERT: E 242 MET cc_start: 0.7594 (mtm) cc_final: 0.7341 (mtt) REVERT: E 254 LYS cc_start: 0.7655 (tptm) cc_final: 0.7297 (tppp) REVERT: E 350 ASN cc_start: 0.6097 (m110) cc_final: 0.5742 (m110) REVERT: E 436 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8254 (mp10) REVERT: E 438 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8164 (mm) REVERT: E 595 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: E 603 GLN cc_start: 0.6944 (mt0) cc_final: 0.6699 (mp10) outliers start: 45 outliers final: 16 residues processed: 191 average time/residue: 0.3573 time to fit residues: 75.7195 Evaluate side-chains 150 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 180 TRP Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 595 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 20 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.179305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.145597 restraints weight = 12291.339| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.26 r_work: 0.3761 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9349 Z= 0.138 Angle : 0.582 16.220 12757 Z= 0.285 Chirality : 0.039 0.137 1418 Planarity : 0.004 0.030 1554 Dihedral : 7.798 141.578 1235 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.94 % Allowed : 18.07 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.31 (0.25), residues: 1126 helix: 0.90 (0.19), residues: 739 sheet: None (None), residues: 0 loop : -1.09 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 512 TYR 0.017 0.001 TYR E 340 PHE 0.020 0.001 PHE A 362 TRP 0.011 0.001 TRP A 80 HIS 0.007 0.001 HIS E 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 9349) covalent geometry : angle 0.58182 / 0.28 (12757) hydrogen bonds : bond 0.04206 / 2.65 ( 527) hydrogen bonds : angle 4.36525 / 3.12 ( 1572) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 130 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 LYS cc_start: 0.8214 (pptt) cc_final: 0.7963 (pptt) REVERT: A 297 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7916 (pt) REVERT: A 439 LYS cc_start: 0.8768 (mttt) cc_final: 0.8396 (mtpm) REVERT: A 585 TRP cc_start: 0.7220 (m100) cc_final: 0.6645 (m-10) REVERT: A 597 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7631 (mt-10) REVERT: E 100 LEU cc_start: 0.8457 (tt) cc_final: 0.7399 (mm) REVERT: E 119 TYR cc_start: 0.6935 (t80) cc_final: 0.6468 (t80) REVERT: E 120 ASN cc_start: 0.8217 (m110) cc_final: 0.7986 (m110) REVERT: E 121 ARG cc_start: 0.8093 (tpp80) cc_final: 0.7771 (mmm160) REVERT: E 242 MET cc_start: 0.7613 (mtm) cc_final: 0.7339 (mtt) REVERT: E 254 LYS cc_start: 0.7747 (tptm) cc_final: 0.7364 (tppp) REVERT: E 337 ASN cc_start: 0.6966 (OUTLIER) cc_final: 0.6448 (p0) REVERT: E 350 ASN cc_start: 0.6236 (m110) cc_final: 0.5921 (m110) REVERT: E 438 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8186 (mm) REVERT: E 600 LEU cc_start: 0.7351 (mm) cc_final: 0.6893 (mp) REVERT: E 603 GLN cc_start: 0.6849 (mt0) cc_final: 0.6599 (mp10) outliers start: 47 outliers final: 18 residues processed: 165 average time/residue: 0.3169 time to fit residues: 58.5776 Evaluate side-chains 139 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 296 HIS Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 486 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.177887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.141256 restraints weight = 12476.617| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.34 r_work: 0.3740 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9349 Z= 0.131 Angle : 0.567 14.719 12757 Z= 0.278 Chirality : 0.039 0.130 1418 Planarity : 0.003 0.030 1554 Dihedral : 7.670 141.251 1233 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.73 % Allowed : 18.70 % Favored : 76.58 % 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 (0.26), residues: 1126 helix: 1.14 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -0.90 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 512 TYR 0.013 0.001 TYR A 340 PHE 0.021 0.001 PHE E 275 TRP 0.010 0.001 TRP A 80 HIS 0.006 0.001 HIS E 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 9349) covalent geometry : angle 0.56656 / 0.28 (12757) hydrogen bonds : bond 0.04142 / 2.60 ( 527) hydrogen bonds : angle 4.31451 / 3.08 ( 1572) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 125 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 LYS cc_start: 0.8137 (pptt) cc_final: 0.7875 (pptt) REVERT: A 236 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7902 (mt0) REVERT: A 297 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.7999 (pt) REVERT: A 439 LYS cc_start: 0.8755 (mttt) cc_final: 0.8370 (mtpm) REVERT: A 581 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7929 (tm-30) REVERT: A 585 TRP cc_start: 0.7226 (m100) cc_final: 0.6668 (m-10) REVERT: E 100 LEU cc_start: 0.8497 (tt) cc_final: 0.7481 (mm) REVERT: E 119 TYR cc_start: 0.6997 (t80) cc_final: 0.6537 (t80) REVERT: E 120 ASN cc_start: 0.8114 (m110) cc_final: 0.7843 (m110) REVERT: E 190 LEU cc_start: 0.6531 (tp) cc_final: 0.6248 (pt) REVERT: E 242 MET cc_start: 0.7625 (mtm) cc_final: 0.7337 (mtt) REVERT: E 254 LYS cc_start: 0.7735 (tptm) cc_final: 0.7167 (tppt) REVERT: E 257 LYS cc_start: 0.5900 (OUTLIER) cc_final: 0.5341 (mmmt) REVERT: E 337 ASN cc_start: 0.7016 (OUTLIER) cc_final: 0.6380 (p0) REVERT: E 350 ASN cc_start: 0.6284 (m110) cc_final: 0.6004 (m110) REVERT: E 370 HIS cc_start: 0.5044 (OUTLIER) cc_final: 0.4810 (p90) REVERT: E 438 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8151 (mm) REVERT: E 479 THR cc_start: 0.6887 (m) cc_final: 0.6147 (t) REVERT: E 508 MET cc_start: 0.5879 (ttm) cc_final: 0.5641 (ttm) REVERT: E 600 LEU cc_start: 0.7376 (mm) cc_final: 0.6898 (mp) REVERT: E 603 GLN cc_start: 0.6841 (mt0) cc_final: 0.6573 (mp10) outliers start: 45 outliers final: 19 residues processed: 161 average time/residue: 0.3266 time to fit residues: 59.0997 Evaluate side-chains 142 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 581 GLN Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 180 TRP Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 296 HIS Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 370 HIS Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 486 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 86 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 70 optimal weight: 0.0370 chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 0.0970 chunk 48 optimal weight: 0.9980 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 GLN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.178584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.144645 restraints weight = 12241.589| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.20 r_work: 0.3776 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9349 Z= 0.111 Angle : 0.549 14.187 12757 Z= 0.266 Chirality : 0.038 0.136 1418 Planarity : 0.003 0.028 1554 Dihedral : 7.575 140.962 1232 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.99 % Allowed : 19.85 % Favored : 76.16 % 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: 0.83 (0.26), residues: 1126 helix: 1.27 (0.20), residues: 747 sheet: None (None), residues: 0 loop : -0.85 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 512 TYR 0.018 0.001 TYR E 340 PHE 0.018 0.001 PHE A 362 TRP 0.009 0.001 TRP E 585 HIS 0.005 0.001 HIS E 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 9349) covalent geometry : angle 0.54912 / 0.27 (12757) hydrogen bonds : bond 0.03756 / 2.36 ( 527) hydrogen bonds : angle 4.26461 / 3.06 ( 1572) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7997 (pptt) cc_final: 0.7649 (pptt) REVERT: A 236 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7824 (mt0) REVERT: A 297 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8026 (pt) REVERT: A 439 LYS cc_start: 0.8745 (mttt) cc_final: 0.8401 (mtpm) REVERT: A 585 TRP cc_start: 0.7165 (m100) cc_final: 0.6643 (m-10) REVERT: A 595 GLU cc_start: 0.7805 (mp0) cc_final: 0.7567 (mp0) REVERT: E 100 LEU cc_start: 0.8477 (tt) cc_final: 0.7369 (mm) REVERT: E 112 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7967 (ttp) REVERT: E 119 TYR cc_start: 0.7013 (t80) cc_final: 0.6498 (t80) REVERT: E 120 ASN cc_start: 0.7968 (m110) cc_final: 0.7699 (m110) REVERT: E 242 MET cc_start: 0.7612 (mtm) cc_final: 0.7324 (mtt) REVERT: E 254 LYS cc_start: 0.7714 (tptm) cc_final: 0.7136 (tppt) REVERT: E 257 LYS cc_start: 0.5939 (OUTLIER) cc_final: 0.5386 (mmmt) REVERT: E 337 ASN cc_start: 0.6934 (OUTLIER) cc_final: 0.6600 (p0) REVERT: E 350 ASN cc_start: 0.6177 (m110) cc_final: 0.5894 (m110) REVERT: E 370 HIS cc_start: 0.5030 (OUTLIER) cc_final: 0.4762 (p90) REVERT: E 438 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8112 (mm) REVERT: E 479 THR cc_start: 0.6755 (m) cc_final: 0.6080 (t) REVERT: E 508 MET cc_start: 0.5831 (ttm) cc_final: 0.5552 (ttm) REVERT: E 600 LEU cc_start: 0.7387 (mm) cc_final: 0.6934 (mp) REVERT: E 603 GLN cc_start: 0.6855 (mt0) cc_final: 0.6601 (mp10) outliers start: 38 outliers final: 16 residues processed: 158 average time/residue: 0.3264 time to fit residues: 57.8185 Evaluate side-chains 142 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 180 TRP Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 370 HIS Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 528 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 6.9990 chunk 58 optimal weight: 0.1980 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.175916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.141415 restraints weight = 12285.249| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.19 r_work: 0.3741 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9349 Z= 0.135 Angle : 0.597 16.724 12757 Z= 0.287 Chirality : 0.039 0.140 1418 Planarity : 0.004 0.053 1554 Dihedral : 7.719 140.703 1232 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.89 % Allowed : 19.85 % Favored : 76.26 % 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: 0.86 (0.26), residues: 1126 helix: 1.28 (0.19), residues: 749 sheet: None (None), residues: 0 loop : -0.81 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 512 TYR 0.013 0.001 TYR A 340 PHE 0.020 0.001 PHE A 362 TRP 0.010 0.001 TRP A 80 HIS 0.006 0.001 HIS E 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 9349) covalent geometry : angle 0.59730 / 0.29 (12757) hydrogen bonds : bond 0.04172 / 2.63 ( 527) hydrogen bonds : angle 4.29168 / 3.07 ( 1572) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.8003 (pptt) cc_final: 0.7583 (pptt) REVERT: A 236 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7847 (mt0) REVERT: A 297 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8091 (pt) REVERT: A 439 LYS cc_start: 0.8749 (mttt) cc_final: 0.8398 (mtpm) REVERT: A 581 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7915 (tm-30) REVERT: A 585 TRP cc_start: 0.7157 (m100) cc_final: 0.6664 (m-10) REVERT: A 595 GLU cc_start: 0.7837 (mp0) cc_final: 0.7578 (mp0) REVERT: E 119 TYR cc_start: 0.7007 (t80) cc_final: 0.6556 (t80) REVERT: E 120 ASN cc_start: 0.7977 (m110) cc_final: 0.7722 (m110) REVERT: E 242 MET cc_start: 0.7661 (mtm) cc_final: 0.7374 (mtt) REVERT: E 254 LYS cc_start: 0.7739 (tptm) cc_final: 0.7162 (tppt) REVERT: E 257 LYS cc_start: 0.5878 (OUTLIER) cc_final: 0.5244 (mtpm) REVERT: E 350 ASN cc_start: 0.6258 (m110) cc_final: 0.6002 (m110) REVERT: E 377 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6451 (mt-10) REVERT: E 438 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8152 (mm) REVERT: E 479 THR cc_start: 0.6825 (m) cc_final: 0.6176 (t) REVERT: E 508 MET cc_start: 0.5894 (ttm) cc_final: 0.5653 (ttm) REVERT: E 600 LEU cc_start: 0.7441 (mm) cc_final: 0.6952 (mp) REVERT: E 603 GLN cc_start: 0.6973 (mt0) cc_final: 0.6679 (mp10) outliers start: 37 outliers final: 17 residues processed: 147 average time/residue: 0.3159 time to fit residues: 51.8178 Evaluate side-chains 132 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 581 GLN Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 377 GLU Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 438 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 26 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 12 optimal weight: 0.1980 chunk 0 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.176984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.142778 restraints weight = 12290.012| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.20 r_work: 0.3752 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9349 Z= 0.119 Angle : 0.593 16.898 12757 Z= 0.282 Chirality : 0.039 0.200 1418 Planarity : 0.003 0.040 1554 Dihedral : 7.731 140.576 1232 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.99 % Allowed : 19.75 % Favored : 76.26 % 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: 0.96 (0.26), residues: 1126 helix: 1.35 (0.19), residues: 749 sheet: None (None), residues: 0 loop : -0.77 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 512 TYR 0.019 0.001 TYR E 340 PHE 0.019 0.001 PHE A 362 TRP 0.018 0.001 TRP E 80 HIS 0.009 0.001 HIS E 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 9349) covalent geometry : angle 0.59350 / 0.28 (12757) hydrogen bonds : bond 0.03933 / 2.47 ( 527) hydrogen bonds : angle 4.26219 / 3.05 ( 1572) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7928 (pptt) cc_final: 0.7500 (pptt) REVERT: A 236 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7863 (mt0) REVERT: A 297 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8037 (pt) REVERT: A 439 LYS cc_start: 0.8752 (mttt) cc_final: 0.8397 (mtpm) REVERT: A 585 TRP cc_start: 0.7161 (m100) cc_final: 0.6660 (m-10) REVERT: A 595 GLU cc_start: 0.7809 (mp0) cc_final: 0.7552 (mp0) REVERT: E 112 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.8016 (ttp) REVERT: E 119 TYR cc_start: 0.6967 (t80) cc_final: 0.6509 (t80) REVERT: E 120 ASN cc_start: 0.7940 (m110) cc_final: 0.7692 (m110) REVERT: E 242 MET cc_start: 0.7652 (mtm) cc_final: 0.7340 (mtt) REVERT: E 254 LYS cc_start: 0.7704 (tptm) cc_final: 0.7119 (tppt) REVERT: E 257 LYS cc_start: 0.5924 (OUTLIER) cc_final: 0.5290 (mtpm) REVERT: E 350 ASN cc_start: 0.6209 (m110) cc_final: 0.5914 (m110) REVERT: E 377 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.6338 (mt-10) REVERT: E 438 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8118 (mm) REVERT: E 479 THR cc_start: 0.6694 (m) cc_final: 0.6171 (t) REVERT: E 508 MET cc_start: 0.5898 (ttm) cc_final: 0.5695 (ttm) REVERT: E 584 LEU cc_start: 0.5141 (OUTLIER) cc_final: 0.4752 (tt) REVERT: E 598 HIS cc_start: 0.6084 (OUTLIER) cc_final: 0.5232 (m-70) REVERT: E 600 LEU cc_start: 0.7403 (mm) cc_final: 0.6942 (mp) REVERT: E 603 GLN cc_start: 0.6999 (mt0) cc_final: 0.6676 (mp10) outliers start: 38 outliers final: 16 residues processed: 144 average time/residue: 0.3275 time to fit residues: 52.5396 Evaluate side-chains 133 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 180 TRP Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 377 GLU Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 598 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 0.2980 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 13 optimal weight: 0.4980 chunk 15 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.177286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.143175 restraints weight = 12258.123| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.18 r_work: 0.3758 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9349 Z= 0.121 Angle : 0.609 17.958 12757 Z= 0.287 Chirality : 0.038 0.168 1418 Planarity : 0.003 0.034 1554 Dihedral : 7.679 140.480 1232 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.47 % Allowed : 20.80 % Favored : 75.74 % 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: 1.05 (0.26), residues: 1126 helix: 1.42 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -0.72 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 512 TYR 0.011 0.001 TYR A 340 PHE 0.026 0.001 PHE E 275 TRP 0.024 0.001 TRP E 80 HIS 0.006 0.001 HIS E 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 9349) covalent geometry : angle 0.60870 / 0.29 (12757) hydrogen bonds : bond 0.03940 / 2.48 ( 527) hydrogen bonds : angle 4.24102 / 3.03 ( 1572) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7762 (pptt) cc_final: 0.7309 (pptt) REVERT: A 439 LYS cc_start: 0.8743 (mttt) cc_final: 0.8388 (mtpm) REVERT: A 509 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7290 (mtp) REVERT: A 585 TRP cc_start: 0.7160 (m100) cc_final: 0.6658 (m-10) REVERT: A 595 GLU cc_start: 0.7816 (mp0) cc_final: 0.7549 (mp0) REVERT: E 112 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7984 (ttp) REVERT: E 119 TYR cc_start: 0.6941 (t80) cc_final: 0.6486 (t80) REVERT: E 120 ASN cc_start: 0.7945 (m110) cc_final: 0.7696 (m110) REVERT: E 242 MET cc_start: 0.7648 (mtm) cc_final: 0.7346 (mtt) REVERT: E 254 LYS cc_start: 0.7719 (tptm) cc_final: 0.7121 (tppt) REVERT: E 257 LYS cc_start: 0.6018 (OUTLIER) cc_final: 0.5341 (mtpm) REVERT: E 350 ASN cc_start: 0.6183 (m110) cc_final: 0.5908 (m110) REVERT: E 370 HIS cc_start: 0.4992 (OUTLIER) cc_final: 0.4771 (p-80) REVERT: E 377 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.6325 (mt-10) REVERT: E 438 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8087 (mm) REVERT: E 479 THR cc_start: 0.6607 (m) cc_final: 0.6145 (t) REVERT: E 508 MET cc_start: 0.5901 (ttm) cc_final: 0.5679 (ttm) REVERT: E 584 LEU cc_start: 0.4942 (OUTLIER) cc_final: 0.4587 (tt) REVERT: E 600 LEU cc_start: 0.7447 (mm) cc_final: 0.7150 (mp) outliers start: 33 outliers final: 16 residues processed: 139 average time/residue: 0.3199 time to fit residues: 49.6163 Evaluate side-chains 133 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 370 HIS Chi-restraints excluded: chain E residue 377 GLU Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 584 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 79 optimal weight: 0.0980 chunk 63 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 598 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.177879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.143874 restraints weight = 12265.913| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.19 r_work: 0.3768 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9349 Z= 0.117 Angle : 0.606 17.682 12757 Z= 0.285 Chirality : 0.038 0.168 1418 Planarity : 0.003 0.049 1554 Dihedral : 7.619 140.454 1232 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.05 % Allowed : 21.64 % Favored : 75.32 % 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: 1.11 (0.26), residues: 1126 helix: 1.45 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.66 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 512 TYR 0.018 0.001 TYR E 340 PHE 0.028 0.001 PHE A 275 TRP 0.024 0.001 TRP E 80 HIS 0.005 0.001 HIS E 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 9349) covalent geometry : angle 0.60583 / 0.28 (12757) hydrogen bonds : bond 0.03824 / 2.41 ( 527) hydrogen bonds : angle 4.22266 / 3.02 ( 1572) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7725 (pptt) cc_final: 0.7274 (pptt) REVERT: A 190 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7150 (pt) REVERT: A 439 LYS cc_start: 0.8738 (mttt) cc_final: 0.8383 (mtpm) REVERT: A 585 TRP cc_start: 0.7148 (m100) cc_final: 0.6634 (m-10) REVERT: A 595 GLU cc_start: 0.7837 (mp0) cc_final: 0.7545 (mp0) REVERT: E 112 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7966 (ttp) REVERT: E 119 TYR cc_start: 0.6958 (t80) cc_final: 0.6466 (t80) REVERT: E 120 ASN cc_start: 0.7944 (m110) cc_final: 0.7668 (m110) REVERT: E 242 MET cc_start: 0.7674 (mtm) cc_final: 0.7384 (mtt) REVERT: E 254 LYS cc_start: 0.7702 (tptm) cc_final: 0.7194 (tppp) REVERT: E 257 LYS cc_start: 0.6014 (OUTLIER) cc_final: 0.5437 (mmmt) REVERT: E 329 PHE cc_start: 0.7182 (m-10) cc_final: 0.6915 (m-10) REVERT: E 350 ASN cc_start: 0.6193 (m110) cc_final: 0.5893 (m110) REVERT: E 370 HIS cc_start: 0.4982 (OUTLIER) cc_final: 0.4588 (p-80) REVERT: E 377 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6321 (mt-10) REVERT: E 438 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8058 (mm) REVERT: E 479 THR cc_start: 0.6533 (m) cc_final: 0.6045 (t) REVERT: E 508 MET cc_start: 0.5902 (ttm) cc_final: 0.5690 (ttm) REVERT: E 584 LEU cc_start: 0.5001 (OUTLIER) cc_final: 0.4625 (tt) REVERT: E 600 LEU cc_start: 0.7426 (mm) cc_final: 0.7127 (mp) outliers start: 29 outliers final: 15 residues processed: 141 average time/residue: 0.3230 time to fit residues: 50.5187 Evaluate side-chains 135 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 370 HIS Chi-restraints excluded: chain E residue 377 GLU Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 50 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.176734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.142560 restraints weight = 12214.549| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.18 r_work: 0.3763 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9349 Z= 0.125 Angle : 0.621 16.604 12757 Z= 0.293 Chirality : 0.038 0.144 1418 Planarity : 0.003 0.042 1554 Dihedral : 7.629 140.524 1232 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.42 % Allowed : 22.69 % Favored : 74.89 % 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: 1.15 (0.26), residues: 1126 helix: 1.45 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -0.57 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 442 TYR 0.010 0.001 TYR A 340 PHE 0.024 0.001 PHE E 275 TRP 0.023 0.001 TRP E 80 HIS 0.005 0.001 HIS E 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 9349) covalent geometry : angle 0.62135 / 0.29 (12757) hydrogen bonds : bond 0.03967 / 2.50 ( 527) hydrogen bonds : angle 4.22005 / 3.01 ( 1572) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7723 (pptt) cc_final: 0.6638 (ptmt) REVERT: A 439 LYS cc_start: 0.8735 (mttt) cc_final: 0.8391 (mtpm) REVERT: A 585 TRP cc_start: 0.7172 (m100) cc_final: 0.6667 (m-10) REVERT: A 595 GLU cc_start: 0.7773 (mp0) cc_final: 0.7490 (mp0) REVERT: E 112 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7997 (ttp) REVERT: E 119 TYR cc_start: 0.6950 (t80) cc_final: 0.6469 (t80) REVERT: E 120 ASN cc_start: 0.7931 (m110) cc_final: 0.7620 (m110) REVERT: E 242 MET cc_start: 0.7671 (mtm) cc_final: 0.7393 (mtt) REVERT: E 254 LYS cc_start: 0.7666 (tptm) cc_final: 0.7081 (tppt) REVERT: E 350 ASN cc_start: 0.6226 (m110) cc_final: 0.5940 (m110) REVERT: E 377 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6310 (mt-10) REVERT: E 438 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8034 (mm) REVERT: E 479 THR cc_start: 0.6689 (m) cc_final: 0.6252 (t) REVERT: E 584 LEU cc_start: 0.5000 (OUTLIER) cc_final: 0.4610 (tt) REVERT: E 600 LEU cc_start: 0.7482 (mm) cc_final: 0.7145 (mp) outliers start: 23 outliers final: 14 residues processed: 128 average time/residue: 0.3019 time to fit residues: 43.3710 Evaluate side-chains 129 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 377 GLU Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 23 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 0.2980 chunk 62 optimal weight: 4.9990 chunk 70 optimal weight: 0.0010 chunk 89 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 598 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.172556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.137010 restraints weight = 12123.632| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.23 r_work: 0.3653 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9349 Z= 0.127 Angle : 0.614 16.588 12757 Z= 0.291 Chirality : 0.040 0.446 1418 Planarity : 0.003 0.037 1554 Dihedral : 7.628 140.472 1231 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.84 % Allowed : 22.27 % Favored : 74.89 % 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: 1.15 (0.26), residues: 1126 helix: 1.44 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.55 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 442 TYR 0.017 0.001 TYR E 340 PHE 0.033 0.001 PHE A 275 TRP 0.023 0.001 TRP E 80 HIS 0.010 0.001 HIS E 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 9349) covalent geometry : angle 0.61378 / 0.29 (12757) hydrogen bonds : bond 0.04020 / 2.53 ( 527) hydrogen bonds : angle 4.23836 / 3.02 ( 1572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2924.00 seconds wall clock time: 50 minutes 36.84 seconds (3036.84 seconds total)