Starting phenix.real_space_refine on Thu Jul 2 14:26:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y90_39065/07_2026/8y90_39065.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y90_39065/07_2026/8y90_39065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y90_39065/07_2026/8y90_39065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y90_39065/07_2026/8y90_39065.map" model { file = "/net/cci-nas-00/data/ceres_data/8y90_39065/07_2026/8y90_39065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y90_39065/07_2026/8y90_39065.cif" } resolution = 3.15 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= 0.045 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 6069 2.51 5 N 1413 2.21 5 O 1534 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: 9058 Number of models: 1 Model: "" Number of chains: 3 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: 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: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 24 Ad-hoc single atom residues: {' NA': 1, ' CL': 1} Unusual residues: {'A1LX6': 1} Classifications: {'undetermined': 1, 'water': 5} Link IDs: {None: 4} Chain breaks: 2 Time building chain proxies: 1.52, per 1000 atoms: 0.17 Number of scatterers: 9058 At special positions: 0 Unit cell: (96.36, 86.87, 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 1534 8.00 N 1413 7.00 C 6069 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: 0.57 Conformation dependent library (CDL) restraints added in 296.5 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: 55 helices and 0 sheets defined 74.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'E' and resid 61 through 74 removed outlier: 3.758A pdb=" N PHE E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU E 66 " --> pdb=" O LYS E 62 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL E 70 " --> pdb=" O LEU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 105 Processing helix chain 'E' and resid 105 through 121 Processing helix chain 'E' and resid 125 through 134 removed outlier: 3.614A pdb=" N TRP E 128 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS E 129 " --> pdb=" O THR E 126 " (cutoff:3.500A) Proline residue: E 132 - end of helix Processing helix chain 'E' and resid 135 through 166 removed outlier: 4.094A pdb=" N TYR E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR E 151 " --> pdb=" O TYR E 147 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL E 154 " --> pdb=" O PHE E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 216 Processing helix chain 'E' and resid 234 through 253 Processing helix chain 'E' and resid 255 through 279 removed outlier: 4.132A pdb=" N LYS E 261 " --> pdb=" O LYS E 257 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL E 262 " --> pdb=" O THR E 258 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP E 264 " --> pdb=" O GLY E 260 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE E 265 " --> pdb=" O LYS E 261 " (cutoff:3.500A) Proline residue: E 270 - end of helix removed outlier: 3.973A pdb=" N PHE E 275 " --> pdb=" O TYR E 271 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL E 276 " --> pdb=" O PHE E 272 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU E 277 " --> pdb=" O VAL E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 295 removed outlier: 3.784A pdb=" N ILE E 291 " --> pdb=" O ALA E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 320 Processing helix chain 'E' and resid 324 through 333 removed outlier: 3.530A 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 removed outlier: 3.614A pdb=" N THR E 397 " --> pdb=" O GLU E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 435 removed outlier: 3.557A pdb=" N TRP E 404 " --> pdb=" O GLY E 400 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL E 427 " --> pdb=" O GLY E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 441 Processing helix chain 'E' and resid 441 through 457 Processing helix chain 'E' and resid 457 through 462 Processing helix chain 'E' and resid 464 through 492 removed outlier: 3.985A pdb=" N VAL E 468 " --> pdb=" O GLY E 464 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU E 471 " --> pdb=" O TYR E 467 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP E 473 " --> pdb=" O LEU E 469 " (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: 3.811A pdb=" N ASN E 555 " --> pdb=" O PRO E 551 " (cutoff:3.500A) removed outlier: 3.706A 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: 3.931A pdb=" N ALA E 602 " --> pdb=" O HIS E 598 " (cutoff:3.500A) Processing helix chain 'E' and resid 610 through 616 removed outlier: 4.052A pdb=" N TRP E 614 " --> pdb=" O GLN E 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 74 removed outlier: 3.954A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 94 through 105 removed outlier: 3.594A pdb=" N LEU A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 120 removed outlier: 3.516A pdb=" N LEU A 116 " --> pdb=" O MET A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 134 Processing helix chain 'A' and resid 135 through 167 removed outlier: 3.675A pdb=" N TYR A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.632A pdb=" N GLU A 223 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 255 through 284 removed outlier: 3.727A pdb=" N GLY A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LYS A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 286 through 295 removed outlier: 4.051A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 320 removed outlier: 4.486A pdb=" N TRP A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 3.567A 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 373 removed outlier: 3.627A pdb=" N ALA A 360 " --> pdb=" O VAL A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 removed outlier: 3.860A pdb=" N VAL A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 398 removed outlier: 3.894A pdb=" N LEU A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.769A pdb=" N ASP A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 439 Processing helix chain 'A' and resid 441 through 456 removed outlier: 3.608A pdb=" N PHE A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 494 removed outlier: 4.211A 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 520 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 580 removed outlier: 3.824A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) Proline residue: A 570 - end of helix Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 598 through 604 removed outlier: 4.375A pdb=" N ALA A 602 " --> pdb=" O HIS A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 removed outlier: 3.507A 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: 4.030A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) 551 hydrogen bonds defined for protein. 1638 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: 1.24 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2647 1.34 - 1.46: 1907 1.46 - 1.57: 4730 1.57 - 1.69: 1 1.69 - 1.81: 62 Bond restraints: 9347 Sorted by residual: bond pdb=" C01 A1LX6 A 701 " pdb=" N02 A1LX6 A 701 " ideal model delta sigma weight residual 1.449 1.273 0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" C03 A1LX6 A 701 " pdb=" N02 A1LX6 A 701 " ideal model delta sigma weight residual 1.450 1.366 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C12 A1LX6 A 701 " pdb=" C13 A1LX6 A 701 " ideal model delta sigma weight residual 1.515 1.582 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C07 A1LX6 A 701 " pdb=" C08 A1LX6 A 701 " ideal model delta sigma weight residual 1.396 1.449 -0.053 2.00e-02 2.50e+03 6.97e+00 bond pdb=" C11 A1LX6 A 701 " pdb=" C12 A1LX6 A 701 " ideal model delta sigma weight residual 1.398 1.449 -0.051 2.00e-02 2.50e+03 6.49e+00 ... (remaining 9342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 12534 1.77 - 3.53: 186 3.53 - 5.30: 26 5.30 - 7.06: 7 7.06 - 8.83: 1 Bond angle restraints: 12754 Sorted by residual: angle pdb=" N VAL E 74 " pdb=" CA VAL E 74 " pdb=" C VAL E 74 " ideal model delta sigma weight residual 106.21 109.57 -3.36 1.07e+00 8.73e-01 9.87e+00 angle pdb=" C ASP A 546 " pdb=" CA ASP A 546 " pdb=" CB ASP A 546 " ideal model delta sigma weight residual 110.81 115.78 -4.97 1.60e+00 3.91e-01 9.64e+00 angle pdb=" C LEU A 191 " pdb=" CA LEU A 191 " pdb=" CB LEU A 191 " ideal model delta sigma weight residual 110.92 115.83 -4.91 1.59e+00 3.96e-01 9.55e+00 angle pdb=" C12 A1LX6 A 701 " pdb=" C13 A1LX6 A 701 " pdb=" N02 A1LX6 A 701 " ideal model delta sigma weight residual 113.93 122.76 -8.83 3.00e+00 1.11e-01 8.66e+00 angle pdb=" N ASP A 546 " pdb=" CA ASP A 546 " pdb=" C ASP A 546 " ideal model delta sigma weight residual 111.11 107.69 3.42 1.20e+00 6.94e-01 8.14e+00 ... (remaining 12749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 4901 16.53 - 33.05: 223 33.05 - 49.58: 76 49.58 - 66.11: 20 66.11 - 82.63: 6 Dihedral angle restraints: 5226 sinusoidal: 1962 harmonic: 3264 Sorted by residual: dihedral pdb=" CA VAL E 374 " pdb=" C VAL E 374 " pdb=" N ASN E 375 " pdb=" CA ASN E 375 " ideal model delta harmonic sigma weight residual 180.00 152.69 27.31 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA TRP E 128 " pdb=" C TRP E 128 " pdb=" N LYS E 129 " pdb=" CA LYS E 129 " ideal model delta harmonic sigma weight residual 180.00 158.51 21.49 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA LYS E 373 " pdb=" C LYS E 373 " pdb=" N VAL E 374 " pdb=" CA VAL E 374 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1064 0.038 - 0.076: 304 0.076 - 0.114: 47 0.114 - 0.152: 3 0.152 - 0.189: 1 Chirality restraints: 1419 Sorted by residual: chirality pdb=" C06 A1LX6 A 701 " pdb=" C07 A1LX6 A 701 " pdb=" C14 A1LX6 A 701 " pdb=" O05 A1LX6 A 701 " both_signs ideal model delta sigma weight residual False 2.38 2.19 0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" CA LEU A 269 " pdb=" N LEU A 269 " pdb=" C LEU A 269 " pdb=" CB LEU A 269 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA PRO A 570 " pdb=" N PRO A 570 " pdb=" C PRO A 570 " pdb=" CB PRO A 570 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.60e-01 ... (remaining 1416 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 477 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.88e+00 pdb=" C ALA E 477 " -0.049 2.00e-02 2.50e+03 pdb=" O ALA E 477 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY E 478 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 476 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C ALA E 476 " 0.048 2.00e-02 2.50e+03 pdb=" O ALA E 476 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA E 477 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 475 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C PHE E 475 " 0.043 2.00e-02 2.50e+03 pdb=" O PHE E 475 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA E 476 " -0.015 2.00e-02 2.50e+03 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 235 2.71 - 3.26: 9740 3.26 - 3.81: 15390 3.81 - 4.35: 19083 4.35 - 4.90: 32295 Nonbonded interactions: 76743 Sorted by model distance: nonbonded pdb=" OH TYR E 205 " pdb=" O LYS E 373 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR E 332 " pdb=" OG1 THR E 429 " model vdw 2.202 3.040 nonbonded pdb=" O ALA E 328 " pdb=" OG SER E 331 " model vdw 2.236 3.040 nonbonded pdb=" O LEU E 471 " pdb=" OG1 THR E 474 " model vdw 2.253 3.040 nonbonded pdb=" O SER A 251 " pdb=" OG SER A 259 " model vdw 2.261 3.040 ... (remaining 76738 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: 2.240 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.540 Find NCS groups from input model: 0.140 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 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 0.176 9347 Z= 0.175 Angle : 0.565 8.828 12754 Z= 0.344 Chirality : 0.034 0.189 1419 Planarity : 0.004 0.038 1554 Dihedral : 11.765 82.634 3150 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 6.09 % Allowed : 8.19 % Favored : 85.71 % 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: -1.83 (0.22), residues: 1126 helix: -0.83 (0.17), residues: 758 sheet: None (None), residues: 0 loop : -1.76 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 216 TYR 0.008 0.001 TYR A 98 PHE 0.008 0.001 PHE E 475 TRP 0.009 0.001 TRP E 128 HIS 0.002 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.18 ( 9347) covalent geometry : angle 0.56533 / 0.34 (12754) hydrogen bonds : bond 0.15051 / 10.35 ( 551) hydrogen bonds : angle 6.30655 / 4.47 ( 1638) *********************** 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 371 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 313 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 152 TYR cc_start: 0.6618 (t80) cc_final: 0.5904 (t80) REVERT: E 173 TRP cc_start: 0.5954 (OUTLIER) cc_final: 0.4968 (m-90) REVERT: E 250 PHE cc_start: 0.7255 (m-80) cc_final: 0.6910 (t80) REVERT: E 314 GLN cc_start: 0.6721 (OUTLIER) cc_final: 0.6423 (mm110) REVERT: E 347 SER cc_start: 0.7763 (m) cc_final: 0.7296 (m) REVERT: A 111 TYR cc_start: 0.7911 (t80) cc_final: 0.7564 (t80) REVERT: A 122 GLU cc_start: 0.6167 (mt-10) cc_final: 0.5884 (mt-10) REVERT: A 147 TYR cc_start: 0.7789 (m-10) cc_final: 0.7303 (m-10) REVERT: A 212 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7167 (mt-10) REVERT: A 263 VAL cc_start: 0.6406 (OUTLIER) cc_final: 0.6123 (m) REVERT: A 397 THR cc_start: 0.8075 (m) cc_final: 0.7710 (p) REVERT: A 418 ASP cc_start: 0.7875 (t0) cc_final: 0.7581 (t0) REVERT: A 490 ILE cc_start: 0.8208 (mt) cc_final: 0.7999 (mp) REVERT: A 519 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8344 (tt) REVERT: A 556 TRP cc_start: 0.6713 (m100) cc_final: 0.6213 (m100) REVERT: A 576 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6866 (tptt) outliers start: 58 outliers final: 12 residues processed: 354 average time/residue: 0.0720 time to fit residues: 36.3048 Evaluate side-chains 195 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain A residue 576 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4454 r_free = 0.4454 target = 0.202196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.168707 restraints weight = 13896.707| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.27 r_work: 0.3946 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9347 Z= 0.137 Angle : 0.597 13.067 12754 Z= 0.303 Chirality : 0.041 0.232 1419 Planarity : 0.005 0.083 1554 Dihedral : 6.973 57.500 1264 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.99 % Allowed : 14.29 % Favored : 79.73 % 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: -0.43 (0.24), residues: 1126 helix: 0.34 (0.18), residues: 768 sheet: None (None), residues: 0 loop : -1.54 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 216 TYR 0.016 0.001 TYR A 575 PHE 0.020 0.002 PHE E 272 TRP 0.019 0.001 TRP E 80 HIS 0.004 0.001 HIS E 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 9347) covalent geometry : angle 0.59705 / 0.30 (12754) hydrogen bonds : bond 0.04404 / 2.98 ( 551) hydrogen bonds : angle 4.73109 / 3.29 ( 1638) *********************** 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 259 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 202 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: E 152 TYR cc_start: 0.7145 (OUTLIER) cc_final: 0.6179 (t80) REVERT: E 155 ILE cc_start: 0.6203 (OUTLIER) cc_final: 0.6002 (mm) REVERT: E 173 TRP cc_start: 0.6059 (OUTLIER) cc_final: 0.4792 (m-90) REVERT: E 189 LYS cc_start: 0.6812 (mmtt) cc_final: 0.6571 (mptt) REVERT: E 250 PHE cc_start: 0.7734 (m-80) cc_final: 0.6863 (t80) REVERT: E 314 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6344 (mm-40) REVERT: E 347 SER cc_start: 0.7951 (m) cc_final: 0.7134 (m) REVERT: E 517 TRP cc_start: 0.6561 (m100) cc_final: 0.6201 (m100) REVERT: E 520 CYS cc_start: 0.4634 (m) cc_final: 0.4187 (p) REVERT: A 111 TYR cc_start: 0.8204 (t80) cc_final: 0.7811 (t80) REVERT: A 147 TYR cc_start: 0.8086 (m-10) cc_final: 0.7721 (m-10) REVERT: A 263 VAL cc_start: 0.8033 (OUTLIER) cc_final: 0.7791 (m) REVERT: A 418 ASP cc_start: 0.8209 (t0) cc_final: 0.7894 (t0) REVERT: A 556 TRP cc_start: 0.6934 (m100) cc_final: 0.6406 (m100) REVERT: A 566 MET cc_start: 0.6366 (mtp) cc_final: 0.6010 (mtt) REVERT: A 576 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.7160 (mmmt) outliers start: 57 outliers final: 26 residues processed: 237 average time/residue: 0.0745 time to fit residues: 25.5826 Evaluate side-chains 196 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 152 TYR Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 451 PHE Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 597 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 0.0370 chunk 91 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 14 optimal weight: 0.0570 chunk 38 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4350 r_free = 0.4350 target = 0.192120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.158728 restraints weight = 13793.098| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.12 r_work: 0.3841 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9347 Z= 0.150 Angle : 0.617 12.742 12754 Z= 0.309 Chirality : 0.041 0.222 1419 Planarity : 0.004 0.041 1554 Dihedral : 6.206 58.116 1250 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.94 % Allowed : 16.60 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.07 (0.25), residues: 1126 helix: 0.56 (0.18), residues: 761 sheet: None (None), residues: 0 loop : -1.22 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 81 TYR 0.019 0.001 TYR E 249 PHE 0.028 0.002 PHE A 445 TRP 0.037 0.002 TRP E 80 HIS 0.005 0.001 HIS E 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 9347) covalent geometry : angle 0.61719 / 0.31 (12754) hydrogen bonds : bond 0.04516 / 2.98 ( 551) hydrogen bonds : angle 4.60035 / 3.19 ( 1638) *********************** 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 231 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 184 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 80 TRP cc_start: 0.4920 (t60) cc_final: 0.4694 (t60) REVERT: E 111 TYR cc_start: 0.7287 (t80) cc_final: 0.7082 (t80) REVERT: E 152 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.6729 (t80) REVERT: E 155 ILE cc_start: 0.6662 (OUTLIER) cc_final: 0.6430 (mm) REVERT: E 173 TRP cc_start: 0.6727 (OUTLIER) cc_final: 0.4949 (m-90) REVERT: E 189 LYS cc_start: 0.7001 (mmtt) cc_final: 0.6663 (mmtt) REVERT: E 250 PHE cc_start: 0.7784 (m-80) cc_final: 0.6724 (t80) REVERT: E 259 SER cc_start: 0.7588 (OUTLIER) cc_final: 0.7062 (t) REVERT: E 347 SER cc_start: 0.7730 (m) cc_final: 0.7274 (m) REVERT: E 367 TYR cc_start: 0.4663 (t80) cc_final: 0.4349 (t80) REVERT: E 509 MET cc_start: 0.7447 (mmm) cc_final: 0.7240 (mmm) REVERT: E 518 ARG cc_start: 0.7417 (ptm160) cc_final: 0.6990 (ptm160) REVERT: A 111 TYR cc_start: 0.8235 (t80) cc_final: 0.7622 (t80) REVERT: A 147 TYR cc_start: 0.8377 (m-10) cc_final: 0.7944 (m-10) REVERT: A 418 ASP cc_start: 0.8395 (t0) cc_final: 0.8145 (t0) REVERT: A 556 TRP cc_start: 0.7127 (m100) cc_final: 0.6526 (m100) REVERT: A 588 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8116 (mm) outliers start: 47 outliers final: 28 residues processed: 217 average time/residue: 0.0713 time to fit residues: 22.7283 Evaluate side-chains 185 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 152 TYR Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 109 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4368 r_free = 0.4368 target = 0.193139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.156346 restraints weight = 13960.701| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.36 r_work: 0.3800 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9347 Z= 0.137 Angle : 0.584 11.355 12754 Z= 0.293 Chirality : 0.039 0.152 1419 Planarity : 0.004 0.038 1554 Dihedral : 5.508 54.936 1240 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 5.25 % Allowed : 17.02 % Favored : 77.73 % 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: 0.20 (0.25), residues: 1126 helix: 0.72 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -0.99 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 81 TYR 0.018 0.001 TYR A 572 PHE 0.022 0.001 PHE E 272 TRP 0.016 0.001 TRP E 80 HIS 0.004 0.001 HIS E 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 9347) covalent geometry : angle 0.58415 / 0.29 (12754) hydrogen bonds : bond 0.04299 / 2.87 ( 551) hydrogen bonds : angle 4.48630 / 3.10 ( 1638) *********************** 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 220 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 170 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: E 111 TYR cc_start: 0.7273 (t80) cc_final: 0.6994 (t80) REVERT: E 112 MET cc_start: 0.7516 (ttm) cc_final: 0.7277 (ttt) REVERT: E 113 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6701 (mt-10) REVERT: E 142 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7293 (mp) REVERT: E 152 TYR cc_start: 0.7750 (OUTLIER) cc_final: 0.6856 (t80) REVERT: E 173 TRP cc_start: 0.6486 (OUTLIER) cc_final: 0.5708 (m-90) REVERT: E 189 LYS cc_start: 0.7011 (mmtt) cc_final: 0.6714 (mmtt) REVERT: E 250 PHE cc_start: 0.7674 (m-80) cc_final: 0.6711 (t80) REVERT: E 367 TYR cc_start: 0.4461 (t80) cc_final: 0.4219 (t80) REVERT: E 471 LEU cc_start: 0.5094 (OUTLIER) cc_final: 0.4579 (tt) REVERT: E 518 ARG cc_start: 0.7376 (ptm160) cc_final: 0.6888 (ptm160) REVERT: E 520 CYS cc_start: 0.4787 (m) cc_final: 0.4434 (p) REVERT: E 556 TRP cc_start: 0.6946 (m100) cc_final: 0.6610 (m100) REVERT: A 111 TYR cc_start: 0.8249 (t80) cc_final: 0.7511 (t80) REVERT: A 147 TYR cc_start: 0.8378 (m-10) cc_final: 0.7871 (m-10) REVERT: A 391 TYR cc_start: 0.7164 (OUTLIER) cc_final: 0.6664 (m-10) REVERT: A 556 TRP cc_start: 0.7053 (m100) cc_final: 0.6470 (m100) REVERT: A 588 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8082 (mm) outliers start: 50 outliers final: 29 residues processed: 206 average time/residue: 0.0721 time to fit residues: 22.4023 Evaluate side-chains 182 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 152 TYR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 355 PHE Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 108 optimal weight: 0.0980 chunk 52 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4339 r_free = 0.4339 target = 0.191269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.157895 restraints weight = 13986.801| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.30 r_work: 0.3799 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9347 Z= 0.124 Angle : 0.569 10.262 12754 Z= 0.285 Chirality : 0.039 0.173 1419 Planarity : 0.004 0.064 1554 Dihedral : 5.393 55.666 1239 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.73 % Allowed : 19.01 % 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: 0.38 (0.25), residues: 1126 helix: 0.87 (0.19), residues: 765 sheet: None (None), residues: 0 loop : -0.99 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 121 TYR 0.017 0.001 TYR A 575 PHE 0.026 0.001 PHE E 329 TRP 0.024 0.001 TRP E 80 HIS 0.002 0.000 HIS E 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 9347) covalent geometry : angle 0.56886 / 0.28 (12754) hydrogen bonds : bond 0.04186 / 2.79 ( 551) hydrogen bonds : angle 4.43839 / 3.06 ( 1638) *********************** 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 220 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: E 111 TYR cc_start: 0.7301 (t80) cc_final: 0.7000 (t80) REVERT: E 173 TRP cc_start: 0.6703 (OUTLIER) cc_final: 0.5983 (m-90) REVERT: E 189 LYS cc_start: 0.7145 (mmtt) cc_final: 0.6819 (mmtt) REVERT: E 250 PHE cc_start: 0.7569 (m-80) cc_final: 0.6635 (t80) REVERT: E 307 VAL cc_start: 0.6039 (OUTLIER) cc_final: 0.5836 (m) REVERT: E 471 LEU cc_start: 0.5073 (OUTLIER) cc_final: 0.4589 (tt) REVERT: E 518 ARG cc_start: 0.7402 (ptm160) cc_final: 0.6913 (ptm160) REVERT: E 520 CYS cc_start: 0.4707 (m) cc_final: 0.4485 (p) REVERT: A 111 TYR cc_start: 0.8177 (t80) cc_final: 0.7498 (t80) REVERT: A 147 TYR cc_start: 0.8287 (m-10) cc_final: 0.7704 (m-10) REVERT: A 391 TYR cc_start: 0.6842 (OUTLIER) cc_final: 0.6569 (m-10) REVERT: A 556 TRP cc_start: 0.6970 (m100) cc_final: 0.6458 (m100) outliers start: 45 outliers final: 30 residues processed: 207 average time/residue: 0.0827 time to fit residues: 24.8914 Evaluate side-chains 186 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 451 PHE Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 2.9990 chunk 88 optimal weight: 0.0170 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 49 optimal weight: 0.0980 chunk 38 optimal weight: 4.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.194349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.161302 restraints weight = 14033.572| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.11 r_work: 0.3829 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9347 Z= 0.119 Angle : 0.577 12.487 12754 Z= 0.286 Chirality : 0.039 0.193 1419 Planarity : 0.004 0.052 1554 Dihedral : 5.343 56.095 1239 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.20 % Allowed : 19.96 % Favored : 75.84 % 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: 0.57 (0.25), residues: 1126 helix: 1.01 (0.19), residues: 765 sheet: None (None), residues: 0 loop : -0.92 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 440 TYR 0.018 0.001 TYR A 575 PHE 0.017 0.001 PHE A 362 TRP 0.013 0.001 TRP E 80 HIS 0.004 0.000 HIS E 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 9347) covalent geometry : angle 0.57682 / 0.29 (12754) hydrogen bonds : bond 0.04029 / 2.69 ( 551) hydrogen bonds : angle 4.40607 / 3.02 ( 1638) *********************** 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 214 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.335 Fit side-chains REVERT: E 111 TYR cc_start: 0.7330 (t80) cc_final: 0.7003 (t80) REVERT: E 133 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7874 (m-10) REVERT: E 155 ILE cc_start: 0.6687 (OUTLIER) cc_final: 0.6446 (mm) REVERT: E 189 LYS cc_start: 0.7149 (mmtt) cc_final: 0.6790 (mmtt) REVERT: E 250 PHE cc_start: 0.7644 (m-80) cc_final: 0.6703 (t80) REVERT: E 307 VAL cc_start: 0.6084 (OUTLIER) cc_final: 0.5873 (m) REVERT: E 471 LEU cc_start: 0.5151 (OUTLIER) cc_final: 0.4668 (tt) REVERT: E 518 ARG cc_start: 0.7345 (ptm160) cc_final: 0.6849 (ptm160) REVERT: A 111 TYR cc_start: 0.8288 (t80) cc_final: 0.7761 (t80) REVERT: A 147 TYR cc_start: 0.8519 (m-10) cc_final: 0.7862 (m-10) REVERT: A 556 TRP cc_start: 0.7181 (m100) cc_final: 0.6533 (m100) outliers start: 40 outliers final: 28 residues processed: 203 average time/residue: 0.0830 time to fit residues: 24.4718 Evaluate side-chains 184 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 451 PHE Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 598 HIS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 86 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4358 r_free = 0.4358 target = 0.192161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.158722 restraints weight = 13967.435| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.39 r_work: 0.3793 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9347 Z= 0.135 Angle : 0.598 12.136 12754 Z= 0.298 Chirality : 0.040 0.205 1419 Planarity : 0.004 0.046 1554 Dihedral : 5.289 56.417 1237 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.83 % Allowed : 19.54 % Favored : 75.63 % 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: 0.56 (0.25), residues: 1126 helix: 1.02 (0.19), residues: 764 sheet: None (None), residues: 0 loop : -0.93 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 216 TYR 0.017 0.001 TYR A 391 PHE 0.026 0.001 PHE A 408 TRP 0.013 0.001 TRP E 264 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 9347) covalent geometry : angle 0.59801 / 0.30 (12754) hydrogen bonds : bond 0.04254 / 2.82 ( 551) hydrogen bonds : angle 4.44954 / 3.05 ( 1638) *********************** 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 208 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 162 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: E 111 TYR cc_start: 0.7323 (t80) cc_final: 0.6929 (t80) REVERT: E 133 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7747 (m-10) REVERT: E 155 ILE cc_start: 0.6400 (OUTLIER) cc_final: 0.6199 (mm) REVERT: E 173 TRP cc_start: 0.6830 (OUTLIER) cc_final: 0.6098 (m-90) REVERT: E 189 LYS cc_start: 0.7100 (mmtt) cc_final: 0.6794 (mmtt) REVERT: E 250 PHE cc_start: 0.7489 (m-80) cc_final: 0.6635 (t80) REVERT: E 471 LEU cc_start: 0.4940 (OUTLIER) cc_final: 0.4451 (tt) REVERT: E 518 ARG cc_start: 0.7398 (ptm160) cc_final: 0.6927 (ptm160) REVERT: A 111 TYR cc_start: 0.8275 (t80) cc_final: 0.7537 (t80) REVERT: A 147 TYR cc_start: 0.8375 (m-10) cc_final: 0.7874 (m-10) REVERT: A 207 PHE cc_start: 0.7799 (m-80) cc_final: 0.7331 (m-80) REVERT: A 299 PHE cc_start: 0.7988 (m-80) cc_final: 0.7764 (m-80) REVERT: A 391 TYR cc_start: 0.7077 (OUTLIER) cc_final: 0.6422 (m-10) REVERT: A 556 TRP cc_start: 0.7044 (m100) cc_final: 0.6457 (m100) outliers start: 46 outliers final: 34 residues processed: 193 average time/residue: 0.0808 time to fit residues: 22.8059 Evaluate side-chains 195 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 367 TYR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 451 PHE Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 598 HIS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 102 optimal weight: 0.0030 chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 80 optimal weight: 7.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- 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 = 0.4356 r_free = 0.4356 target = 0.191788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.158517 restraints weight = 13876.783| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.30 r_work: 0.3765 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9347 Z= 0.134 Angle : 0.597 11.097 12754 Z= 0.298 Chirality : 0.040 0.194 1419 Planarity : 0.004 0.052 1554 Dihedral : 5.345 57.699 1237 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.73 % Allowed : 20.17 % Favored : 75.11 % 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: 0.60 (0.25), residues: 1126 helix: 1.01 (0.19), residues: 769 sheet: None (None), residues: 0 loop : -0.83 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 216 TYR 0.021 0.001 TYR A 391 PHE 0.023 0.001 PHE A 362 TRP 0.014 0.001 TRP E 264 HIS 0.008 0.001 HIS E 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 9347) covalent geometry : angle 0.59733 / 0.30 (12754) hydrogen bonds : bond 0.04296 / 2.86 ( 551) hydrogen bonds : angle 4.44542 / 3.03 ( 1638) *********************** 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 208 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: E 111 TYR cc_start: 0.7356 (t80) cc_final: 0.6960 (t80) REVERT: E 133 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7706 (m-10) REVERT: E 155 ILE cc_start: 0.6449 (OUTLIER) cc_final: 0.6245 (mm) REVERT: E 173 TRP cc_start: 0.7003 (OUTLIER) cc_final: 0.6254 (m-90) REVERT: E 189 LYS cc_start: 0.7051 (mmtt) cc_final: 0.6763 (mmtt) REVERT: E 250 PHE cc_start: 0.7483 (m-80) cc_final: 0.6632 (t80) REVERT: E 471 LEU cc_start: 0.4939 (OUTLIER) cc_final: 0.4438 (tt) REVERT: E 518 ARG cc_start: 0.7421 (ptm160) cc_final: 0.6936 (ptm160) REVERT: A 147 TYR cc_start: 0.8332 (m-10) cc_final: 0.7897 (m-10) REVERT: A 391 TYR cc_start: 0.6971 (OUTLIER) cc_final: 0.6346 (m-10) REVERT: A 556 TRP cc_start: 0.6971 (m100) cc_final: 0.6419 (m100) REVERT: A 566 MET cc_start: 0.7719 (mtp) cc_final: 0.7301 (mtp) outliers start: 45 outliers final: 34 residues processed: 195 average time/residue: 0.0778 time to fit residues: 22.2343 Evaluate side-chains 192 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 598 HIS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4354 r_free = 0.4354 target = 0.191435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.157702 restraints weight = 13881.631| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.36 r_work: 0.3764 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9347 Z= 0.134 Angle : 0.619 13.153 12754 Z= 0.304 Chirality : 0.040 0.180 1419 Planarity : 0.004 0.047 1554 Dihedral : 5.343 58.177 1237 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.62 % Allowed : 20.38 % Favored : 75.00 % 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: 0.65 (0.25), residues: 1126 helix: 1.03 (0.19), residues: 769 sheet: None (None), residues: 0 loop : -0.79 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 216 TYR 0.020 0.001 TYR A 391 PHE 0.022 0.001 PHE A 362 TRP 0.020 0.001 TRP E 264 HIS 0.006 0.001 HIS E 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 9347) covalent geometry : angle 0.61887 / 0.30 (12754) hydrogen bonds : bond 0.04277 / 2.85 ( 551) hydrogen bonds : angle 4.45540 / 3.04 ( 1638) *********************** 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 204 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 0.253 Fit side-chains REVERT: E 111 TYR cc_start: 0.7386 (t80) cc_final: 0.6962 (t80) REVERT: E 133 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7638 (m-10) REVERT: E 189 LYS cc_start: 0.7045 (mmtt) cc_final: 0.6747 (mmtt) REVERT: E 250 PHE cc_start: 0.7486 (m-80) cc_final: 0.6588 (t80) REVERT: E 332 TYR cc_start: 0.6985 (m-80) cc_final: 0.6735 (m-10) REVERT: E 471 LEU cc_start: 0.4868 (OUTLIER) cc_final: 0.4360 (tt) REVERT: E 518 ARG cc_start: 0.7407 (ptm160) cc_final: 0.6906 (ptm160) REVERT: A 147 TYR cc_start: 0.8394 (m-10) cc_final: 0.7974 (m-10) REVERT: A 207 PHE cc_start: 0.7696 (m-80) cc_final: 0.7400 (m-80) REVERT: A 391 TYR cc_start: 0.7061 (OUTLIER) cc_final: 0.6380 (m-10) REVERT: A 556 TRP cc_start: 0.7037 (m100) cc_final: 0.6437 (m100) REVERT: A 566 MET cc_start: 0.7741 (mtp) cc_final: 0.7323 (mtp) outliers start: 44 outliers final: 37 residues processed: 190 average time/residue: 0.0796 time to fit residues: 21.9791 Evaluate side-chains 191 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 367 TYR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 451 PHE Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 598 HIS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4329 r_free = 0.4329 target = 0.189055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.154456 restraints weight = 13868.277| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.34 r_work: 0.3721 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9347 Z= 0.157 Angle : 0.652 13.741 12754 Z= 0.323 Chirality : 0.041 0.196 1419 Planarity : 0.004 0.045 1554 Dihedral : 5.442 59.021 1237 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.20 % Allowed : 21.53 % Favored : 74.26 % 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: 0.58 (0.25), residues: 1126 helix: 0.98 (0.19), residues: 771 sheet: None (None), residues: 0 loop : -0.84 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 216 TYR 0.018 0.001 TYR A 391 PHE 0.025 0.002 PHE A 362 TRP 0.020 0.001 TRP E 264 HIS 0.005 0.001 HIS E 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 9347) covalent geometry : angle 0.65238 / 0.32 (12754) hydrogen bonds : bond 0.04580 / 3.01 ( 551) hydrogen bonds : angle 4.54050 / 3.10 ( 1638) ********************** 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 192 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.404 Fit side-chains REVERT: E 111 TYR cc_start: 0.7397 (t80) cc_final: 0.6944 (t80) REVERT: E 133 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7612 (m-10) REVERT: E 189 LYS cc_start: 0.7118 (mmtt) cc_final: 0.6813 (mmtt) REVERT: E 250 PHE cc_start: 0.7534 (m-80) cc_final: 0.6553 (t80) REVERT: E 332 TYR cc_start: 0.7023 (m-80) cc_final: 0.6766 (m-10) REVERT: E 471 LEU cc_start: 0.4880 (OUTLIER) cc_final: 0.4337 (tt) REVERT: E 518 ARG cc_start: 0.7466 (ptm160) cc_final: 0.6990 (ptm160) REVERT: A 147 TYR cc_start: 0.8413 (m-10) cc_final: 0.8144 (m-10) REVERT: A 207 PHE cc_start: 0.7734 (m-80) cc_final: 0.7482 (m-80) REVERT: A 391 TYR cc_start: 0.7033 (OUTLIER) cc_final: 0.6467 (m-10) REVERT: A 556 TRP cc_start: 0.7145 (m100) cc_final: 0.6529 (m100) outliers start: 40 outliers final: 35 residues processed: 182 average time/residue: 0.0735 time to fit residues: 20.2194 Evaluate side-chains 187 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 367 TYR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 598 HIS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 chunk 98 optimal weight: 1.9990 chunk 73 optimal weight: 0.0670 chunk 3 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 70 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 24 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.2322 ------------------------------------------------------------------------------- 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 = 0.4285 r_free = 0.4285 target = 0.185795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.150867 restraints weight = 13796.885| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.18 r_work: 0.3722 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9347 Z= 0.162 Angle : 0.652 13.146 12754 Z= 0.324 Chirality : 0.041 0.203 1419 Planarity : 0.004 0.045 1554 Dihedral : 5.241 59.655 1237 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.31 % Allowed : 21.11 % Favored : 74.58 % 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: 0.57 (0.25), residues: 1126 helix: 1.00 (0.19), residues: 763 sheet: None (None), residues: 0 loop : -0.84 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 216 TYR 0.018 0.002 TYR A 391 PHE 0.026 0.002 PHE A 362 TRP 0.034 0.001 TRP E 264 HIS 0.004 0.001 HIS E 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 9347) covalent geometry : angle 0.65227 / 0.32 (12754) hydrogen bonds : bond 0.04674 / 3.08 ( 551) hydrogen bonds : angle 4.57263 / 3.12 ( 1638) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2284.71 seconds wall clock time: 39 minutes 31.59 seconds (2371.59 seconds total)