Starting phenix.real_space_refine on Tue Apr 29 23:10:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y90_39065/04_2025/8y90_39065.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y90_39065/04_2025/8y90_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_39065/04_2025/8y90_39065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y90_39065/04_2025/8y90_39065.map" model { file = "/net/cci-nas-00/data/ceres_data/8y90_39065/04_2025/8y90_39065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y90_39065/04_2025/8y90_39065.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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, 26 Unusual residues: {' CL': 1, ' NA': 1, 'A1LX6': 1} Classifications: {'undetermined': 3, 'water': 5} Link IDs: {None: 7} Time building chain proxies: 6.09, per 1000 atoms: 0.67 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: 2.62 Conformation dependent library (CDL) restraints added in 986.6 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: 0.76 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: 2.39 Time building geometry restraints manager: 3.07 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: 2.470 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: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 23.830 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 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 : 8.97 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (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 TRP 0.009 0.001 TRP E 128 HIS 0.002 0.000 HIS A 228 PHE 0.008 0.001 PHE E 475 TYR 0.008 0.001 TYR A 98 ARG 0.002 0.000 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.15051 ( 551) hydrogen bonds : angle 6.30655 ( 1638) covalent geometry : bond 0.00318 ( 9347) covalent geometry : angle 0.56533 (12754) *********************** 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 : 0.865 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: 0.6124 (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: 0.2031 time to fit residues: 100.7816 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 : 0.915 ------------------------------------------------------------------------------- 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 94 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.195437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.159928 restraints weight = 13750.821| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.26 r_work: 0.3880 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9347 Z= 0.160 Angle : 0.611 12.803 12754 Z= 0.314 Chirality : 0.041 0.205 1419 Planarity : 0.005 0.077 1554 Dihedral : 7.019 58.530 1264 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.67 % Allowed : 14.39 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.24), residues: 1126 helix: 0.30 (0.18), residues: 768 sheet: None (None), residues: 0 loop : -1.55 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 80 HIS 0.007 0.001 HIS E 222 PHE 0.020 0.002 PHE E 272 TYR 0.014 0.001 TYR A 575 ARG 0.007 0.001 ARG E 81 Details of bonding type rmsd hydrogen bonds : bond 0.04689 ( 551) hydrogen bonds : angle 4.76602 ( 1638) covalent geometry : bond 0.00357 ( 9347) covalent geometry : angle 0.61133 (12754) *********************** 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 254 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 200 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 152 TYR cc_start: 0.7287 (OUTLIER) cc_final: 0.6248 (t80) REVERT: E 155 ILE cc_start: 0.6207 (OUTLIER) cc_final: 0.5960 (mm) REVERT: E 173 TRP cc_start: 0.6227 (OUTLIER) cc_final: 0.4832 (m-90) REVERT: E 189 LYS cc_start: 0.6941 (mmtt) cc_final: 0.6662 (mptt) REVERT: E 250 PHE cc_start: 0.7829 (m-80) cc_final: 0.6856 (t80) REVERT: E 347 SER cc_start: 0.7931 (m) cc_final: 0.7104 (m) REVERT: E 517 TRP cc_start: 0.6663 (m100) cc_final: 0.6270 (m100) REVERT: E 520 CYS cc_start: 0.4783 (m) cc_final: 0.4281 (p) REVERT: A 111 TYR cc_start: 0.8294 (t80) cc_final: 0.7776 (t80) REVERT: A 147 TYR cc_start: 0.8223 (m-10) cc_final: 0.7835 (m-10) REVERT: A 204 LYS cc_start: 0.7801 (mmtm) cc_final: 0.7591 (pptt) REVERT: A 418 ASP cc_start: 0.8258 (t0) cc_final: 0.8011 (t0) REVERT: A 556 TRP cc_start: 0.6992 (m100) cc_final: 0.6461 (m100) REVERT: A 576 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7234 (mmmt) outliers start: 54 outliers final: 24 residues processed: 235 average time/residue: 0.1819 time to fit residues: 61.3317 Evaluate side-chains 185 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 337 ASN Chi-restraints excluded: chain E residue 444 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 262 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 67 optimal weight: 0.2980 chunk 38 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.195349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.159298 restraints weight = 13774.127| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.32 r_work: 0.3838 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9347 Z= 0.137 Angle : 0.586 12.360 12754 Z= 0.294 Chirality : 0.040 0.163 1419 Planarity : 0.004 0.040 1554 Dihedral : 5.879 58.394 1246 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.83 % Allowed : 16.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1126 helix: 0.54 (0.19), residues: 763 sheet: None (None), residues: 0 loop : -1.15 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP E 80 HIS 0.006 0.001 HIS E 222 PHE 0.021 0.001 PHE E 272 TYR 0.020 0.001 TYR E 249 ARG 0.004 0.001 ARG E 81 Details of bonding type rmsd hydrogen bonds : bond 0.04392 ( 551) hydrogen bonds : angle 4.56531 ( 1638) covalent geometry : bond 0.00301 ( 9347) covalent geometry : angle 0.58613 (12754) *********************** 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 221 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 175 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: E 111 TYR cc_start: 0.7245 (t80) cc_final: 0.7024 (t80) REVERT: E 113 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6633 (mt-10) REVERT: E 152 TYR cc_start: 0.7619 (OUTLIER) cc_final: 0.6519 (t80) REVERT: E 155 ILE cc_start: 0.6390 (OUTLIER) cc_final: 0.6146 (mp) REVERT: E 173 TRP cc_start: 0.6448 (OUTLIER) cc_final: 0.4671 (m-90) REVERT: E 189 LYS cc_start: 0.6950 (mmtt) cc_final: 0.6654 (mmtt) REVERT: E 250 PHE cc_start: 0.7709 (m-80) cc_final: 0.6681 (t80) REVERT: E 259 SER cc_start: 0.7520 (OUTLIER) cc_final: 0.6967 (t) REVERT: E 347 SER cc_start: 0.7603 (m) cc_final: 0.7106 (m) REVERT: E 518 ARG cc_start: 0.7379 (ptm160) cc_final: 0.6930 (ptm160) REVERT: A 111 TYR cc_start: 0.8229 (t80) cc_final: 0.7647 (t80) REVERT: A 147 TYR cc_start: 0.8255 (m-10) cc_final: 0.7841 (m-10) REVERT: A 205 TYR cc_start: 0.5931 (m-80) cc_final: 0.5588 (m-80) REVERT: A 556 TRP cc_start: 0.6977 (m100) cc_final: 0.6460 (m100) REVERT: A 588 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8095 (mm) outliers start: 46 outliers final: 26 residues processed: 208 average time/residue: 0.1776 time to fit residues: 54.5465 Evaluate side-chains 183 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 VAL 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 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 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 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 386 LEU Chi-restraints excluded: chain A residue 519 LEU 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 15 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 94 optimal weight: 0.0670 chunk 102 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.195248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.159098 restraints weight = 13812.119| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.36 r_work: 0.3829 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9347 Z= 0.125 Angle : 0.577 11.263 12754 Z= 0.287 Chirality : 0.039 0.197 1419 Planarity : 0.004 0.039 1554 Dihedral : 5.431 53.610 1240 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.25 % Allowed : 17.44 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.25), residues: 1126 helix: 0.72 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -0.98 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP E 80 HIS 0.002 0.000 HIS E 598 PHE 0.023 0.001 PHE E 272 TYR 0.017 0.001 TYR A 572 ARG 0.003 0.000 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 551) hydrogen bonds : angle 4.48131 ( 1638) covalent geometry : bond 0.00266 ( 9347) covalent geometry : angle 0.57663 (12754) *********************** 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 215 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 165 time to evaluate : 0.949 Fit side-chains REVERT: E 111 TYR cc_start: 0.7262 (t80) cc_final: 0.6984 (t80) REVERT: E 112 MET cc_start: 0.7401 (ttm) cc_final: 0.7200 (ttt) REVERT: E 133 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7771 (m-10) REVERT: E 152 TYR cc_start: 0.7694 (OUTLIER) cc_final: 0.6639 (t80) REVERT: E 173 TRP cc_start: 0.6429 (OUTLIER) cc_final: 0.5678 (m-90) REVERT: E 189 LYS cc_start: 0.6994 (mmtt) cc_final: 0.6688 (mmtt) REVERT: E 239 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8059 (mp) REVERT: E 250 PHE cc_start: 0.7658 (m-80) cc_final: 0.6739 (t80) REVERT: E 314 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6199 (mm110) REVERT: E 347 SER cc_start: 0.7684 (m) cc_final: 0.7389 (m) REVERT: E 367 TYR cc_start: 0.4378 (t80) cc_final: 0.4151 (t80) REVERT: E 471 LEU cc_start: 0.4980 (OUTLIER) cc_final: 0.4550 (tt) REVERT: E 518 ARG cc_start: 0.7369 (ptm160) cc_final: 0.6877 (ptm160) REVERT: E 520 CYS cc_start: 0.4813 (m) cc_final: 0.4437 (p) REVERT: A 111 TYR cc_start: 0.8226 (t80) cc_final: 0.7597 (t80) REVERT: A 147 TYR cc_start: 0.8361 (m-10) cc_final: 0.7835 (m-10) REVERT: A 206 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7757 (mtpp) REVERT: A 323 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7201 (t80) REVERT: A 391 TYR cc_start: 0.7183 (OUTLIER) cc_final: 0.6614 (m-10) REVERT: A 556 TRP cc_start: 0.7060 (m100) cc_final: 0.6462 (m100) REVERT: A 588 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8087 (mm) outliers start: 50 outliers final: 25 residues processed: 204 average time/residue: 0.1738 time to fit residues: 52.8960 Evaluate side-chains 184 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 LEU 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 169 LEU Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 239 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 309 ILE Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 355 PHE Chi-restraints excluded: chain E residue 387 VAL 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 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 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 323 PHE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain A residue 563 LEU 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 104 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 12 optimal weight: 0.0570 chunk 35 optimal weight: 7.9990 chunk 15 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.193822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.159699 restraints weight = 13816.216| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.24 r_work: 0.3818 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4369 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= 0.123 Angle : 0.580 12.431 12754 Z= 0.287 Chirality : 0.040 0.185 1419 Planarity : 0.004 0.064 1554 Dihedral : 5.367 55.400 1239 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.94 % Allowed : 18.38 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1126 helix: 0.88 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -0.90 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 80 HIS 0.003 0.000 HIS E 598 PHE 0.026 0.001 PHE E 329 TYR 0.015 0.001 TYR A 575 ARG 0.002 0.000 ARG E 440 Details of bonding type rmsd hydrogen bonds : bond 0.04169 ( 551) hydrogen bonds : angle 4.44133 ( 1638) covalent geometry : bond 0.00266 ( 9347) covalent geometry : angle 0.57988 (12754) *********************** 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 209 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 162 time to evaluate : 0.965 Fit side-chains REVERT: E 111 TYR cc_start: 0.7326 (t80) cc_final: 0.7011 (t80) REVERT: E 113 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6770 (mt-10) REVERT: E 133 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7924 (m-10) REVERT: E 152 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.7283 (t80) REVERT: E 173 TRP cc_start: 0.6858 (OUTLIER) cc_final: 0.6068 (m-90) REVERT: E 189 LYS cc_start: 0.7181 (mmtt) cc_final: 0.6795 (mmtt) REVERT: E 250 PHE cc_start: 0.7679 (m-80) cc_final: 0.6757 (t80) REVERT: E 471 LEU cc_start: 0.5110 (OUTLIER) cc_final: 0.4627 (tt) REVERT: E 520 CYS cc_start: 0.4871 (m) cc_final: 0.4569 (p) REVERT: A 111 TYR cc_start: 0.8276 (t80) cc_final: 0.7708 (t80) REVERT: A 147 TYR cc_start: 0.8537 (m-10) cc_final: 0.7971 (m-10) REVERT: A 323 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7305 (t80) REVERT: A 556 TRP cc_start: 0.7214 (m100) cc_final: 0.6552 (m100) outliers start: 47 outliers final: 27 residues processed: 195 average time/residue: 0.2602 time to fit residues: 75.1907 Evaluate side-chains 182 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 148 VAL 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 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 309 ILE Chi-restraints excluded: chain E residue 387 VAL 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 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 323 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.186552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.151453 restraints weight = 13872.222| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.22 r_work: 0.3744 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9347 Z= 0.163 Angle : 0.615 11.553 12754 Z= 0.310 Chirality : 0.041 0.188 1419 Planarity : 0.004 0.053 1554 Dihedral : 5.538 56.364 1239 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.46 % Allowed : 18.59 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.25), residues: 1126 helix: 0.85 (0.19), residues: 767 sheet: None (None), residues: 0 loop : -1.03 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 264 HIS 0.003 0.001 HIS E 222 PHE 0.029 0.002 PHE A 362 TYR 0.014 0.002 TYR A 391 ARG 0.008 0.001 ARG E 440 Details of bonding type rmsd hydrogen bonds : bond 0.04695 ( 551) hydrogen bonds : angle 4.57248 ( 1638) covalent geometry : bond 0.00367 ( 9347) covalent geometry : angle 0.61518 (12754) *********************** 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 211 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 159 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: E 111 TYR cc_start: 0.7392 (t80) cc_final: 0.6994 (t80) REVERT: E 113 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6655 (mt-10) REVERT: E 133 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7908 (m-10) REVERT: E 155 ILE cc_start: 0.6833 (OUTLIER) cc_final: 0.6569 (mm) REVERT: E 189 LYS cc_start: 0.7173 (mmtt) cc_final: 0.6822 (mmtt) REVERT: E 250 PHE cc_start: 0.7783 (m-80) cc_final: 0.6646 (t80) REVERT: E 264 TRP cc_start: 0.5673 (t60) cc_final: 0.5415 (t60) REVERT: E 471 LEU cc_start: 0.5116 (OUTLIER) cc_final: 0.4585 (tt) REVERT: E 556 TRP cc_start: 0.6997 (m100) cc_final: 0.6627 (m100) REVERT: A 147 TYR cc_start: 0.8665 (m-10) cc_final: 0.8230 (m-10) REVERT: A 299 PHE cc_start: 0.7981 (m-80) cc_final: 0.7764 (m-80) REVERT: A 323 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7355 (t80) REVERT: A 361 ILE cc_start: 0.8944 (mm) cc_final: 0.8728 (mm) REVERT: A 391 TYR cc_start: 0.7305 (OUTLIER) cc_final: 0.6955 (m-10) REVERT: A 556 TRP cc_start: 0.7247 (m100) cc_final: 0.6540 (m100) outliers start: 52 outliers final: 33 residues processed: 197 average time/residue: 0.1857 time to fit residues: 54.7003 Evaluate side-chains 189 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 196 LEU Chi-restraints excluded: chain E residue 246 ILE 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 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 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 323 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.187424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.152763 restraints weight = 14036.029| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.25 r_work: 0.3766 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9347 Z= 0.141 Angle : 0.600 12.103 12754 Z= 0.297 Chirality : 0.040 0.199 1419 Planarity : 0.004 0.047 1554 Dihedral : 5.340 57.999 1239 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.62 % Allowed : 19.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1126 helix: 0.93 (0.19), residues: 767 sheet: None (None), residues: 0 loop : -1.01 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 264 HIS 0.002 0.001 HIS E 222 PHE 0.023 0.001 PHE A 362 TYR 0.015 0.001 TYR A 391 ARG 0.005 0.000 ARG E 440 Details of bonding type rmsd hydrogen bonds : bond 0.04486 ( 551) hydrogen bonds : angle 4.51684 ( 1638) covalent geometry : bond 0.00316 ( 9347) covalent geometry : angle 0.60011 (12754) *********************** 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 210 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 166 time to evaluate : 1.065 Fit side-chains REVERT: E 111 TYR cc_start: 0.7350 (t80) cc_final: 0.6985 (t80) REVERT: E 133 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7770 (m-10) REVERT: E 155 ILE cc_start: 0.6821 (OUTLIER) cc_final: 0.6583 (mm) REVERT: E 189 LYS cc_start: 0.7216 (mmtt) cc_final: 0.6852 (mmtt) REVERT: E 250 PHE cc_start: 0.7749 (m-80) cc_final: 0.6641 (t80) REVERT: E 264 TRP cc_start: 0.5663 (t60) cc_final: 0.5382 (t60) REVERT: E 332 TYR cc_start: 0.6970 (m-80) cc_final: 0.6626 (m-10) REVERT: E 471 LEU cc_start: 0.5081 (OUTLIER) cc_final: 0.4558 (tt) REVERT: E 518 ARG cc_start: 0.7336 (ptm160) cc_final: 0.6581 (ptm160) REVERT: E 556 TRP cc_start: 0.7007 (m100) cc_final: 0.6682 (m100) REVERT: A 147 TYR cc_start: 0.8617 (m-10) cc_final: 0.8142 (m-10) REVERT: A 207 PHE cc_start: 0.7894 (m-80) cc_final: 0.7651 (m-80) REVERT: A 323 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7287 (t80) REVERT: A 361 ILE cc_start: 0.8885 (mm) cc_final: 0.8463 (mm) REVERT: A 391 TYR cc_start: 0.7162 (OUTLIER) cc_final: 0.6686 (m-10) REVERT: A 556 TRP cc_start: 0.7297 (m100) cc_final: 0.6606 (m100) outliers start: 44 outliers final: 33 residues processed: 198 average time/residue: 0.1902 time to fit residues: 55.3096 Evaluate side-chains 185 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 196 LEU Chi-restraints excluded: chain E residue 246 ILE 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 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 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 323 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.185304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.149659 restraints weight = 14204.807| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.23 r_work: 0.3724 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9347 Z= 0.169 Angle : 0.648 12.789 12754 Z= 0.321 Chirality : 0.041 0.191 1419 Planarity : 0.004 0.046 1554 Dihedral : 5.355 58.220 1237 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.73 % Allowed : 20.48 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.25), residues: 1126 helix: 0.84 (0.19), residues: 771 sheet: None (None), residues: 0 loop : -1.02 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 80 HIS 0.003 0.001 HIS E 598 PHE 0.026 0.002 PHE A 362 TYR 0.014 0.001 TYR A 391 ARG 0.007 0.001 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.04827 ( 551) hydrogen bonds : angle 4.56375 ( 1638) covalent geometry : bond 0.00390 ( 9347) covalent geometry : angle 0.64799 (12754) *********************** 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 199 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 0.958 Fit side-chains REVERT: E 111 TYR cc_start: 0.7387 (t80) cc_final: 0.6943 (t80) REVERT: E 122 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6616 (mp0) REVERT: E 133 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7695 (m-10) REVERT: E 155 ILE cc_start: 0.6553 (OUTLIER) cc_final: 0.6334 (mm) REVERT: E 189 LYS cc_start: 0.7188 (mmtt) cc_final: 0.6893 (mmtt) REVERT: E 250 PHE cc_start: 0.7692 (m-80) cc_final: 0.6516 (t80) REVERT: E 264 TRP cc_start: 0.5737 (t60) cc_final: 0.5417 (t60) REVERT: E 280 HIS cc_start: 0.7510 (t-90) cc_final: 0.7279 (t-90) REVERT: E 332 TYR cc_start: 0.7040 (m-80) cc_final: 0.6739 (m-10) REVERT: E 471 LEU cc_start: 0.4840 (OUTLIER) cc_final: 0.4291 (tt) REVERT: E 518 ARG cc_start: 0.7342 (ptm160) cc_final: 0.6570 (ptm160) REVERT: A 147 TYR cc_start: 0.8452 (m-10) cc_final: 0.8174 (m-10) REVERT: A 323 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7218 (t80) REVERT: A 361 ILE cc_start: 0.8800 (mm) cc_final: 0.8262 (mm) REVERT: A 391 TYR cc_start: 0.7103 (OUTLIER) cc_final: 0.6775 (m-10) REVERT: A 556 TRP cc_start: 0.7191 (m100) cc_final: 0.6537 (m100) outliers start: 45 outliers final: 36 residues processed: 187 average time/residue: 0.2342 time to fit residues: 66.3100 Evaluate side-chains 191 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 1.530 ------------------------------------------------------------------------------- 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 196 LEU Chi-restraints excluded: chain E residue 246 ILE 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 349 ILE Chi-restraints excluded: chain E residue 370 HIS Chi-restraints excluded: chain E residue 387 VAL 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 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 323 PHE 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 85 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.186852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.152174 restraints weight = 13811.596| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.22 r_work: 0.3754 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9347 Z= 0.136 Angle : 0.612 11.358 12754 Z= 0.303 Chirality : 0.040 0.189 1419 Planarity : 0.004 0.068 1554 Dihedral : 5.272 59.323 1237 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.31 % Allowed : 21.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1126 helix: 0.92 (0.19), residues: 770 sheet: None (None), residues: 0 loop : -0.93 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 264 HIS 0.005 0.001 HIS E 222 PHE 0.022 0.001 PHE A 362 TYR 0.017 0.001 TYR A 575 ARG 0.009 0.001 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.04448 ( 551) hydrogen bonds : angle 4.49839 ( 1638) covalent geometry : bond 0.00303 ( 9347) covalent geometry : angle 0.61165 (12754) *********************** 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 197 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 0.960 Fit side-chains REVERT: E 111 TYR cc_start: 0.7370 (t80) cc_final: 0.6972 (t80) REVERT: E 133 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7702 (m-10) REVERT: E 155 ILE cc_start: 0.6806 (OUTLIER) cc_final: 0.6584 (mm) REVERT: E 189 LYS cc_start: 0.7244 (mmtt) cc_final: 0.6820 (mmtt) REVERT: E 250 PHE cc_start: 0.7770 (m-80) cc_final: 0.6593 (t80) REVERT: E 264 TRP cc_start: 0.5692 (t60) cc_final: 0.5381 (t60) REVERT: E 332 TYR cc_start: 0.7060 (m-80) cc_final: 0.6692 (m-10) REVERT: E 471 LEU cc_start: 0.4851 (OUTLIER) cc_final: 0.4303 (tt) REVERT: E 518 ARG cc_start: 0.7429 (ptm160) cc_final: 0.6669 (ptm160) REVERT: A 147 TYR cc_start: 0.8542 (m-10) cc_final: 0.8219 (m-10) REVERT: A 207 PHE cc_start: 0.7704 (m-80) cc_final: 0.7326 (m-80) REVERT: A 323 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.7308 (t80) REVERT: A 361 ILE cc_start: 0.8836 (mm) cc_final: 0.8323 (mm) REVERT: A 391 TYR cc_start: 0.7113 (OUTLIER) cc_final: 0.6906 (m-10) REVERT: A 556 TRP cc_start: 0.7322 (m100) cc_final: 0.6637 (m100) outliers start: 41 outliers final: 33 residues processed: 186 average time/residue: 0.1667 time to fit residues: 45.8981 Evaluate side-chains 185 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 246 ILE 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 370 HIS 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 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 323 PHE 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 106 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 67 optimal weight: 0.0770 chunk 92 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.191740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.158197 restraints weight = 13904.904| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.32 r_work: 0.3769 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.5313 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= 0.128 Angle : 0.622 11.360 12754 Z= 0.306 Chirality : 0.040 0.219 1419 Planarity : 0.004 0.061 1554 Dihedral : 5.257 59.667 1237 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.31 % Allowed : 21.53 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1126 helix: 0.98 (0.19), residues: 769 sheet: None (None), residues: 0 loop : -0.90 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 264 HIS 0.024 0.001 HIS E 280 PHE 0.022 0.001 PHE A 362 TYR 0.019 0.001 TYR A 575 ARG 0.008 0.001 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 551) hydrogen bonds : angle 4.47954 ( 1638) covalent geometry : bond 0.00275 ( 9347) covalent geometry : angle 0.62154 (12754) ********************** 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 191 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 0.942 Fit side-chains REVERT: E 95 LEU cc_start: 0.6005 (mt) cc_final: 0.4713 (pp) REVERT: E 111 TYR cc_start: 0.7371 (t80) cc_final: 0.6953 (t80) REVERT: E 133 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7597 (m-10) REVERT: E 189 LYS cc_start: 0.7181 (mmtt) cc_final: 0.6789 (mmtt) REVERT: E 250 PHE cc_start: 0.7534 (m-80) cc_final: 0.6509 (t80) REVERT: E 264 TRP cc_start: 0.5733 (t60) cc_final: 0.5426 (t60) REVERT: E 332 TYR cc_start: 0.7054 (m-80) cc_final: 0.6724 (m-10) REVERT: E 471 LEU cc_start: 0.4668 (OUTLIER) cc_final: 0.4126 (tt) REVERT: A 147 TYR cc_start: 0.8325 (m-10) cc_final: 0.7983 (m-10) REVERT: A 207 PHE cc_start: 0.7580 (m-80) cc_final: 0.7300 (m-80) REVERT: A 323 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.7209 (t80) REVERT: A 361 ILE cc_start: 0.8730 (mm) cc_final: 0.8334 (mm) REVERT: A 391 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.6534 (m-10) REVERT: A 556 TRP cc_start: 0.7124 (m100) cc_final: 0.6536 (m100) outliers start: 41 outliers final: 32 residues processed: 180 average time/residue: 0.1769 time to fit residues: 48.2322 Evaluate side-chains 181 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 196 LEU Chi-restraints excluded: chain E residue 246 ILE 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 370 HIS 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 179 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 323 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 0.0980 chunk 105 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 87 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.190582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.156684 restraints weight = 13904.086| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.30 r_work: 0.3755 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9347 Z= 0.138 Angle : 0.620 11.186 12754 Z= 0.307 Chirality : 0.041 0.314 1419 Planarity : 0.004 0.056 1554 Dihedral : 5.246 59.840 1237 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.89 % Allowed : 22.06 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1126 helix: 1.00 (0.19), residues: 769 sheet: None (None), residues: 0 loop : -0.86 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 80 HIS 0.022 0.001 HIS E 280 PHE 0.021 0.001 PHE A 362 TYR 0.017 0.001 TYR A 391 ARG 0.008 0.001 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.04375 ( 551) hydrogen bonds : angle 4.48230 ( 1638) covalent geometry : bond 0.00309 ( 9347) covalent geometry : angle 0.61976 (12754) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 5363.00 seconds wall clock time: 93 minutes 54.57 seconds (5634.57 seconds total)