Starting phenix.real_space_refine on Mon May 12 09:54:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fuv_50779/05_2025/9fuv_50779.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fuv_50779/05_2025/9fuv_50779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fuv_50779/05_2025/9fuv_50779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fuv_50779/05_2025/9fuv_50779.map" model { file = "/net/cci-nas-00/data/ceres_data/9fuv_50779/05_2025/9fuv_50779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fuv_50779/05_2025/9fuv_50779.cif" } resolution = 4.0 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= 0.001 sd= 0.008 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5590 2.51 5 N 1536 2.21 5 O 1642 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-5687/modules/chem_data/mon_lib" Total number of atoms: 8822 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4411 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 13, 'TRANS': 555} Chain: "B" Number of atoms: 4411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4411 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 13, 'TRANS': 555} Time building chain proxies: 6.33, per 1000 atoms: 0.72 Number of scatterers: 8822 At special positions: 0 Unit cell: (116.96, 101.32, 136.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1642 8.00 N 1536 7.00 C 5590 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: 2.22 Conformation dependent library (CDL) restraints added in 991.8 milliseconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 4 sheets defined 68.4% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 23 through 47 removed outlier: 3.888A pdb=" N ILE A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N MET A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.549A pdb=" N ASP A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 111 removed outlier: 3.943A pdb=" N TRP A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Proline residue: A 68 - end of helix removed outlier: 3.554A pdb=" N GLY A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 129 removed outlier: 3.974A pdb=" N LEU A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 126 " --> pdb=" O GLY A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 164 removed outlier: 3.852A pdb=" N GLU A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 213 Proline residue: A 176 - end of helix removed outlier: 3.637A pdb=" N THR A 199 " --> pdb=" O ASN A 195 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 221 removed outlier: 3.553A pdb=" N ILE A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 269 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 281 through 323 removed outlier: 4.086A pdb=" N THR A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 3.592A pdb=" N THR A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASN A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A 314 " --> pdb=" O ARG A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 390 removed outlier: 3.535A pdb=" N ALA A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 Processing helix chain 'A' and resid 432 through 438 removed outlier: 3.852A pdb=" N ALA A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 457 Processing helix chain 'A' and resid 459 through 466 removed outlier: 4.086A pdb=" N ILE A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 removed outlier: 3.764A pdb=" N THR A 472 " --> pdb=" O GLY A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 498 Processing helix chain 'A' and resid 515 through 528 Processing helix chain 'A' and resid 538 through 545 Processing helix chain 'A' and resid 561 through 568 Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'B' and resid 16 through 21 Processing helix chain 'B' and resid 23 through 55 removed outlier: 4.419A pdb=" N ASP B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 48 " --> pdb=" O MET B 44 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 61 through 110 removed outlier: 4.188A pdb=" N TRP B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) Proline residue: B 68 - end of helix removed outlier: 3.970A pdb=" N THR B 99 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 129 through 147 Processing helix chain 'B' and resid 147 through 164 Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 173 through 213 removed outlier: 4.111A pdb=" N ILE B 177 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 220 Processing helix chain 'B' and resid 222 through 272 removed outlier: 3.898A pdb=" N ASP B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 281 through 323 removed outlier: 3.785A pdb=" N THR B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Proline residue: B 297 - end of helix removed outlier: 4.239A pdb=" N ASN B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ALA B 314 " --> pdb=" O ARG B 310 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS B 315 " --> pdb=" O GLY B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 391 removed outlier: 3.837A pdb=" N ALA B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 387 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 Processing helix chain 'B' and resid 432 through 438 Processing helix chain 'B' and resid 446 through 457 removed outlier: 3.669A pdb=" N ILE B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 466 removed outlier: 4.363A pdb=" N ILE B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 472 Processing helix chain 'B' and resid 482 through 498 Processing helix chain 'B' and resid 515 through 528 Processing helix chain 'B' and resid 538 through 545 Processing helix chain 'B' and resid 561 through 568 Processing helix chain 'B' and resid 571 through 580 Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.528A pdb=" N GLU A 343 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL A 347 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLU A 397 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 422 removed outlier: 3.510A pdb=" N ILE A 503 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 422 " --> pdb=" O ILE A 503 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LEU A 502 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL A 372 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR A 371 " --> pdb=" O GLU A 547 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL A 549 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ALA A 373 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A 551 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 342 through 345 Processing sheet with id=AA4, first strand: chain 'B' and resid 419 through 422 removed outlier: 6.123A pdb=" N ALA B 420 " --> pdb=" O ILE B 503 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU B 502 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE B 535 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU B 504 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL B 372 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU B 547 " --> pdb=" O THR B 371 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1650 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: 2.62 Time building geometry restraints manager: 2.58 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: 2867 1.34 - 1.45: 1039 1.45 - 1.57: 4940 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 8950 Sorted by residual: bond pdb=" N VAL A 65 " pdb=" CA VAL A 65 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.23e+00 bond pdb=" N VAL B 63 " pdb=" CA VAL B 63 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.29e-02 6.01e+03 7.39e+00 bond pdb=" N VAL B 356 " pdb=" CA VAL B 356 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.23e-02 6.61e+03 7.30e+00 bond pdb=" N VAL A 63 " pdb=" CA VAL A 63 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.26e-02 6.30e+03 7.16e+00 bond pdb=" N THR B 472 " pdb=" CA THR B 472 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.22e-02 6.72e+03 7.11e+00 ... (remaining 8945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 11296 1.23 - 2.47: 629 2.47 - 3.70: 120 3.70 - 4.93: 34 4.93 - 6.16: 13 Bond angle restraints: 12092 Sorted by residual: angle pdb=" N ALA B 358 " pdb=" CA ALA B 358 " pdb=" C ALA B 358 " ideal model delta sigma weight residual 113.16 108.07 5.09 1.24e+00 6.50e-01 1.69e+01 angle pdb=" C THR B 472 " pdb=" CA THR B 472 " pdb=" CB THR B 472 " ideal model delta sigma weight residual 109.89 103.73 6.16 1.60e+00 3.91e-01 1.48e+01 angle pdb=" N ASP B 341 " pdb=" CA ASP B 341 " pdb=" C ASP B 341 " ideal model delta sigma weight residual 109.59 115.16 -5.57 1.47e+00 4.63e-01 1.44e+01 angle pdb=" N GLU B 327 " pdb=" CA GLU B 327 " pdb=" CB GLU B 327 " ideal model delta sigma weight residual 109.19 114.76 -5.57 1.54e+00 4.22e-01 1.31e+01 angle pdb=" N LEU B 125 " pdb=" CA LEU B 125 " pdb=" C LEU B 125 " ideal model delta sigma weight residual 111.36 107.53 3.83 1.09e+00 8.42e-01 1.24e+01 ... (remaining 12087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 4614 16.94 - 33.87: 610 33.87 - 50.81: 184 50.81 - 67.74: 37 67.74 - 84.68: 9 Dihedral angle restraints: 5454 sinusoidal: 2164 harmonic: 3290 Sorted by residual: dihedral pdb=" CA TRP A 17 " pdb=" C TRP A 17 " pdb=" N PRO A 18 " pdb=" CA PRO A 18 " ideal model delta harmonic sigma weight residual 180.00 156.51 23.49 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA PHE A 272 " pdb=" C PHE A 272 " pdb=" N PRO A 273 " pdb=" CA PRO A 273 " ideal model delta harmonic sigma weight residual 180.00 157.20 22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA PHE A 13 " pdb=" C PHE A 13 " pdb=" N ARG A 14 " pdb=" CA ARG A 14 " ideal model delta harmonic sigma weight residual 180.00 160.12 19.88 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1034 0.036 - 0.073: 286 0.073 - 0.109: 90 0.109 - 0.146: 21 0.146 - 0.182: 9 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CA LEU B 125 " pdb=" N LEU B 125 " pdb=" C LEU B 125 " pdb=" CB LEU B 125 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CA VAL A 63 " pdb=" N VAL A 63 " pdb=" C VAL A 63 " pdb=" CB VAL A 63 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" CB VAL A 63 " pdb=" CA VAL A 63 " pdb=" CG1 VAL A 63 " pdb=" CG2 VAL A 63 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.02e-01 ... (remaining 1437 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 296 " 0.051 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO A 297 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 297 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 297 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 49 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO B 50 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 50 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 50 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 133 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C GLU B 133 " -0.035 2.00e-02 2.50e+03 pdb=" O GLU B 133 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN B 134 " 0.012 2.00e-02 2.50e+03 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 866 2.73 - 3.27: 10297 3.27 - 3.82: 15382 3.82 - 4.36: 17502 4.36 - 4.90: 28205 Nonbonded interactions: 72252 Sorted by model distance: nonbonded pdb=" OD1 ASP A 467 " pdb=" N ASN A 468 " model vdw 2.190 3.120 nonbonded pdb=" O GLY A 282 " pdb=" OG1 THR A 285 " model vdw 2.222 3.040 nonbonded pdb=" O GLN A 202 " pdb=" OG1 THR A 205 " model vdw 2.232 3.040 nonbonded pdb=" OD1 ASP A 231 " pdb=" NH2 ARG B 102 " model vdw 2.235 3.120 nonbonded pdb=" O ARG A 377 " pdb=" NE ARG A 377 " model vdw 2.250 3.120 ... (remaining 72247 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 4.030 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.590 Find NCS groups from input model: 0.290 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8950 Z= 0.214 Angle : 0.690 6.163 12092 Z= 0.407 Chirality : 0.041 0.182 1440 Planarity : 0.005 0.076 1532 Dihedral : 17.155 84.677 3326 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.03 % Favored : 94.71 % Rotamer: Outliers : 0.62 % Allowed : 31.30 % Favored : 68.08 % 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: -0.04 (0.25), residues: 1134 helix: 0.93 (0.20), residues: 702 sheet: -1.16 (0.75), residues: 56 loop : -1.65 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 91 HIS 0.006 0.001 HIS B 214 PHE 0.014 0.002 PHE A 56 TYR 0.013 0.001 TYR B 439 ARG 0.009 0.000 ARG B 377 Details of bonding type rmsd hydrogen bonds : bond 0.15279 ( 557) hydrogen bonds : angle 6.71115 ( 1650) covalent geometry : bond 0.00369 ( 8950) covalent geometry : angle 0.68965 (12092) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 163 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8210 (tpp) cc_final: 0.7934 (ttt) REVERT: A 149 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7784 (mm-30) REVERT: A 295 MET cc_start: 0.8203 (ttm) cc_final: 0.7915 (ttm) REVERT: A 312 MET cc_start: 0.8618 (mmm) cc_final: 0.8100 (mmm) REVERT: A 495 LEU cc_start: 0.9092 (mm) cc_final: 0.8859 (mm) REVERT: B 98 MET cc_start: 0.8232 (ppp) cc_final: 0.7793 (tmm) REVERT: B 456 MET cc_start: 0.9047 (ttp) cc_final: 0.8841 (ptm) REVERT: B 481 LEU cc_start: 0.8859 (mt) cc_final: 0.8525 (pt) REVERT: B 495 LEU cc_start: 0.9042 (tt) cc_final: 0.8806 (tt) outliers start: 6 outliers final: 3 residues processed: 167 average time/residue: 0.1780 time to fit residues: 42.5688 Evaluate side-chains 146 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 470 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 28 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 363 ASN B 430 ASN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.099848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.077381 restraints weight = 29018.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.079765 restraints weight = 15866.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.081345 restraints weight = 10621.071| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8950 Z= 0.145 Angle : 0.650 10.171 12092 Z= 0.337 Chirality : 0.042 0.176 1440 Planarity : 0.004 0.046 1532 Dihedral : 5.156 56.192 1243 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.23 % Favored : 95.50 % Rotamer: Outliers : 3.82 % Allowed : 29.13 % Favored : 67.05 % 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: 0.21 (0.25), residues: 1134 helix: 1.06 (0.19), residues: 726 sheet: -0.87 (0.85), residues: 44 loop : -1.60 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 165 HIS 0.008 0.002 HIS A 214 PHE 0.017 0.002 PHE A 23 TYR 0.020 0.001 TYR A 439 ARG 0.003 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.04693 ( 557) hydrogen bonds : angle 4.82313 ( 1650) covalent geometry : bond 0.00304 ( 8950) covalent geometry : angle 0.65040 (12092) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8843 (tpp) cc_final: 0.8479 (tpp) REVERT: A 108 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8303 (mtt) REVERT: A 111 MET cc_start: 0.8444 (tpp) cc_final: 0.8115 (ttt) REVERT: A 295 MET cc_start: 0.8153 (ttm) cc_final: 0.7875 (ttm) REVERT: A 495 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8734 (mm) REVERT: B 98 MET cc_start: 0.8488 (ppp) cc_final: 0.7922 (tmm) REVERT: B 133 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7521 (tm-30) REVERT: B 325 GLU cc_start: 0.7842 (pm20) cc_final: 0.7608 (pm20) REVERT: B 428 LEU cc_start: 0.9117 (tp) cc_final: 0.8777 (tp) REVERT: B 481 LEU cc_start: 0.8847 (mt) cc_final: 0.8559 (pt) outliers start: 37 outliers final: 18 residues processed: 196 average time/residue: 0.1811 time to fit residues: 50.5564 Evaluate side-chains 168 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 524 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 16 optimal weight: 0.0980 chunk 48 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.100633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.078136 restraints weight = 29370.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.080496 restraints weight = 16116.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.082142 restraints weight = 10778.354| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8950 Z= 0.135 Angle : 0.622 10.152 12092 Z= 0.321 Chirality : 0.042 0.185 1440 Planarity : 0.004 0.036 1532 Dihedral : 4.836 48.628 1241 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.41 % Favored : 95.33 % Rotamer: Outliers : 5.27 % Allowed : 28.93 % Favored : 65.81 % 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: 0.29 (0.25), residues: 1134 helix: 1.13 (0.19), residues: 728 sheet: -0.79 (0.84), residues: 44 loop : -1.61 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 66 HIS 0.012 0.002 HIS B 214 PHE 0.015 0.002 PHE A 23 TYR 0.017 0.001 TYR A 439 ARG 0.004 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 557) hydrogen bonds : angle 4.51706 ( 1650) covalent geometry : bond 0.00289 ( 8950) covalent geometry : angle 0.62212 (12092) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 158 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8906 (tpp) cc_final: 0.8353 (tpp) REVERT: A 111 MET cc_start: 0.8317 (tpp) cc_final: 0.8095 (ttt) REVERT: A 149 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7553 (mm-30) REVERT: A 209 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8020 (mp10) REVERT: A 295 MET cc_start: 0.8158 (ttm) cc_final: 0.7853 (ttm) REVERT: A 495 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8712 (mm) REVERT: B 98 MET cc_start: 0.8556 (ppp) cc_final: 0.8223 (tmm) REVERT: B 107 HIS cc_start: 0.8429 (OUTLIER) cc_final: 0.8033 (t-90) REVERT: B 133 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: B 149 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7517 (mm-30) REVERT: B 481 LEU cc_start: 0.8821 (mt) cc_final: 0.8519 (pt) outliers start: 51 outliers final: 31 residues processed: 194 average time/residue: 0.1740 time to fit residues: 48.4997 Evaluate side-chains 182 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 578 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 99 optimal weight: 0.9980 chunk 107 optimal weight: 0.0060 chunk 2 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.101170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.078565 restraints weight = 29396.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.080922 restraints weight = 16420.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.082541 restraints weight = 11079.651| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8950 Z= 0.135 Angle : 0.634 10.343 12092 Z= 0.322 Chirality : 0.041 0.180 1440 Planarity : 0.004 0.036 1532 Dihedral : 4.854 58.289 1241 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.23 % Favored : 95.50 % Rotamer: Outliers : 4.44 % Allowed : 30.06 % Favored : 65.50 % 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: 0.36 (0.25), residues: 1134 helix: 1.19 (0.19), residues: 730 sheet: -0.78 (0.83), residues: 44 loop : -1.60 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 66 HIS 0.009 0.001 HIS A 214 PHE 0.014 0.002 PHE A 23 TYR 0.021 0.001 TYR A 439 ARG 0.004 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.04193 ( 557) hydrogen bonds : angle 4.35117 ( 1650) covalent geometry : bond 0.00296 ( 8950) covalent geometry : angle 0.63414 (12092) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.6295 (mmp) cc_final: 0.6084 (mmt) REVERT: A 98 MET cc_start: 0.8893 (tpp) cc_final: 0.8264 (tpp) REVERT: A 149 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7594 (mm-30) REVERT: A 295 MET cc_start: 0.8097 (ttm) cc_final: 0.7800 (ttm) REVERT: A 495 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8707 (mm) REVERT: A 517 ARG cc_start: 0.8991 (ttt180) cc_final: 0.8760 (ptp90) REVERT: A 562 HIS cc_start: 0.8601 (p-80) cc_final: 0.8251 (p-80) REVERT: B 100 MET cc_start: 0.8942 (mmp) cc_final: 0.8637 (tpp) REVERT: B 133 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8037 (tm-30) REVERT: B 149 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7553 (mm-30) REVERT: B 174 LEU cc_start: 0.9087 (mt) cc_final: 0.8821 (mt) REVERT: B 458 TYR cc_start: 0.8391 (t80) cc_final: 0.7983 (t80) outliers start: 43 outliers final: 35 residues processed: 190 average time/residue: 0.1863 time to fit residues: 51.1633 Evaluate side-chains 185 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 17 TRP Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 576 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN B 436 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.100509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.078139 restraints weight = 29214.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.080485 restraints weight = 16214.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.082096 restraints weight = 10904.957| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8950 Z= 0.136 Angle : 0.621 11.007 12092 Z= 0.317 Chirality : 0.041 0.176 1440 Planarity : 0.004 0.038 1532 Dihedral : 4.822 59.734 1241 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.41 % Favored : 95.33 % Rotamer: Outliers : 5.68 % Allowed : 29.03 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.43 (0.25), residues: 1134 helix: 1.28 (0.19), residues: 730 sheet: -0.85 (0.82), residues: 44 loop : -1.64 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 66 HIS 0.009 0.001 HIS A 214 PHE 0.015 0.002 PHE A 23 TYR 0.016 0.001 TYR A 439 ARG 0.004 0.000 ARG B 377 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 557) hydrogen bonds : angle 4.31004 ( 1650) covalent geometry : bond 0.00301 ( 8950) covalent geometry : angle 0.62116 (12092) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 156 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8880 (tpp) cc_final: 0.8208 (tpp) REVERT: A 107 HIS cc_start: 0.7801 (OUTLIER) cc_final: 0.7427 (t-90) REVERT: A 149 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7576 (mm-30) REVERT: A 295 MET cc_start: 0.8049 (ttm) cc_final: 0.7721 (ttm) REVERT: A 460 MET cc_start: 0.7903 (tpt) cc_final: 0.7656 (tmm) REVERT: A 487 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8801 (tp40) REVERT: A 495 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8691 (mm) REVERT: A 517 ARG cc_start: 0.8966 (ttt180) cc_final: 0.8733 (ptp90) REVERT: A 562 HIS cc_start: 0.8592 (p-80) cc_final: 0.8257 (p-80) REVERT: B 98 MET cc_start: 0.8507 (tmm) cc_final: 0.8026 (tmm) REVERT: B 100 MET cc_start: 0.8942 (mmp) cc_final: 0.8581 (tpp) REVERT: B 107 HIS cc_start: 0.8448 (OUTLIER) cc_final: 0.8036 (t-90) REVERT: B 133 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8038 (tm-30) REVERT: B 149 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7621 (mm-30) REVERT: B 160 MET cc_start: 0.8250 (tpp) cc_final: 0.7914 (tpp) REVERT: B 174 LEU cc_start: 0.9098 (mt) cc_final: 0.8895 (mp) REVERT: B 416 ARG cc_start: 0.8453 (mmt90) cc_final: 0.7800 (mpt-90) REVERT: B 458 TYR cc_start: 0.8395 (t80) cc_final: 0.8038 (t80) REVERT: B 481 LEU cc_start: 0.8421 (mm) cc_final: 0.8095 (mt) REVERT: B 486 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8488 (mtt90) outliers start: 55 outliers final: 38 residues processed: 197 average time/residue: 0.1788 time to fit residues: 50.3436 Evaluate side-chains 189 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 144 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 17 TRP Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 66 TRP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 486 ARG Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 576 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 GLN B 436 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.100852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.078287 restraints weight = 29153.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.080607 restraints weight = 16391.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.082233 restraints weight = 11103.189| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8950 Z= 0.133 Angle : 0.643 13.639 12092 Z= 0.320 Chirality : 0.041 0.144 1440 Planarity : 0.004 0.040 1532 Dihedral : 4.790 58.860 1241 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.32 % Favored : 95.50 % Rotamer: Outliers : 5.48 % Allowed : 29.24 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1134 helix: 1.33 (0.19), residues: 730 sheet: -0.93 (0.81), residues: 44 loop : -1.66 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 17 HIS 0.010 0.001 HIS A 214 PHE 0.014 0.001 PHE A 23 TYR 0.015 0.001 TYR A 439 ARG 0.004 0.000 ARG B 377 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 557) hydrogen bonds : angle 4.25679 ( 1650) covalent geometry : bond 0.00295 ( 8950) covalent geometry : angle 0.64273 (12092) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 149 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8877 (tpp) cc_final: 0.8158 (tpp) REVERT: A 107 HIS cc_start: 0.7721 (OUTLIER) cc_final: 0.7357 (t-90) REVERT: A 149 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7589 (mm-30) REVERT: A 295 MET cc_start: 0.8044 (ttm) cc_final: 0.7726 (ttm) REVERT: A 487 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8810 (tp40) REVERT: A 495 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8674 (mm) REVERT: A 517 ARG cc_start: 0.8970 (ttt180) cc_final: 0.8746 (ptp90) REVERT: A 562 HIS cc_start: 0.8588 (p-80) cc_final: 0.8275 (p-80) REVERT: B 17 TRP cc_start: 0.6655 (OUTLIER) cc_final: 0.6447 (t60) REVERT: B 98 MET cc_start: 0.8409 (tmm) cc_final: 0.8028 (tmm) REVERT: B 100 MET cc_start: 0.8910 (mmp) cc_final: 0.8592 (tpp) REVERT: B 107 HIS cc_start: 0.8432 (OUTLIER) cc_final: 0.8052 (t-90) REVERT: B 133 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8071 (tm-30) REVERT: B 149 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7599 (mm-30) REVERT: B 160 MET cc_start: 0.8219 (tpp) cc_final: 0.7949 (tpp) REVERT: B 174 LEU cc_start: 0.9108 (mt) cc_final: 0.8901 (mp) REVERT: B 481 LEU cc_start: 0.8521 (mm) cc_final: 0.8227 (mt) outliers start: 53 outliers final: 40 residues processed: 187 average time/residue: 0.1851 time to fit residues: 48.9325 Evaluate side-chains 187 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 140 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 17 TRP Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 66 TRP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 17 TRP Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 576 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 103 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.100393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.077663 restraints weight = 29762.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.080023 restraints weight = 16747.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.081649 restraints weight = 11357.411| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8950 Z= 0.133 Angle : 0.632 11.505 12092 Z= 0.317 Chirality : 0.041 0.156 1440 Planarity : 0.004 0.041 1532 Dihedral : 4.640 57.548 1239 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.32 % Favored : 95.50 % Rotamer: Outliers : 5.17 % Allowed : 30.48 % Favored : 64.36 % 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: 1134 helix: 1.37 (0.19), residues: 730 sheet: -1.54 (0.63), residues: 64 loop : -1.63 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 91 HIS 0.012 0.001 HIS A 214 PHE 0.014 0.001 PHE A 23 TYR 0.013 0.001 TYR A 439 ARG 0.003 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.04062 ( 557) hydrogen bonds : angle 4.23859 ( 1650) covalent geometry : bond 0.00295 ( 8950) covalent geometry : angle 0.63211 (12092) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 148 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8848 (tpp) cc_final: 0.8109 (tpp) REVERT: A 149 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7587 (mm-30) REVERT: A 295 MET cc_start: 0.8057 (ttm) cc_final: 0.7692 (ttm) REVERT: A 487 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8592 (tp40) REVERT: A 495 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8672 (mm) REVERT: A 517 ARG cc_start: 0.8996 (ttt180) cc_final: 0.8772 (ptp90) REVERT: A 562 HIS cc_start: 0.8584 (p-80) cc_final: 0.8274 (p-80) REVERT: B 17 TRP cc_start: 0.6631 (OUTLIER) cc_final: 0.6403 (t60) REVERT: B 98 MET cc_start: 0.8350 (tmm) cc_final: 0.8059 (tmm) REVERT: B 100 MET cc_start: 0.8892 (mmp) cc_final: 0.8607 (tpp) REVERT: B 107 HIS cc_start: 0.8449 (OUTLIER) cc_final: 0.8057 (t-90) REVERT: B 133 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: B 149 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7586 (mm-30) REVERT: B 160 MET cc_start: 0.8265 (tpp) cc_final: 0.7894 (tpp) REVERT: B 374 LEU cc_start: 0.9056 (mm) cc_final: 0.8724 (tp) REVERT: B 465 LYS cc_start: 0.8357 (pttt) cc_final: 0.7918 (pptt) REVERT: B 481 LEU cc_start: 0.8552 (mm) cc_final: 0.8195 (mt) REVERT: B 486 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8714 (mtt90) outliers start: 50 outliers final: 41 residues processed: 186 average time/residue: 0.1797 time to fit residues: 48.6963 Evaluate side-chains 191 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 143 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 17 TRP Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 66 TRP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 17 TRP Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 486 ARG Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 576 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 40 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 102 optimal weight: 0.0040 chunk 99 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 464 ASN B 436 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.099044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.076124 restraints weight = 30032.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.078438 restraints weight = 16986.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.080030 restraints weight = 11580.587| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8950 Z= 0.157 Angle : 0.670 11.679 12092 Z= 0.334 Chirality : 0.042 0.149 1440 Planarity : 0.004 0.041 1532 Dihedral : 4.641 56.693 1239 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.41 % Favored : 95.41 % Rotamer: Outliers : 5.89 % Allowed : 30.27 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1134 helix: 1.36 (0.19), residues: 730 sheet: -1.55 (0.62), residues: 64 loop : -1.60 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 17 HIS 0.011 0.001 HIS A 214 PHE 0.018 0.002 PHE A 23 TYR 0.013 0.001 TYR A 439 ARG 0.003 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 557) hydrogen bonds : angle 4.31615 ( 1650) covalent geometry : bond 0.00352 ( 8950) covalent geometry : angle 0.67042 (12092) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 141 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8862 (tpp) cc_final: 0.8088 (tpp) REVERT: A 149 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7601 (mm-30) REVERT: A 295 MET cc_start: 0.8059 (ttm) cc_final: 0.7693 (ttm) REVERT: A 450 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.9123 (mm) REVERT: A 458 TYR cc_start: 0.8354 (OUTLIER) cc_final: 0.8105 (m-80) REVERT: A 487 GLN cc_start: 0.9214 (OUTLIER) cc_final: 0.8611 (tp40) REVERT: A 495 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8693 (mm) REVERT: A 562 HIS cc_start: 0.8606 (p-80) cc_final: 0.8296 (p-80) REVERT: B 100 MET cc_start: 0.8910 (mmp) cc_final: 0.8648 (tpp) REVERT: B 107 HIS cc_start: 0.8547 (OUTLIER) cc_final: 0.8080 (t-90) REVERT: B 133 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7779 (tm-30) REVERT: B 149 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7644 (mm-30) REVERT: B 160 MET cc_start: 0.8336 (tpp) cc_final: 0.8116 (tpp) REVERT: B 276 MET cc_start: 0.7193 (mmp) cc_final: 0.6726 (mmt) REVERT: B 465 LYS cc_start: 0.8374 (pttt) cc_final: 0.7965 (pptt) REVERT: B 481 LEU cc_start: 0.8598 (mm) cc_final: 0.8241 (mt) REVERT: B 486 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8720 (mtt90) outliers start: 57 outliers final: 44 residues processed: 183 average time/residue: 0.1714 time to fit residues: 45.2648 Evaluate side-chains 189 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 137 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 17 TRP Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 66 TRP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 486 ARG Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 576 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS B 436 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.097687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.074790 restraints weight = 29655.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.077063 restraints weight = 16745.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.078646 restraints weight = 11415.711| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8950 Z= 0.178 Angle : 0.700 11.741 12092 Z= 0.351 Chirality : 0.043 0.237 1440 Planarity : 0.004 0.040 1532 Dihedral : 4.676 48.571 1239 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.59 % Favored : 95.24 % Rotamer: Outliers : 5.48 % Allowed : 30.99 % Favored : 63.53 % 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: 0.36 (0.25), residues: 1134 helix: 1.25 (0.19), residues: 730 sheet: -1.48 (0.62), residues: 64 loop : -1.60 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 17 HIS 0.015 0.002 HIS A 214 PHE 0.020 0.002 PHE A 23 TYR 0.014 0.001 TYR B 439 ARG 0.003 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 557) hydrogen bonds : angle 4.42886 ( 1650) covalent geometry : bond 0.00399 ( 8950) covalent geometry : angle 0.69965 (12092) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 135 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.6220 (mmt) cc_final: 0.5585 (mmt) REVERT: A 98 MET cc_start: 0.8850 (tpp) cc_final: 0.8067 (tpp) REVERT: A 149 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7795 (mm-30) REVERT: A 295 MET cc_start: 0.8048 (ttm) cc_final: 0.7686 (ttm) REVERT: A 487 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8588 (tp40) REVERT: A 495 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8746 (mm) REVERT: A 562 HIS cc_start: 0.8650 (p-80) cc_final: 0.8343 (p-80) REVERT: B 100 MET cc_start: 0.8911 (mmp) cc_final: 0.8656 (tpp) REVERT: B 107 HIS cc_start: 0.8574 (OUTLIER) cc_final: 0.8083 (t-90) REVERT: B 133 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7646 (tm-30) REVERT: B 149 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7690 (mm-30) REVERT: B 481 LEU cc_start: 0.8638 (mm) cc_final: 0.8210 (mt) REVERT: B 486 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8637 (mtt90) outliers start: 53 outliers final: 44 residues processed: 175 average time/residue: 0.1749 time to fit residues: 44.2965 Evaluate side-chains 185 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 135 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 17 TRP Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 66 TRP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 486 ARG Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 576 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 72 optimal weight: 0.0070 chunk 70 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 88 optimal weight: 20.0000 chunk 100 optimal weight: 0.0980 chunk 68 optimal weight: 2.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.101319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.078378 restraints weight = 29669.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.080748 restraints weight = 16719.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.082407 restraints weight = 11380.735| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8950 Z= 0.129 Angle : 0.697 12.221 12092 Z= 0.340 Chirality : 0.041 0.198 1440 Planarity : 0.004 0.041 1532 Dihedral : 4.570 45.442 1239 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.32 % Favored : 95.50 % Rotamer: Outliers : 3.82 % Allowed : 32.64 % Favored : 63.53 % 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: 0.46 (0.25), residues: 1134 helix: 1.33 (0.19), residues: 730 sheet: -2.31 (0.61), residues: 44 loop : -1.49 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 165 HIS 0.017 0.002 HIS A 214 PHE 0.015 0.001 PHE A 105 TYR 0.008 0.001 TYR A 439 ARG 0.003 0.000 ARG B 377 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 557) hydrogen bonds : angle 4.27069 ( 1650) covalent geometry : bond 0.00285 ( 8950) covalent geometry : angle 0.69657 (12092) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8855 (tpp) cc_final: 0.8159 (tpp) REVERT: A 149 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7688 (mm-30) REVERT: A 210 MET cc_start: 0.8703 (mmt) cc_final: 0.8326 (tpp) REVERT: A 295 MET cc_start: 0.7985 (ttm) cc_final: 0.7632 (ttm) REVERT: A 487 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8694 (mm-40) REVERT: A 495 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8680 (mm) REVERT: A 562 HIS cc_start: 0.8662 (p-80) cc_final: 0.8365 (p-80) REVERT: B 100 MET cc_start: 0.8833 (mmp) cc_final: 0.8590 (tpp) REVERT: B 107 HIS cc_start: 0.8425 (OUTLIER) cc_final: 0.7981 (t-90) REVERT: B 133 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7718 (tm-30) REVERT: B 149 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7619 (mm-30) REVERT: B 465 LYS cc_start: 0.8462 (pttt) cc_final: 0.8079 (pptt) REVERT: B 481 LEU cc_start: 0.8562 (mm) cc_final: 0.8228 (mt) outliers start: 37 outliers final: 31 residues processed: 174 average time/residue: 0.1756 time to fit residues: 43.8621 Evaluate side-chains 176 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 486 ARG Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 576 HIS Chi-restraints excluded: chain B residue 578 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.098702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.076018 restraints weight = 29768.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.078312 restraints weight = 16770.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.079883 restraints weight = 11416.999| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8950 Z= 0.162 Angle : 0.705 11.977 12092 Z= 0.350 Chirality : 0.042 0.172 1440 Planarity : 0.004 0.040 1532 Dihedral : 4.616 46.298 1239 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.67 % Favored : 95.24 % Rotamer: Outliers : 4.65 % Allowed : 31.82 % Favored : 63.53 % 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: 0.43 (0.25), residues: 1134 helix: 1.29 (0.19), residues: 718 sheet: -2.30 (0.62), residues: 44 loop : -1.36 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 17 HIS 0.018 0.002 HIS A 214 PHE 0.019 0.002 PHE A 23 TYR 0.011 0.001 TYR B 439 ARG 0.002 0.000 ARG B 377 Details of bonding type rmsd hydrogen bonds : bond 0.04271 ( 557) hydrogen bonds : angle 4.35768 ( 1650) covalent geometry : bond 0.00367 ( 8950) covalent geometry : angle 0.70511 (12092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3134.84 seconds wall clock time: 56 minutes 23.10 seconds (3383.10 seconds total)