Starting phenix.real_space_refine on Wed Mar 4 03:14:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s8x_24928/03_2026/7s8x_24928.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s8x_24928/03_2026/7s8x_24928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s8x_24928/03_2026/7s8x_24928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s8x_24928/03_2026/7s8x_24928.map" model { file = "/net/cci-nas-00/data/ceres_data/7s8x_24928/03_2026/7s8x_24928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s8x_24928/03_2026/7s8x_24928.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 50 5.16 5 C 6838 2.51 5 N 1676 2.21 5 O 1862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10426 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5213 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 33, 'TRANS': 641} Chain breaks: 1 Chain: "B" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5213 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 33, 'TRANS': 641} Chain breaks: 1 Time building chain proxies: 2.30, per 1000 atoms: 0.22 Number of scatterers: 10426 At special positions: 0 Unit cell: (115.867, 107.363, 119.056, 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 50 16.00 O 1862 8.00 N 1676 7.00 C 6838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 559.4 milliseconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2492 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 4 sheets defined 68.1% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 removed outlier: 3.577A pdb=" N LEU A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 49 removed outlier: 3.648A pdb=" N GLN A 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA A 49 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 75 through 105 removed outlier: 5.160A pdb=" N LEU A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 109 through 127 removed outlier: 3.711A pdb=" N LEU A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 137 through 152 removed outlier: 3.522A pdb=" N SER A 141 " --> pdb=" O PHE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 196 removed outlier: 4.698A pdb=" N ARG A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 204 removed outlier: 3.875A pdb=" N PHE A 200 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 230 removed outlier: 4.450A pdb=" N LYS A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 258 through 282 Processing helix chain 'A' and resid 291 through 307 removed outlier: 3.651A pdb=" N PHE A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 335 through 366 removed outlier: 6.440A pdb=" N VAL A 341 " --> pdb=" O HIS A 337 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ASP A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N HIS A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 Processing helix chain 'A' and resid 396 through 407 Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 430 through 434 removed outlier: 3.774A pdb=" N GLU A 433 " --> pdb=" O PHE A 430 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A 434 " --> pdb=" O LEU A 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 430 through 434' Processing helix chain 'A' and resid 436 through 448 removed outlier: 3.797A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 456 through 465 removed outlier: 3.734A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 483 through 505 removed outlier: 3.918A pdb=" N VAL A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 527 removed outlier: 4.109A pdb=" N GLU A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 523 through 527' Processing helix chain 'A' and resid 548 through 560 Processing helix chain 'A' and resid 563 through 578 Processing helix chain 'A' and resid 653 through 671 Processing helix chain 'A' and resid 680 through 690 removed outlier: 3.675A pdb=" N ASN A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 721 Processing helix chain 'B' and resid 24 through 32 removed outlier: 3.577A pdb=" N LEU B 32 " --> pdb=" O LEU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 49 removed outlier: 3.648A pdb=" N GLN B 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA B 49 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 75 through 105 removed outlier: 5.160A pdb=" N LEU B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) Proline residue: B 96 - end of helix Processing helix chain 'B' and resid 109 through 127 removed outlier: 3.711A pdb=" N LEU B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 137 through 152 removed outlier: 3.523A pdb=" N SER B 141 " --> pdb=" O PHE B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 196 removed outlier: 4.698A pdb=" N ARG B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 204 removed outlier: 3.874A pdb=" N PHE B 200 " --> pdb=" O ARG B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 230 removed outlier: 4.450A pdb=" N LYS B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 253 Processing helix chain 'B' and resid 258 through 282 Processing helix chain 'B' and resid 291 through 307 removed outlier: 3.651A pdb=" N PHE B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 335 through 366 removed outlier: 6.443A pdb=" N VAL B 341 " --> pdb=" O HIS B 337 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ASP B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS B 364 " --> pdb=" O THR B 360 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS B 365 " --> pdb=" O LEU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 396 through 407 Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 430 through 434 removed outlier: 3.774A pdb=" N GLU B 433 " --> pdb=" O PHE B 430 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER B 434 " --> pdb=" O LEU B 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 430 through 434' Processing helix chain 'B' and resid 436 through 448 removed outlier: 3.797A pdb=" N LEU B 440 " --> pdb=" O PRO B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 456 through 465 removed outlier: 3.736A pdb=" N PHE B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 482 Processing helix chain 'B' and resid 483 through 505 removed outlier: 3.917A pdb=" N VAL B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.109A pdb=" N GLU B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 523 through 527' Processing helix chain 'B' and resid 548 through 560 Processing helix chain 'B' and resid 563 through 578 Processing helix chain 'B' and resid 653 through 671 Processing helix chain 'B' and resid 680 through 690 removed outlier: 3.675A pdb=" N ASN B 690 " --> pdb=" O ASP B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 721 Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.561A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N GLN A 513 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N ILE A 535 " --> pdb=" O GLN A 513 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS A 536 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASP A 645 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE A 538 " --> pdb=" O ASP A 645 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N PHE A 703 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A 676 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 135 Processing sheet with id=AA4, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.562A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN B 513 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N ILE B 535 " --> pdb=" O GLN B 513 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS B 536 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASP B 645 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE B 538 " --> pdb=" O ASP B 645 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N PHE B 703 " --> pdb=" O VAL B 674 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 676 " --> pdb=" O PHE B 703 " (cutoff:3.500A) 650 hydrogen bonds defined for protein. 1908 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 1.13 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: 3218 1.34 - 1.46: 2255 1.46 - 1.58: 5107 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 10662 Sorted by residual: bond pdb=" N VAL B 18 " pdb=" CA VAL B 18 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.42e+00 bond pdb=" N TYR A 17 " pdb=" CA TYR A 17 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.21e-02 6.83e+03 4.93e+00 bond pdb=" N TYR B 17 " pdb=" CA TYR B 17 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.20e-02 6.94e+03 4.70e+00 bond pdb=" CA LEU B 448 " pdb=" C LEU B 448 " ideal model delta sigma weight residual 1.522 1.550 -0.028 1.72e-02 3.38e+03 2.72e+00 bond pdb=" CA LEU A 448 " pdb=" C LEU A 448 " ideal model delta sigma weight residual 1.522 1.550 -0.028 1.72e-02 3.38e+03 2.71e+00 ... (remaining 10657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 13985 1.69 - 3.38: 411 3.38 - 5.06: 77 5.06 - 6.75: 15 6.75 - 8.44: 6 Bond angle restraints: 14494 Sorted by residual: angle pdb=" C PRO B 515 " pdb=" N ASP B 516 " pdb=" CA ASP B 516 " ideal model delta sigma weight residual 121.54 128.06 -6.52 1.91e+00 2.74e-01 1.17e+01 angle pdb=" C PRO A 515 " pdb=" N ASP A 516 " pdb=" CA ASP A 516 " ideal model delta sigma weight residual 121.54 128.00 -6.46 1.91e+00 2.74e-01 1.14e+01 angle pdb=" N ALA B 138 " pdb=" CA ALA B 138 " pdb=" C ALA B 138 " ideal model delta sigma weight residual 110.80 117.73 -6.93 2.13e+00 2.20e-01 1.06e+01 angle pdb=" N ALA A 138 " pdb=" CA ALA A 138 " pdb=" C ALA A 138 " ideal model delta sigma weight residual 110.80 117.70 -6.90 2.13e+00 2.20e-01 1.05e+01 angle pdb=" CA VAL B 18 " pdb=" C VAL B 18 " pdb=" O VAL B 18 " ideal model delta sigma weight residual 120.78 117.19 3.59 1.25e+00 6.40e-01 8.25e+00 ... (remaining 14489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 5712 17.78 - 35.55: 500 35.55 - 53.33: 70 53.33 - 71.11: 16 71.11 - 88.89: 14 Dihedral angle restraints: 6312 sinusoidal: 2418 harmonic: 3894 Sorted by residual: dihedral pdb=" CA PHE A 23 " pdb=" C PHE A 23 " pdb=" N SER A 24 " pdb=" CA SER A 24 " ideal model delta harmonic sigma weight residual 180.00 157.76 22.24 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA PHE B 23 " pdb=" C PHE B 23 " pdb=" N SER B 24 " pdb=" CA SER B 24 " ideal model delta harmonic sigma weight residual 180.00 157.80 22.20 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA PHE B 76 " pdb=" C PHE B 76 " pdb=" N LYS B 77 " pdb=" CA LYS B 77 " ideal model delta harmonic sigma weight residual 180.00 -158.61 -21.39 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 6309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1140 0.041 - 0.083: 435 0.083 - 0.124: 126 0.124 - 0.165: 19 0.165 - 0.206: 2 Chirality restraints: 1722 Sorted by residual: chirality pdb=" CB THR A 390 " pdb=" CA THR A 390 " pdb=" OG1 THR A 390 " pdb=" CG2 THR A 390 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB THR B 390 " pdb=" CA THR B 390 " pdb=" OG1 THR B 390 " pdb=" CG2 THR B 390 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ASP B 516 " pdb=" N ASP B 516 " pdb=" C ASP B 516 " pdb=" CB ASP B 516 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.34e-01 ... (remaining 1719 not shown) Planarity restraints: 1806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 135 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO A 136 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 136 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 136 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 135 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO B 136 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 136 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 136 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 286 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO B 287 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 287 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 287 " 0.023 5.00e-02 4.00e+02 ... (remaining 1803 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2094 2.77 - 3.30: 10857 3.30 - 3.83: 17417 3.83 - 4.37: 20218 4.37 - 4.90: 34690 Nonbonded interactions: 85276 Sorted by model distance: nonbonded pdb=" OH TYR A 123 " pdb=" OE1 GLU A 374 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR B 123 " pdb=" OE1 GLU B 374 " model vdw 2.238 3.040 nonbonded pdb=" OG1 THR A 503 " pdb=" OH TYR A 545 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR B 503 " pdb=" OH TYR B 545 " model vdw 2.263 3.040 nonbonded pdb=" OG1 THR A 128 " pdb=" OE2 GLU A 374 " model vdw 2.264 3.040 ... (remaining 85271 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: 0.02 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.510 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 : 0.005 0.047 10662 Z= 0.222 Angle : 0.726 8.441 14494 Z= 0.401 Chirality : 0.046 0.206 1722 Planarity : 0.005 0.042 1806 Dihedral : 14.048 88.885 3820 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.56 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.23), residues: 1342 helix: 0.88 (0.18), residues: 874 sheet: 1.17 (0.87), residues: 36 loop : -1.89 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 130 TYR 0.016 0.002 TYR B 545 PHE 0.028 0.002 PHE B 111 TRP 0.016 0.002 TRP A 472 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00508 (10662) covalent geometry : angle 0.72584 (14494) hydrogen bonds : bond 0.10780 ( 650) hydrogen bonds : angle 5.53977 ( 1908) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.322 Fit side-chains REVERT: A 334 SER cc_start: 0.8071 (p) cc_final: 0.7689 (p) REVERT: A 453 MET cc_start: 0.8131 (mmp) cc_final: 0.7873 (mmm) REVERT: B 180 MET cc_start: 0.6892 (mmm) cc_final: 0.6653 (mmp) REVERT: B 453 MET cc_start: 0.8100 (mmp) cc_final: 0.7894 (mmm) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.0805 time to fit residues: 18.8847 Evaluate side-chains 121 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0060 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN A 447 ASN B 279 ASN B 447 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.149030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.116165 restraints weight = 13252.657| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.66 r_work: 0.2902 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10662 Z= 0.140 Angle : 0.599 7.094 14494 Z= 0.313 Chirality : 0.044 0.156 1722 Planarity : 0.005 0.044 1806 Dihedral : 4.644 19.372 1444 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.79 % Allowed : 6.11 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.23), residues: 1342 helix: 1.35 (0.18), residues: 864 sheet: 1.08 (0.88), residues: 36 loop : -1.74 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 572 TYR 0.010 0.001 TYR B 367 PHE 0.023 0.001 PHE A 278 TRP 0.006 0.001 TRP A 70 HIS 0.002 0.001 HIS B 704 Details of bonding type rmsd covalent geometry : bond 0.00307 (10662) covalent geometry : angle 0.59891 (14494) hydrogen bonds : bond 0.04323 ( 650) hydrogen bonds : angle 4.51640 ( 1908) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.406 Fit side-chains REVERT: A 83 ASP cc_start: 0.7406 (m-30) cc_final: 0.7006 (m-30) REVERT: A 180 MET cc_start: 0.7324 (mmp) cc_final: 0.6889 (mmm) REVERT: A 267 MET cc_start: 0.8364 (tmm) cc_final: 0.7955 (ttt) REVERT: A 453 MET cc_start: 0.8762 (mmp) cc_final: 0.8475 (mmm) REVERT: A 548 ASN cc_start: 0.8475 (t0) cc_final: 0.8003 (t0) REVERT: B 58 ARG cc_start: 0.7191 (ptm160) cc_final: 0.6935 (mpt180) REVERT: B 83 ASP cc_start: 0.7385 (m-30) cc_final: 0.7006 (m-30) REVERT: B 267 MET cc_start: 0.8388 (tmm) cc_final: 0.8029 (ttt) REVERT: B 453 MET cc_start: 0.8816 (mmp) cc_final: 0.8551 (mmm) REVERT: B 548 ASN cc_start: 0.8303 (t0) cc_final: 0.7744 (t0) outliers start: 9 outliers final: 8 residues processed: 142 average time/residue: 0.0848 time to fit residues: 18.0351 Evaluate side-chains 134 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 76 PHE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 344 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 56 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 63 optimal weight: 0.0050 chunk 22 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 112 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 ASN B 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.150095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117246 restraints weight = 13272.829| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.61 r_work: 0.2916 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10662 Z= 0.132 Angle : 0.560 7.152 14494 Z= 0.293 Chirality : 0.042 0.162 1722 Planarity : 0.004 0.046 1806 Dihedral : 4.420 19.536 1444 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.57 % Allowed : 7.68 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.23), residues: 1342 helix: 1.52 (0.17), residues: 866 sheet: 1.20 (0.89), residues: 36 loop : -1.66 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 572 TYR 0.009 0.001 TYR A 545 PHE 0.021 0.001 PHE B 278 TRP 0.007 0.001 TRP A 70 HIS 0.002 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00290 (10662) covalent geometry : angle 0.55952 (14494) hydrogen bonds : bond 0.03985 ( 650) hydrogen bonds : angle 4.36423 ( 1908) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.505 Fit side-chains REVERT: A 180 MET cc_start: 0.7426 (mmp) cc_final: 0.7043 (mmm) REVERT: A 267 MET cc_start: 0.8327 (tmm) cc_final: 0.8043 (mmp) REVERT: A 548 ASN cc_start: 0.8428 (t0) cc_final: 0.7904 (t0) REVERT: B 75 ARG cc_start: 0.7380 (mtm-85) cc_final: 0.7088 (mmt90) REVERT: B 83 ASP cc_start: 0.7407 (m-30) cc_final: 0.6999 (m-30) REVERT: B 267 MET cc_start: 0.8371 (tmm) cc_final: 0.8071 (mmp) REVERT: B 299 MET cc_start: 0.7740 (mmt) cc_final: 0.7525 (mmm) REVERT: B 548 ASN cc_start: 0.8237 (t0) cc_final: 0.7650 (t0) outliers start: 18 outliers final: 11 residues processed: 145 average time/residue: 0.0779 time to fit residues: 17.0444 Evaluate side-chains 141 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 76 PHE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 337 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 26 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 116 optimal weight: 0.0870 chunk 71 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.149124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.115528 restraints weight = 13360.944| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.73 r_work: 0.2875 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10662 Z= 0.147 Angle : 0.563 7.283 14494 Z= 0.293 Chirality : 0.043 0.162 1722 Planarity : 0.005 0.046 1806 Dihedral : 4.376 19.269 1444 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.40 % Allowed : 10.38 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.23), residues: 1342 helix: 1.61 (0.18), residues: 868 sheet: 1.32 (0.89), residues: 36 loop : -1.60 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 75 TYR 0.009 0.001 TYR B 367 PHE 0.023 0.001 PHE A 278 TRP 0.006 0.001 TRP A 70 HIS 0.002 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00343 (10662) covalent geometry : angle 0.56348 (14494) hydrogen bonds : bond 0.03946 ( 650) hydrogen bonds : angle 4.28589 ( 1908) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.379 Fit side-chains REVERT: A 83 ASP cc_start: 0.7399 (m-30) cc_final: 0.7123 (m-30) REVERT: A 267 MET cc_start: 0.8308 (tmm) cc_final: 0.8017 (mmp) REVERT: A 548 ASN cc_start: 0.8567 (t0) cc_final: 0.8027 (t0) REVERT: B 75 ARG cc_start: 0.7298 (mtm-85) cc_final: 0.7064 (mmt90) REVERT: B 83 ASP cc_start: 0.7432 (m-30) cc_final: 0.7030 (m-30) REVERT: B 548 ASN cc_start: 0.8435 (t0) cc_final: 0.7842 (t0) outliers start: 16 outliers final: 15 residues processed: 141 average time/residue: 0.0818 time to fit residues: 17.7824 Evaluate side-chains 144 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 76 PHE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 659 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 22 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 3 optimal weight: 0.3980 chunk 75 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.150151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.116746 restraints weight = 13343.823| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.76 r_work: 0.2900 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10662 Z= 0.129 Angle : 0.545 7.273 14494 Z= 0.284 Chirality : 0.043 0.170 1722 Planarity : 0.004 0.047 1806 Dihedral : 4.292 19.528 1444 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.09 % Allowed : 11.08 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.24), residues: 1342 helix: 1.73 (0.18), residues: 866 sheet: 1.38 (0.89), residues: 36 loop : -1.58 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 571 TYR 0.007 0.001 TYR A 545 PHE 0.020 0.001 PHE A 278 TRP 0.005 0.001 TRP B 472 HIS 0.002 0.000 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00296 (10662) covalent geometry : angle 0.54484 (14494) hydrogen bonds : bond 0.03755 ( 650) hydrogen bonds : angle 4.21213 ( 1908) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.308 Fit side-chains REVERT: A 58 ARG cc_start: 0.7262 (ptm160) cc_final: 0.7050 (mpt180) REVERT: A 75 ARG cc_start: 0.7334 (mtm-85) cc_final: 0.6999 (mmt90) REVERT: A 453 MET cc_start: 0.8802 (mmp) cc_final: 0.8589 (mmp) REVERT: A 548 ASN cc_start: 0.8462 (t0) cc_final: 0.7899 (t0) REVERT: B 83 ASP cc_start: 0.7563 (m-30) cc_final: 0.7259 (m-30) REVERT: B 267 MET cc_start: 0.8328 (tmm) cc_final: 0.8120 (mmp) REVERT: B 548 ASN cc_start: 0.8324 (t0) cc_final: 0.7724 (t0) outliers start: 24 outliers final: 17 residues processed: 148 average time/residue: 0.0761 time to fit residues: 17.3027 Evaluate side-chains 146 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 76 PHE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 659 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 71 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 132 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.148857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114949 restraints weight = 13389.025| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.82 r_work: 0.2878 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10662 Z= 0.148 Angle : 0.554 7.317 14494 Z= 0.288 Chirality : 0.043 0.163 1722 Planarity : 0.004 0.046 1806 Dihedral : 4.305 19.149 1444 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.79 % Allowed : 11.17 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.24), residues: 1342 helix: 1.70 (0.18), residues: 866 sheet: 1.50 (0.90), residues: 36 loop : -1.57 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 75 TYR 0.009 0.001 TYR B 508 PHE 0.017 0.001 PHE A 278 TRP 0.005 0.001 TRP A 70 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00352 (10662) covalent geometry : angle 0.55364 (14494) hydrogen bonds : bond 0.03833 ( 650) hydrogen bonds : angle 4.19482 ( 1908) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.379 Fit side-chains REVERT: A 83 ASP cc_start: 0.7400 (m-30) cc_final: 0.7116 (m-30) REVERT: A 251 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7724 (mp) REVERT: A 267 MET cc_start: 0.8307 (tmm) cc_final: 0.8093 (mmp) REVERT: A 453 MET cc_start: 0.8805 (mmp) cc_final: 0.8576 (mmp) REVERT: A 548 ASN cc_start: 0.8554 (t0) cc_final: 0.7977 (t0) REVERT: B 83 ASP cc_start: 0.7501 (m-30) cc_final: 0.7222 (m-30) REVERT: B 267 MET cc_start: 0.8349 (tmm) cc_final: 0.8102 (mmp) REVERT: B 548 ASN cc_start: 0.8480 (t0) cc_final: 0.7887 (t0) outliers start: 32 outliers final: 16 residues processed: 146 average time/residue: 0.0791 time to fit residues: 18.1152 Evaluate side-chains 145 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 76 PHE Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 659 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 91 optimal weight: 0.2980 chunk 63 optimal weight: 0.5980 chunk 114 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 111 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 99 optimal weight: 0.0870 chunk 125 optimal weight: 5.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.150985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.120032 restraints weight = 13154.340| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.46 r_work: 0.2931 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10662 Z= 0.120 Angle : 0.533 7.265 14494 Z= 0.278 Chirality : 0.042 0.163 1722 Planarity : 0.004 0.046 1806 Dihedral : 4.240 19.727 1444 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.44 % Allowed : 11.78 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.24), residues: 1342 helix: 1.79 (0.18), residues: 866 sheet: 1.45 (0.87), residues: 36 loop : -1.50 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 31 TYR 0.007 0.001 TYR A 545 PHE 0.016 0.001 PHE A 278 TRP 0.007 0.001 TRP A 472 HIS 0.002 0.000 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00270 (10662) covalent geometry : angle 0.53333 (14494) hydrogen bonds : bond 0.03602 ( 650) hydrogen bonds : angle 4.12641 ( 1908) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.399 Fit side-chains REVERT: A 251 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7611 (mp) REVERT: A 453 MET cc_start: 0.8787 (mmp) cc_final: 0.8533 (mmp) REVERT: A 548 ASN cc_start: 0.8353 (t0) cc_final: 0.7778 (t0) REVERT: B 83 ASP cc_start: 0.7458 (m-30) cc_final: 0.7181 (m-30) REVERT: B 251 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7529 (mp) REVERT: B 267 MET cc_start: 0.8317 (tmm) cc_final: 0.8076 (mmp) REVERT: B 548 ASN cc_start: 0.8293 (t0) cc_final: 0.7823 (t0) outliers start: 28 outliers final: 16 residues processed: 144 average time/residue: 0.0841 time to fit residues: 18.7061 Evaluate side-chains 139 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain B residue 76 PHE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 659 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 100 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.150693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.119892 restraints weight = 13102.730| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.37 r_work: 0.2937 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10662 Z= 0.126 Angle : 0.536 7.236 14494 Z= 0.278 Chirality : 0.042 0.169 1722 Planarity : 0.004 0.047 1806 Dihedral : 4.179 19.402 1444 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.66 % Allowed : 13.18 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.24), residues: 1342 helix: 1.82 (0.18), residues: 870 sheet: 1.48 (0.86), residues: 36 loop : -1.44 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 399 TYR 0.010 0.001 TYR B 237 PHE 0.017 0.001 PHE B 111 TRP 0.005 0.001 TRP A 472 HIS 0.003 0.000 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00289 (10662) covalent geometry : angle 0.53554 (14494) hydrogen bonds : bond 0.03591 ( 650) hydrogen bonds : angle 4.09177 ( 1908) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.398 Fit side-chains REVERT: A 83 ASP cc_start: 0.7535 (m-30) cc_final: 0.7303 (m-30) REVERT: A 453 MET cc_start: 0.8777 (mmp) cc_final: 0.8538 (mmp) REVERT: A 548 ASN cc_start: 0.8385 (t0) cc_final: 0.7788 (t0) REVERT: B 83 ASP cc_start: 0.7512 (m-30) cc_final: 0.7249 (m-30) REVERT: B 180 MET cc_start: 0.7529 (mmp) cc_final: 0.6958 (mmp) REVERT: B 251 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7490 (mp) REVERT: B 548 ASN cc_start: 0.8337 (t0) cc_final: 0.7739 (t0) outliers start: 19 outliers final: 14 residues processed: 138 average time/residue: 0.0842 time to fit residues: 18.0003 Evaluate side-chains 139 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain B residue 76 PHE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 639 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 23 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 99 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.150305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.120604 restraints weight = 13185.808| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.35 r_work: 0.2925 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10662 Z= 0.129 Angle : 0.534 7.217 14494 Z= 0.276 Chirality : 0.042 0.141 1722 Planarity : 0.004 0.047 1806 Dihedral : 4.178 19.360 1444 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.01 % Allowed : 13.18 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.24), residues: 1342 helix: 1.83 (0.18), residues: 870 sheet: 1.44 (0.85), residues: 36 loop : -1.42 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 399 TYR 0.008 0.001 TYR A 508 PHE 0.016 0.001 PHE B 111 TRP 0.005 0.001 TRP A 472 HIS 0.002 0.000 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00302 (10662) covalent geometry : angle 0.53399 (14494) hydrogen bonds : bond 0.03603 ( 650) hydrogen bonds : angle 4.07734 ( 1908) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.384 Fit side-chains REVERT: A 83 ASP cc_start: 0.7514 (m-30) cc_final: 0.7291 (m-30) REVERT: A 267 MET cc_start: 0.6579 (mmp) cc_final: 0.6307 (mmm) REVERT: A 548 ASN cc_start: 0.8390 (t0) cc_final: 0.7776 (t0) REVERT: B 83 ASP cc_start: 0.7488 (m-30) cc_final: 0.7187 (m-30) REVERT: B 180 MET cc_start: 0.7572 (mmp) cc_final: 0.7151 (mmp) REVERT: B 251 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7527 (mp) REVERT: B 267 MET cc_start: 0.8307 (tmm) cc_final: 0.8082 (mmp) REVERT: B 299 MET cc_start: 0.7699 (mmt) cc_final: 0.7246 (ptm) REVERT: B 548 ASN cc_start: 0.8404 (t0) cc_final: 0.7800 (t0) outliers start: 23 outliers final: 17 residues processed: 147 average time/residue: 0.0854 time to fit residues: 19.1800 Evaluate side-chains 142 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain B residue 76 PHE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 639 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 45 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.150485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120325 restraints weight = 13131.391| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.36 r_work: 0.2934 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10662 Z= 0.126 Angle : 0.541 7.195 14494 Z= 0.279 Chirality : 0.043 0.149 1722 Planarity : 0.004 0.047 1806 Dihedral : 4.223 19.493 1444 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.83 % Allowed : 13.79 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.24), residues: 1342 helix: 1.83 (0.18), residues: 872 sheet: 1.40 (0.84), residues: 36 loop : -1.45 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 399 TYR 0.037 0.001 TYR B 526 PHE 0.015 0.001 PHE B 111 TRP 0.006 0.001 TRP A 472 HIS 0.002 0.000 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00291 (10662) covalent geometry : angle 0.54055 (14494) hydrogen bonds : bond 0.03558 ( 650) hydrogen bonds : angle 4.07102 ( 1908) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.287 Fit side-chains REVERT: A 267 MET cc_start: 0.6648 (mmp) cc_final: 0.6413 (mmm) REVERT: A 453 MET cc_start: 0.8817 (mmp) cc_final: 0.8586 (mmp) REVERT: A 548 ASN cc_start: 0.8392 (t0) cc_final: 0.7790 (t0) REVERT: B 83 ASP cc_start: 0.7461 (m-30) cc_final: 0.7220 (m-30) REVERT: B 180 MET cc_start: 0.7631 (mmp) cc_final: 0.7269 (mmp) REVERT: B 267 MET cc_start: 0.8315 (tmm) cc_final: 0.8090 (mmp) REVERT: B 299 MET cc_start: 0.7632 (mmt) cc_final: 0.7228 (ptm) REVERT: B 548 ASN cc_start: 0.8355 (t0) cc_final: 0.7768 (t0) outliers start: 21 outliers final: 18 residues processed: 143 average time/residue: 0.0809 time to fit residues: 17.6352 Evaluate side-chains 146 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain B residue 76 PHE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 639 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 9 optimal weight: 0.2980 chunk 84 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 102 optimal weight: 0.0870 chunk 62 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.151697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.118521 restraints weight = 13181.846| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.43 r_work: 0.2950 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10662 Z= 0.118 Angle : 0.529 7.173 14494 Z= 0.273 Chirality : 0.042 0.153 1722 Planarity : 0.004 0.048 1806 Dihedral : 4.174 19.581 1444 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.92 % Allowed : 13.87 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.24), residues: 1342 helix: 1.90 (0.18), residues: 870 sheet: 1.39 (0.83), residues: 36 loop : -1.44 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 571 TYR 0.014 0.001 TYR A 526 PHE 0.015 0.001 PHE A 278 TRP 0.007 0.001 TRP A 472 HIS 0.002 0.000 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00271 (10662) covalent geometry : angle 0.52866 (14494) hydrogen bonds : bond 0.03455 ( 650) hydrogen bonds : angle 4.04272 ( 1908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2225.03 seconds wall clock time: 39 minutes 0.57 seconds (2340.57 seconds total)