Starting phenix.real_space_refine on Mon Jul 28 13:45:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s8x_24928/07_2025/7s8x_24928.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s8x_24928/07_2025/7s8x_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_24928/07_2025/7s8x_24928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s8x_24928/07_2025/7s8x_24928.map" model { file = "/net/cci-nas-00/data/ceres_data/7s8x_24928/07_2025/7s8x_24928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s8x_24928/07_2025/7s8x_24928.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.50, per 1000 atoms: 0.62 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: 2.69 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.05 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: 3.45 Time building geometry restraints manager: 3.18 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: 0.05 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: 48.320 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: 0.100 Process input model: 26.910 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.890 ------------------------------------------------------------------------------- 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 (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: 0.01 (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 TRP 0.016 0.002 TRP A 472 HIS 0.003 0.001 HIS A 131 PHE 0.028 0.002 PHE B 111 TYR 0.016 0.002 TYR B 545 ARG 0.010 0.001 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.10780 ( 650) hydrogen bonds : angle 5.53977 ( 1908) covalent geometry : bond 0.00508 (10662) covalent geometry : angle 0.72584 (14494) *********************** 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 : 2.024 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: 0.2098 time to fit residues: 48.5690 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 : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.146010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.113567 restraints weight = 13234.187| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.58 r_work: 0.2838 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10662 Z= 0.196 Angle : 0.639 7.355 14494 Z= 0.335 Chirality : 0.045 0.161 1722 Planarity : 0.005 0.043 1806 Dihedral : 4.764 19.195 1444 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.87 % Allowed : 7.42 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.23), residues: 1342 helix: 1.20 (0.18), residues: 866 sheet: 1.15 (0.88), residues: 36 loop : -1.82 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 70 HIS 0.002 0.001 HIS B 131 PHE 0.024 0.002 PHE B 111 TYR 0.012 0.002 TYR A 16 ARG 0.004 0.001 ARG B 572 Details of bonding type rmsd hydrogen bonds : bond 0.04620 ( 650) hydrogen bonds : angle 4.56118 ( 1908) covalent geometry : bond 0.00470 (10662) covalent geometry : angle 0.63890 (14494) *********************** 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 147 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 1.256 Fit side-chains REVERT: A 83 ASP cc_start: 0.7469 (m-30) cc_final: 0.7095 (m-30) REVERT: A 180 MET cc_start: 0.7489 (mmp) cc_final: 0.7084 (mmm) REVERT: A 267 MET cc_start: 0.8431 (tmm) cc_final: 0.8001 (ttt) REVERT: A 453 MET cc_start: 0.8855 (mmp) cc_final: 0.8596 (mmm) REVERT: A 548 ASN cc_start: 0.8644 (t0) cc_final: 0.8210 (t0) REVERT: B 83 ASP cc_start: 0.7442 (m-30) cc_final: 0.7075 (m-30) REVERT: B 267 MET cc_start: 0.8453 (tmm) cc_final: 0.8070 (ttt) REVERT: B 453 MET cc_start: 0.8877 (mmp) cc_final: 0.8634 (mmm) REVERT: B 548 ASN cc_start: 0.8545 (t0) cc_final: 0.8052 (t0) outliers start: 10 outliers final: 10 residues processed: 138 average time/residue: 0.2045 time to fit residues: 42.6377 Evaluate side-chains 138 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 1.518 ------------------------------------------------------------------------------- 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 A residue 423 LEU Chi-restraints excluded: chain B residue 76 PHE 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 28 optimal weight: 0.0770 chunk 39 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 63 optimal weight: 0.0270 chunk 130 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.149622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.116516 restraints weight = 13347.345| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.62 r_work: 0.2892 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1399 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= 0.128 Angle : 0.558 7.207 14494 Z= 0.294 Chirality : 0.042 0.162 1722 Planarity : 0.005 0.045 1806 Dihedral : 4.475 19.462 1444 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.57 % Allowed : 9.16 % Favored : 89.27 % 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: 0.69 (0.23), residues: 1342 helix: 1.48 (0.18), residues: 866 sheet: 1.10 (0.89), residues: 36 loop : -1.73 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 70 HIS 0.002 0.001 HIS B 704 PHE 0.021 0.001 PHE B 278 TYR 0.008 0.001 TYR B 545 ARG 0.005 0.000 ARG B 572 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 650) hydrogen bonds : angle 4.37146 ( 1908) covalent geometry : bond 0.00277 (10662) covalent geometry : angle 0.55757 (14494) *********************** 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 162 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 1.548 Fit side-chains REVERT: A 83 ASP cc_start: 0.7379 (m-30) cc_final: 0.6996 (m-30) REVERT: A 267 MET cc_start: 0.8337 (tmm) cc_final: 0.8016 (mmp) REVERT: A 548 ASN cc_start: 0.8382 (t0) cc_final: 0.7853 (t0) REVERT: B 58 ARG cc_start: 0.7177 (ptm160) cc_final: 0.6948 (mpt180) REVERT: B 75 ARG cc_start: 0.7416 (mtm-85) cc_final: 0.7121 (mmt90) REVERT: B 83 ASP cc_start: 0.7414 (m-30) cc_final: 0.6993 (m-30) REVERT: B 267 MET cc_start: 0.8375 (tmm) cc_final: 0.8056 (mmp) REVERT: B 299 MET cc_start: 0.7749 (mmt) cc_final: 0.7543 (mmm) REVERT: B 453 MET cc_start: 0.8840 (mmp) cc_final: 0.8568 (mmm) REVERT: B 548 ASN cc_start: 0.8260 (t0) cc_final: 0.7697 (t0) outliers start: 18 outliers final: 12 residues processed: 149 average time/residue: 0.2354 time to fit residues: 54.3702 Evaluate side-chains 139 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 1.340 ------------------------------------------------------------------------------- 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 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 271 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 20 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 118 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.148582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.114206 restraints weight = 13258.801| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.58 r_work: 0.2879 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10662 Z= 0.149 Angle : 0.568 7.304 14494 Z= 0.296 Chirality : 0.043 0.162 1722 Planarity : 0.004 0.045 1806 Dihedral : 4.421 19.234 1444 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.66 % Allowed : 11.52 % 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 (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: 0.80 (0.23), residues: 1342 helix: 1.56 (0.18), residues: 866 sheet: 1.24 (0.90), residues: 36 loop : -1.67 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 70 HIS 0.003 0.001 HIS B 131 PHE 0.022 0.001 PHE A 278 TYR 0.009 0.001 TYR A 367 ARG 0.004 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 650) hydrogen bonds : angle 4.30439 ( 1908) covalent geometry : bond 0.00352 (10662) covalent geometry : angle 0.56792 (14494) *********************** 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 162 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 1.195 Fit side-chains REVERT: A 58 ARG cc_start: 0.7245 (ptm160) cc_final: 0.7020 (mpt180) REVERT: A 83 ASP cc_start: 0.7435 (m-30) cc_final: 0.7094 (m-30) REVERT: A 267 MET cc_start: 0.8274 (tmm) cc_final: 0.8018 (mmp) REVERT: A 548 ASN cc_start: 0.8503 (t0) cc_final: 0.7941 (t0) REVERT: B 58 ARG cc_start: 0.7204 (ptm160) cc_final: 0.6951 (mpt180) REVERT: B 75 ARG cc_start: 0.7301 (mtm-85) cc_final: 0.7067 (mmt90) REVERT: B 83 ASP cc_start: 0.7425 (m-30) cc_final: 0.7023 (m-30) REVERT: B 548 ASN cc_start: 0.8419 (t0) cc_final: 0.7843 (t0) outliers start: 19 outliers final: 16 residues processed: 146 average time/residue: 0.2194 time to fit residues: 48.7287 Evaluate side-chains 149 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.517 ------------------------------------------------------------------------------- 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 521 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 271 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 34 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 650 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.147624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.113264 restraints weight = 13173.929| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.52 r_work: 0.2867 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10662 Z= 0.166 Angle : 0.572 7.376 14494 Z= 0.299 Chirality : 0.044 0.158 1722 Planarity : 0.005 0.046 1806 Dihedral : 4.431 18.967 1444 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.79 % Allowed : 11.61 % Favored : 85.60 % 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: 0.87 (0.24), residues: 1342 helix: 1.57 (0.18), residues: 868 sheet: 1.45 (0.92), residues: 36 loop : -1.58 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 472 HIS 0.003 0.001 HIS B 131 PHE 0.020 0.001 PHE A 278 TYR 0.009 0.001 TYR A 508 ARG 0.002 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.04028 ( 650) hydrogen bonds : angle 4.28189 ( 1908) covalent geometry : bond 0.00400 (10662) covalent geometry : angle 0.57162 (14494) *********************** 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 173 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 1.098 Fit side-chains REVERT: A 20 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8508 (ptt90) REVERT: A 58 ARG cc_start: 0.7262 (ptm160) cc_final: 0.7039 (mpt180) REVERT: A 75 ARG cc_start: 0.7421 (mtm-85) cc_final: 0.7076 (mmt90) REVERT: A 83 ASP cc_start: 0.7541 (m-30) cc_final: 0.7227 (m-30) REVERT: A 548 ASN cc_start: 0.8566 (t0) cc_final: 0.7972 (t0) REVERT: B 83 ASP cc_start: 0.7427 (m-30) cc_final: 0.7021 (m-30) REVERT: B 548 ASN cc_start: 0.8527 (t0) cc_final: 0.7945 (t0) outliers start: 32 outliers final: 18 residues processed: 156 average time/residue: 0.1844 time to fit residues: 43.7767 Evaluate side-chains 152 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG 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 A residue 390 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 639 VAL 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 334 SER 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 Chi-restraints excluded: chain B residue 670 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 33 optimal weight: 0.7980 chunk 15 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.148708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.114935 restraints weight = 13331.496| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.65 r_work: 0.2875 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1929 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= 0.138 Angle : 0.558 7.339 14494 Z= 0.291 Chirality : 0.043 0.165 1722 Planarity : 0.004 0.045 1806 Dihedral : 4.389 19.317 1444 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.62 % Allowed : 12.48 % Favored : 84.90 % 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: 0.97 (0.24), residues: 1342 helix: 1.65 (0.18), residues: 866 sheet: 1.49 (0.90), residues: 36 loop : -1.54 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 70 HIS 0.002 0.001 HIS A 131 PHE 0.018 0.001 PHE A 278 TYR 0.010 0.001 TYR B 367 ARG 0.002 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 650) hydrogen bonds : angle 4.23598 ( 1908) covalent geometry : bond 0.00322 (10662) covalent geometry : angle 0.55802 (14494) *********************** 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 165 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 1.188 Fit side-chains REVERT: A 83 ASP cc_start: 0.7465 (m-30) cc_final: 0.7175 (m-30) REVERT: A 548 ASN cc_start: 0.8468 (t0) cc_final: 0.7892 (t0) REVERT: B 83 ASP cc_start: 0.7529 (m-30) cc_final: 0.7154 (m-30) REVERT: B 267 MET cc_start: 0.6507 (mmp) cc_final: 0.6209 (mmm) REVERT: B 548 ASN cc_start: 0.8413 (t0) cc_final: 0.7830 (t0) outliers start: 30 outliers final: 21 residues processed: 149 average time/residue: 0.2095 time to fit residues: 47.7793 Evaluate side-chains 156 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 139 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 A residue 521 ILE Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 20 ARG 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 118 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 27 optimal weight: 20.0000 chunk 84 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 76 optimal weight: 0.0060 chunk 54 optimal weight: 0.1980 chunk 98 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- 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 = 0.149395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.115976 restraints weight = 13348.787| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.58 r_work: 0.2888 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2060 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= 0.134 Angle : 0.552 7.343 14494 Z= 0.287 Chirality : 0.043 0.169 1722 Planarity : 0.004 0.045 1806 Dihedral : 4.316 19.424 1444 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.88 % Allowed : 12.04 % Favored : 85.08 % 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: 1.02 (0.24), residues: 1342 helix: 1.73 (0.18), residues: 866 sheet: 1.49 (0.89), residues: 36 loop : -1.60 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 472 HIS 0.002 0.000 HIS B 131 PHE 0.017 0.001 PHE A 278 TYR 0.007 0.001 TYR B 508 ARG 0.002 0.000 ARG A 631 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 650) hydrogen bonds : angle 4.18410 ( 1908) covalent geometry : bond 0.00311 (10662) covalent geometry : angle 0.55152 (14494) *********************** 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 171 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 1.113 Fit side-chains REVERT: A 20 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8489 (ptt90) REVERT: A 83 ASP cc_start: 0.7452 (m-30) cc_final: 0.7182 (m-30) REVERT: A 548 ASN cc_start: 0.8389 (t0) cc_final: 0.7788 (t0) REVERT: B 83 ASP cc_start: 0.7505 (m-30) cc_final: 0.7178 (m-30) REVERT: B 267 MET cc_start: 0.6582 (mmp) cc_final: 0.6354 (mmm) REVERT: B 548 ASN cc_start: 0.8345 (t0) cc_final: 0.7744 (t0) outliers start: 33 outliers final: 22 residues processed: 154 average time/residue: 0.1907 time to fit residues: 44.2126 Evaluate side-chains 154 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 139 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 A residue 521 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 76 PHE Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 243 VAL 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 521 ILE Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 639 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 40 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 67 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.150194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.118048 restraints weight = 13187.896| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.48 r_work: 0.2908 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2216 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= 0.124 Angle : 0.550 11.613 14494 Z= 0.282 Chirality : 0.042 0.164 1722 Planarity : 0.004 0.045 1806 Dihedral : 4.235 19.716 1444 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.62 % Allowed : 12.83 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.24), residues: 1342 helix: 1.78 (0.18), residues: 866 sheet: 1.36 (0.85), residues: 36 loop : -1.54 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 472 HIS 0.002 0.001 HIS A 131 PHE 0.016 0.001 PHE A 278 TYR 0.010 0.001 TYR B 367 ARG 0.002 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 650) hydrogen bonds : angle 4.13006 ( 1908) covalent geometry : bond 0.00284 (10662) covalent geometry : angle 0.55025 (14494) *********************** 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 165 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 1.148 Fit side-chains REVERT: A 20 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8493 (ptt90) REVERT: A 83 ASP cc_start: 0.7469 (m-30) cc_final: 0.7181 (m-30) REVERT: A 267 MET cc_start: 0.6588 (mmp) cc_final: 0.6333 (mmm) REVERT: A 548 ASN cc_start: 0.8318 (t0) cc_final: 0.7699 (t0) REVERT: B 83 ASP cc_start: 0.7345 (m-30) cc_final: 0.7016 (m-30) REVERT: B 180 MET cc_start: 0.7478 (mmp) cc_final: 0.6878 (mmp) REVERT: B 548 ASN cc_start: 0.8290 (t0) cc_final: 0.7678 (t0) outliers start: 30 outliers final: 21 residues processed: 153 average time/residue: 0.2056 time to fit residues: 47.5620 Evaluate side-chains 149 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 243 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 A residue 419 LEU 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 103 MET Chi-restraints excluded: chain B residue 243 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 75 optimal weight: 2.9990 chunk 27 optimal weight: 30.0000 chunk 96 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 0.0370 chunk 119 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN B 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.150727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117333 restraints weight = 13365.025| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.45 r_work: 0.2920 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10662 Z= 0.119 Angle : 0.545 11.941 14494 Z= 0.278 Chirality : 0.042 0.142 1722 Planarity : 0.004 0.045 1806 Dihedral : 4.189 19.490 1444 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.36 % Allowed : 13.35 % Favored : 84.29 % 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: 1.17 (0.24), residues: 1342 helix: 1.80 (0.18), residues: 870 sheet: 1.37 (0.84), residues: 36 loop : -1.46 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 472 HIS 0.003 0.001 HIS A 131 PHE 0.015 0.001 PHE A 278 TYR 0.007 0.001 TYR B 508 ARG 0.006 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 650) hydrogen bonds : angle 4.09921 ( 1908) covalent geometry : bond 0.00272 (10662) covalent geometry : angle 0.54480 (14494) *********************** 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 163 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.119 Fit side-chains REVERT: A 20 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8505 (ptt90) REVERT: A 83 ASP cc_start: 0.7470 (m-30) cc_final: 0.7214 (m-30) REVERT: A 267 MET cc_start: 0.6682 (mmp) cc_final: 0.6458 (mmm) REVERT: A 548 ASN cc_start: 0.8270 (t0) cc_final: 0.7647 (t0) REVERT: B 20 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8287 (tmm160) REVERT: B 83 ASP cc_start: 0.7432 (m-30) cc_final: 0.7123 (m-30) REVERT: B 180 MET cc_start: 0.7570 (mmp) cc_final: 0.7096 (mmp) REVERT: B 299 MET cc_start: 0.7686 (mmt) cc_final: 0.7225 (ptm) REVERT: B 548 ASN cc_start: 0.8206 (t0) cc_final: 0.7709 (t0) outliers start: 27 outliers final: 18 residues processed: 151 average time/residue: 0.1989 time to fit residues: 44.7185 Evaluate side-chains 146 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 419 LEU 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 20 ARG Chi-restraints excluded: chain B residue 76 PHE 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 88 optimal weight: 0.0970 chunk 55 optimal weight: 0.6980 chunk 98 optimal weight: 8.9990 chunk 31 optimal weight: 0.0870 chunk 115 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 0.0170 chunk 37 optimal weight: 2.9990 overall best weight: 0.3194 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.152314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.118826 restraints weight = 13164.053| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.33 r_work: 0.2963 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 10662 Z= 0.111 Angle : 0.540 12.420 14494 Z= 0.274 Chirality : 0.042 0.146 1722 Planarity : 0.004 0.046 1806 Dihedral : 4.147 20.066 1444 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.92 % Allowed : 14.22 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.24), residues: 1342 helix: 1.93 (0.18), residues: 866 sheet: 1.32 (0.83), residues: 36 loop : -1.52 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 472 HIS 0.002 0.001 HIS B 33 PHE 0.016 0.001 PHE A 278 TYR 0.011 0.001 TYR B 367 ARG 0.004 0.000 ARG B 31 Details of bonding type rmsd hydrogen bonds : bond 0.03406 ( 650) hydrogen bonds : angle 4.04883 ( 1908) covalent geometry : bond 0.00248 (10662) covalent geometry : angle 0.53977 (14494) ********************** 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 158 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.355 Fit side-chains REVERT: A 314 ASN cc_start: 0.8480 (t0) cc_final: 0.8172 (t0) REVERT: A 548 ASN cc_start: 0.8107 (t0) cc_final: 0.7607 (t0) REVERT: B 20 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8296 (tmm160) REVERT: B 180 MET cc_start: 0.7576 (mmp) cc_final: 0.7208 (mmp) REVERT: B 299 MET cc_start: 0.7683 (mmt) cc_final: 0.7298 (ptm) REVERT: B 548 ASN cc_start: 0.8079 (t0) cc_final: 0.7577 (t0) outliers start: 22 outliers final: 17 residues processed: 151 average time/residue: 0.2052 time to fit residues: 46.1579 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 : 1.357 ------------------------------------------------------------------------------- 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 139 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 76 PHE 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 55 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 58 optimal weight: 0.0970 chunk 122 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN A 650 ASN B 258 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.151180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.119273 restraints weight = 13099.644| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.50 r_work: 0.2933 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2530 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= 0.125 Angle : 0.552 12.182 14494 Z= 0.280 Chirality : 0.043 0.157 1722 Planarity : 0.004 0.045 1806 Dihedral : 4.150 19.328 1444 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.18 % Allowed : 13.96 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.24), residues: 1342 helix: 1.90 (0.18), residues: 868 sheet: 1.38 (0.83), residues: 36 loop : -1.48 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 472 HIS 0.002 0.000 HIS A 131 PHE 0.016 0.001 PHE B 111 TYR 0.013 0.001 TYR A 526 ARG 0.003 0.000 ARG B 399 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 650) hydrogen bonds : angle 4.05547 ( 1908) covalent geometry : bond 0.00292 (10662) covalent geometry : angle 0.55173 (14494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5059.91 seconds wall clock time: 90 minutes 28.84 seconds (5428.84 seconds total)