Starting phenix.real_space_refine on Thu Aug 6 13:00:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s3m_54540/08_2026/9s3m_54540.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s3m_54540/08_2026/9s3m_54540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9s3m_54540/08_2026/9s3m_54540.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s3m_54540/08_2026/9s3m_54540.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9s3m_54540/08_2026/9s3m_54540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s3m_54540/08_2026/9s3m_54540.map" } resolution = 2.31 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= 0.012 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: 5 Type Number sf(0) Gaussians S 41 5.16 5 C 4641 2.51 5 N 1275 2.21 5 O 1405 1.98 5 H 7374 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14736 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6339 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 384} Chain: "B" Number of atoms: 6377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6377 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 384} Chain: "C" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2020 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 4, 'TRANS': 130} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 2.99, per 1000 atoms: 0.20 Number of scatterers: 14736 At special positions: 0 Unit cell: (70.2625, 93.9875, 135.963, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 41 16.00 O 1405 8.00 N 1275 7.00 C 4641 6.00 H 7374 1.00 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: 1.44 Conformation dependent library (CDL) restraints added in 552.4 milliseconds 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1764 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 17 sheets defined 28.3% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 478 through 489 Processing helix chain 'A' and resid 525 through 537 Processing helix chain 'A' and resid 550 through 565 Processing helix chain 'A' and resid 580 through 589 Processing helix chain 'A' and resid 601 through 605 removed outlier: 4.228A pdb=" N LEU A 605 " --> pdb=" O LYS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 removed outlier: 3.598A pdb=" N VAL A 632 " --> pdb=" O PRO A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 647 Processing helix chain 'B' and resid 325 through 337 Processing helix chain 'B' and resid 348 through 350 No H-bonds generated for 'chain 'B' and resid 348 through 350' Processing helix chain 'B' and resid 478 through 489 Processing helix chain 'B' and resid 525 through 537 removed outlier: 3.539A pdb=" N HIS B 537 " --> pdb=" O THR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 565 Processing helix chain 'B' and resid 580 through 589 Processing helix chain 'B' and resid 627 through 638 Processing helix chain 'B' and resid 638 through 647 Processing helix chain 'C' and resid 51 through 60 Processing helix chain 'C' and resid 61 through 72 Processing helix chain 'C' and resid 84 through 93 Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 117 through 126 Processing helix chain 'C' and resid 127 through 137 removed outlier: 3.723A pdb=" N GLU C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 133 " --> pdb=" O GLU C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 159 Processing helix chain 'C' and resid 160 through 175 Processing sheet with id=AA1, first strand: chain 'A' and resid 323 through 324 removed outlier: 6.619A pdb=" N ARG A 598 " --> pdb=" O THR A 324 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 342 through 346 Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 360 removed outlier: 3.610A pdb=" N LEU A 471 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 371 Processing sheet with id=AA5, first strand: chain 'A' and resid 423 through 426 removed outlier: 3.534A pdb=" N MET A 409 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ARG A 410 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU A 392 " --> pdb=" O ARG A 410 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU A 443 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU A 442 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLU A 435 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLU A 444 " --> pdb=" O ILE A 433 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 541 through 547 removed outlier: 6.502A pdb=" N VAL A 501 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU A 544 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL A 503 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE A 546 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N SER A 505 " --> pdb=" O ILE A 546 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE A 568 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU A 624 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR A 570 " --> pdb=" O LEU A 624 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE A 609 " --> pdb=" O HIS A 595 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 510 through 511 Processing sheet with id=AA8, first strand: chain 'A' and resid 656 through 661 removed outlier: 7.464A pdb=" N ALA A 689 " --> pdb=" O LYS A 658 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ARG A 660 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N SER A 691 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG A 675 " --> pdb=" O THR A 692 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 672 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP A 729 " --> pdb=" O MET A 711 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 665 through 666 Processing sheet with id=AB1, first strand: chain 'B' and resid 323 through 324 Processing sheet with id=AB2, first strand: chain 'B' and resid 342 through 346 Processing sheet with id=AB3, first strand: chain 'B' and resid 359 through 360 removed outlier: 3.542A pdb=" N LEU B 471 " --> pdb=" O VAL B 359 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 370 through 371 Processing sheet with id=AB5, first strand: chain 'B' and resid 423 through 426 removed outlier: 4.022A pdb=" N MET B 409 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL B 408 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY B 391 " --> pdb=" O VAL B 408 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU B 443 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLU B 442 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLU B 435 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLU B 444 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 433 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 541 through 547 removed outlier: 10.853A pdb=" N VAL B 501 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 9.693A pdb=" N GLY B 545 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N VAL B 503 " --> pdb=" O GLY B 545 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N VAL B 547 " --> pdb=" O VAL B 503 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER B 505 " --> pdb=" O VAL B 547 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ALA B 502 " --> pdb=" O ILE B 569 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N SER B 571 " --> pdb=" O ALA B 502 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N MET B 504 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE B 568 " --> pdb=" O PHE B 622 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU B 624 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR B 570 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHE B 609 " --> pdb=" O HIS B 595 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 510 through 511 Processing sheet with id=AB8, first strand: chain 'B' and resid 656 through 661 removed outlier: 7.492A pdb=" N ALA B 689 " --> pdb=" O LYS B 658 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG B 660 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N SER B 691 " --> pdb=" O ARG B 660 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG B 675 " --> pdb=" O THR B 692 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASP B 729 " --> pdb=" O MET B 711 " (cutoff:3.500A) 280 hydrogen bonds defined for protein. 774 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: 3.94 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7364 1.03 - 1.23: 12 1.23 - 1.42: 2934 1.42 - 1.62: 4492 1.62 - 1.81: 72 Bond restraints: 14874 Sorted by residual: bond pdb=" C MET A 711 " pdb=" N LEU A 712 " ideal model delta sigma weight residual 1.331 1.289 0.042 2.07e-02 2.33e+03 4.20e+00 bond pdb=" CG ARG B 452 " pdb=" CD ARG B 452 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.57e+00 bond pdb=" C ALA A 623 " pdb=" N LEU A 624 " ideal model delta sigma weight residual 1.331 1.307 0.023 1.48e-02 4.57e+03 2.51e+00 bond pdb=" CB GLU C 63 " pdb=" CG GLU C 63 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.54e+00 bond pdb=" CB LYS B 666 " pdb=" CG LYS B 666 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.28e+00 ... (remaining 14869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.15: 27042 7.15 - 14.30: 6 14.30 - 21.44: 0 21.44 - 28.59: 0 28.59 - 35.74: 3 Bond angle restraints: 27051 Sorted by residual: angle pdb=" C HIS B 682 " pdb=" CA HIS B 682 " pdb=" HA HIS B 682 " ideal model delta sigma weight residual 109.00 73.26 35.74 3.00e+00 1.11e-01 1.42e+02 angle pdb=" CB HIS B 682 " pdb=" CA HIS B 682 " pdb=" HA HIS B 682 " ideal model delta sigma weight residual 109.00 74.89 34.11 3.00e+00 1.11e-01 1.29e+02 angle pdb=" N HIS B 682 " pdb=" CA HIS B 682 " pdb=" HA HIS B 682 " ideal model delta sigma weight residual 110.00 76.80 33.20 3.00e+00 1.11e-01 1.22e+02 angle pdb=" CG ARG B 452 " pdb=" CD ARG B 452 " pdb=" NE ARG B 452 " ideal model delta sigma weight residual 112.00 125.69 -13.69 2.20e+00 2.07e-01 3.87e+01 angle pdb=" CB LYS B 666 " pdb=" CG LYS B 666 " pdb=" CD LYS B 666 " ideal model delta sigma weight residual 111.30 120.68 -9.38 2.30e+00 1.89e-01 1.66e+01 ... (remaining 27046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.27: 6039 16.27 - 32.53: 666 32.53 - 48.80: 187 48.80 - 65.06: 96 65.06 - 81.33: 12 Dihedral angle restraints: 7000 sinusoidal: 3947 harmonic: 3053 Sorted by residual: dihedral pdb=" C HIS B 682 " pdb=" N HIS B 682 " pdb=" CA HIS B 682 " pdb=" CB HIS B 682 " ideal model delta harmonic sigma weight residual -122.60 -132.70 10.10 0 2.50e+00 1.60e-01 1.63e+01 dihedral pdb=" CG ARG B 466 " pdb=" CD ARG B 466 " pdb=" NE ARG B 466 " pdb=" CZ ARG B 466 " ideal model delta sinusoidal sigma weight residual -90.00 -45.03 -44.97 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CA ASP C 162 " pdb=" CB ASP C 162 " pdb=" CG ASP C 162 " pdb=" OD1 ASP C 162 " ideal model delta sinusoidal sigma weight residual -30.00 -82.99 52.99 1 2.00e+01 2.50e-03 9.55e+00 ... (remaining 6997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1056 0.071 - 0.143: 135 0.143 - 0.214: 1 0.214 - 0.286: 0 0.286 - 0.357: 1 Chirality restraints: 1193 Sorted by residual: chirality pdb=" CA HIS B 682 " pdb=" N HIS B 682 " pdb=" C HIS B 682 " pdb=" CB HIS B 682 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA ILE B 417 " pdb=" N ILE B 417 " pdb=" C ILE B 417 " pdb=" CB ILE B 417 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CG LEU C 95 " pdb=" CB LEU C 95 " pdb=" CD1 LEU C 95 " pdb=" CD2 LEU C 95 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 1190 not shown) Planarity restraints: 2244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 452 " 0.377 9.50e-02 1.11e+02 1.26e-01 1.73e+01 pdb=" NE ARG B 452 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG B 452 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 452 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 452 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG B 452 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 452 " -0.002 2.00e-02 2.50e+03 pdb="HH21 ARG B 452 " 0.005 2.00e-02 2.50e+03 pdb="HH22 ARG B 452 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 452 " 0.282 9.50e-02 1.11e+02 9.42e-02 1.01e+01 pdb=" NE ARG A 452 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 452 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 452 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 452 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG A 452 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 452 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 452 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 452 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 365 " 0.029 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO B 366 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 366 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 366 " 0.022 5.00e-02 4.00e+02 ... (remaining 2241 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1575 2.23 - 2.83: 33486 2.83 - 3.42: 40037 3.42 - 4.01: 55951 4.01 - 4.60: 84013 Nonbonded interactions: 215062 Sorted by model distance: nonbonded pdb=" HA HIS B 682 " pdb=" HB3 HIS B 682 " model vdw 1.642 1.952 nonbonded pdb=" H HIS B 682 " pdb=" HA HIS B 682 " model vdw 1.753 1.816 nonbonded pdb=" HB3 LYS B 328 " pdb=" HZ1 LYS B 328 " model vdw 1.753 2.270 nonbonded pdb=" HB2 LYS B 579 " pdb=" HZ3 LYS B 579 " model vdw 1.769 2.270 nonbonded pdb=" CD ARG A 699 " pdb=" HE3 MET A 701 " model vdw 1.835 2.920 ... (remaining 215057 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and ((resid 321 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (re \ sid 322 and (name N or name CA or name C or name O or name CB or name CG or name \ CD )) or (resid 323 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD1 or name CD2)) or resid 324 through 669 or (resid 670 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name NE or \ name CZ or name NH1 or name NH2 or name H or name HA )) or resid 671 through 73 \ 6)) } 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=0.00 max=1.00 mean=0.99 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: 1.640 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: 0.110 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.530 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:8.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7500 Z= 0.161 Angle : 0.699 13.692 10205 Z= 0.358 Chirality : 0.044 0.357 1193 Planarity : 0.007 0.165 1347 Dihedral : 15.998 79.606 2816 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.86 % Allowed : 21.11 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.11 (0.27), residues: 961 helix: 0.89 (0.33), residues: 254 sheet: -0.29 (0.37), residues: 170 loop : -0.10 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 452 TYR 0.011 0.001 TYR C 125 PHE 0.010 0.001 PHE A 368 TRP 0.007 0.001 TRP A 680 HIS 0.012 0.001 HIS B 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 7500) covalent geometry : angle 0.69949 / 0.36 (10205) hydrogen bonds : bond 0.20592 / 13.87 ( 280) hydrogen bonds : angle 8.54041 / 6.01 ( 774) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 TYR cc_start: 0.8248 (m-80) cc_final: 0.7753 (m-80) REVERT: A 410 ARG cc_start: 0.8044 (ttm110) cc_final: 0.7675 (ttm110) REVERT: A 601 MET cc_start: 0.8117 (ptm) cc_final: 0.7617 (ptt) REVERT: B 394 GLN cc_start: 0.8485 (mt0) cc_final: 0.8097 (mm110) REVERT: B 401 GLN cc_start: 0.8638 (pt0) cc_final: 0.7898 (pp30) REVERT: B 601 MET cc_start: 0.7405 (ptm) cc_final: 0.7057 (ptm) REVERT: B 684 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8404 (mp0) REVERT: C 128 LEU cc_start: 0.8439 (tp) cc_final: 0.8172 (mp) REVERT: C 129 GLU cc_start: 0.7909 (pt0) cc_final: 0.7636 (mp0) outliers start: 7 outliers final: 4 residues processed: 110 average time/residue: 0.8927 time to fit residues: 104.4889 Evaluate side-chains 104 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 91 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.111027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.071763 restraints weight = 35489.082| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.86 r_work: 0.2887 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7500 Z= 0.152 Angle : 0.587 6.582 10205 Z= 0.293 Chirality : 0.045 0.383 1193 Planarity : 0.005 0.036 1347 Dihedral : 5.178 59.370 1043 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.10 % Allowed : 18.89 % Favored : 79.01 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 3.03 % 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: 0.59 (0.27), residues: 961 helix: 1.82 (0.32), residues: 256 sheet: -0.35 (0.40), residues: 150 loop : -0.00 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 452 TYR 0.010 0.001 TYR C 91 PHE 0.008 0.001 PHE A 368 TRP 0.005 0.001 TRP C 58 HIS 0.009 0.001 HIS B 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 7500) covalent geometry : angle 0.58749 / 0.29 (10205) hydrogen bonds : bond 0.04688 / 3.06 ( 280) hydrogen bonds : angle 5.83672 / 4.02 ( 774) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 TYR cc_start: 0.8325 (m-80) cc_final: 0.7826 (m-80) REVERT: A 410 ARG cc_start: 0.7981 (ttm110) cc_final: 0.7502 (ttm110) REVERT: A 601 MET cc_start: 0.7705 (ptm) cc_final: 0.7107 (ptt) REVERT: A 720 VAL cc_start: 0.8811 (t) cc_final: 0.8561 (t) REVERT: B 394 GLN cc_start: 0.8511 (mt0) cc_final: 0.8104 (mm110) REVERT: B 401 GLN cc_start: 0.8600 (pt0) cc_final: 0.7929 (pp30) REVERT: B 684 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8166 (mp0) REVERT: C 107 ASP cc_start: 0.8601 (t0) cc_final: 0.8261 (t0) REVERT: C 129 GLU cc_start: 0.8161 (pt0) cc_final: 0.7642 (mp0) outliers start: 17 outliers final: 7 residues processed: 117 average time/residue: 0.8487 time to fit residues: 106.3357 Evaluate side-chains 104 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 77 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 80 optimal weight: 0.3980 chunk 72 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.111475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.072343 restraints weight = 35885.018| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.89 r_work: 0.2912 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7500 Z= 0.117 Angle : 0.555 6.547 10205 Z= 0.273 Chirality : 0.044 0.381 1193 Planarity : 0.004 0.034 1347 Dihedral : 5.027 59.628 1041 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.35 % Allowed : 17.90 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.90 (0.27), residues: 961 helix: 2.32 (0.33), residues: 260 sheet: -0.11 (0.45), residues: 130 loop : 0.01 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 598 TYR 0.009 0.001 TYR C 91 PHE 0.006 0.001 PHE B 368 TRP 0.005 0.001 TRP C 58 HIS 0.008 0.001 HIS B 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 7500) covalent geometry : angle 0.55469 / 0.27 (10205) hydrogen bonds : bond 0.03898 / 2.57 ( 280) hydrogen bonds : angle 5.39508 / 3.71 ( 774) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 TYR cc_start: 0.8368 (m-80) cc_final: 0.7925 (m-80) REVERT: A 410 ARG cc_start: 0.7919 (ttm110) cc_final: 0.7507 (ttm110) REVERT: A 601 MET cc_start: 0.7710 (ptm) cc_final: 0.6987 (ptt) REVERT: B 394 GLN cc_start: 0.8529 (mt0) cc_final: 0.8129 (mm-40) REVERT: B 401 GLN cc_start: 0.8579 (pt0) cc_final: 0.7970 (pp30) REVERT: B 684 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8132 (mp0) REVERT: C 132 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8093 (mp0) REVERT: C 136 LYS cc_start: 0.9100 (mttt) cc_final: 0.8851 (mttm) REVERT: C 165 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7647 (mm-30) outliers start: 19 outliers final: 10 residues processed: 111 average time/residue: 0.8596 time to fit residues: 102.2043 Evaluate side-chains 108 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 132 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 61 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.110753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.071139 restraints weight = 35840.064| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.90 r_work: 0.2890 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7500 Z= 0.182 Angle : 0.566 6.955 10205 Z= 0.279 Chirality : 0.045 0.386 1193 Planarity : 0.004 0.035 1347 Dihedral : 5.121 59.554 1041 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.35 % Allowed : 17.65 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.84 (0.27), residues: 961 helix: 2.42 (0.32), residues: 260 sheet: -0.31 (0.41), residues: 150 loop : -0.05 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 598 TYR 0.010 0.001 TYR C 91 PHE 0.008 0.001 PHE A 368 TRP 0.004 0.001 TRP C 58 HIS 0.007 0.001 HIS B 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 ( 7500) covalent geometry : angle 0.56638 / 0.28 (10205) hydrogen bonds : bond 0.03828 / 2.52 ( 280) hydrogen bonds : angle 5.20634 / 3.57 ( 774) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.7802 (mpp) cc_final: 0.7570 (mpp) REVERT: A 376 TYR cc_start: 0.8399 (m-80) cc_final: 0.7991 (m-80) REVERT: A 410 ARG cc_start: 0.7889 (ttm110) cc_final: 0.7497 (ttm110) REVERT: A 601 MET cc_start: 0.7526 (ptm) cc_final: 0.7326 (ptt) REVERT: B 394 GLN cc_start: 0.8489 (mt0) cc_final: 0.8089 (mm-40) REVERT: B 401 GLN cc_start: 0.8582 (pt0) cc_final: 0.7970 (pp30) REVERT: B 684 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: C 132 GLU cc_start: 0.8399 (mp0) cc_final: 0.8037 (mp0) REVERT: C 165 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7657 (mm-30) outliers start: 19 outliers final: 11 residues processed: 109 average time/residue: 0.9971 time to fit residues: 116.0087 Evaluate side-chains 106 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 91 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.111156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.071852 restraints weight = 35767.191| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.88 r_work: 0.2896 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7500 Z= 0.132 Angle : 0.548 7.106 10205 Z= 0.267 Chirality : 0.044 0.384 1193 Planarity : 0.004 0.035 1347 Dihedral : 5.073 59.518 1041 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.59 % Allowed : 17.41 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.91 (0.27), residues: 961 helix: 2.59 (0.33), residues: 260 sheet: -0.42 (0.38), residues: 174 loop : 0.02 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 598 TYR 0.010 0.001 TYR C 91 PHE 0.007 0.001 PHE C 113 TRP 0.004 0.001 TRP C 58 HIS 0.006 0.001 HIS B 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 7500) covalent geometry : angle 0.54831 / 0.27 (10205) hydrogen bonds : bond 0.03393 / 2.21 ( 280) hydrogen bonds : angle 5.00377 / 3.43 ( 774) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.7783 (mpp) cc_final: 0.7504 (mpp) REVERT: A 376 TYR cc_start: 0.8404 (m-80) cc_final: 0.7878 (m-80) REVERT: A 452 ARG cc_start: 0.8467 (ttp80) cc_final: 0.8208 (ttp80) REVERT: A 601 MET cc_start: 0.7521 (ptm) cc_final: 0.7304 (ptt) REVERT: B 394 GLN cc_start: 0.8525 (mt0) cc_final: 0.8111 (mm110) REVERT: B 401 GLN cc_start: 0.8578 (pt0) cc_final: 0.7969 (pp30) REVERT: B 684 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: C 132 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8082 (mp0) outliers start: 21 outliers final: 11 residues processed: 108 average time/residue: 0.8904 time to fit residues: 103.3097 Evaluate side-chains 108 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 132 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 15 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 81 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 694 ASN C 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.111457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.072324 restraints weight = 35835.679| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.89 r_work: 0.2902 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7500 Z= 0.114 Angle : 0.542 7.383 10205 Z= 0.264 Chirality : 0.044 0.380 1193 Planarity : 0.004 0.035 1347 Dihedral : 4.956 59.829 1040 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.10 % Allowed : 17.78 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.27), residues: 961 helix: 2.67 (0.33), residues: 260 sheet: 0.21 (0.48), residues: 106 loop : 0.03 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 598 TYR 0.009 0.001 TYR C 91 PHE 0.007 0.001 PHE A 388 TRP 0.004 0.001 TRP C 58 HIS 0.005 0.001 HIS B 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.11 ( 7500) covalent geometry : angle 0.54189 / 0.26 (10205) hydrogen bonds : bond 0.03157 / 2.06 ( 280) hydrogen bonds : angle 4.86217 / 3.34 ( 774) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.7805 (mpp) cc_final: 0.7545 (mpp) REVERT: A 376 TYR cc_start: 0.8288 (m-80) cc_final: 0.8039 (m-80) REVERT: A 452 ARG cc_start: 0.8500 (ttp80) cc_final: 0.8271 (ttp80) REVERT: A 601 MET cc_start: 0.7495 (ptm) cc_final: 0.7287 (ptt) REVERT: B 394 GLN cc_start: 0.8525 (mt0) cc_final: 0.8125 (mm-40) REVERT: B 401 GLN cc_start: 0.8588 (pt0) cc_final: 0.7969 (pp30) REVERT: B 684 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8057 (mp0) REVERT: C 132 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8032 (mp0) REVERT: C 136 LYS cc_start: 0.9084 (mttt) cc_final: 0.8795 (mttm) outliers start: 17 outliers final: 6 residues processed: 107 average time/residue: 1.1215 time to fit residues: 128.5487 Evaluate side-chains 103 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 132 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 0.0770 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.110514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.070827 restraints weight = 35857.503| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.90 r_work: 0.2889 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7500 Z= 0.195 Angle : 0.580 8.683 10205 Z= 0.284 Chirality : 0.045 0.387 1193 Planarity : 0.005 0.076 1347 Dihedral : 4.724 59.692 1037 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.35 % Allowed : 17.78 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.01 (0.27), residues: 961 helix: 2.56 (0.32), residues: 260 sheet: 0.12 (0.48), residues: 106 loop : -0.04 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 410 TYR 0.016 0.001 TYR C 124 PHE 0.009 0.001 PHE A 368 TRP 0.004 0.001 TRP C 58 HIS 0.005 0.001 HIS B 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 ( 7500) covalent geometry : angle 0.57989 / 0.28 (10205) hydrogen bonds : bond 0.03546 / 2.32 ( 280) hydrogen bonds : angle 4.90941 / 3.37 ( 774) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.7825 (mpp) cc_final: 0.7524 (mpp) REVERT: A 373 LYS cc_start: 0.8830 (ptmt) cc_final: 0.8474 (pmtt) REVERT: A 376 TYR cc_start: 0.8409 (m-80) cc_final: 0.8182 (m-80) REVERT: A 410 ARG cc_start: 0.8207 (mtp-110) cc_final: 0.7935 (mtp85) REVERT: A 682 HIS cc_start: 0.8200 (t70) cc_final: 0.7993 (t70) REVERT: B 394 GLN cc_start: 0.8516 (mt0) cc_final: 0.8110 (mm-40) REVERT: B 401 GLN cc_start: 0.8593 (pt0) cc_final: 0.7970 (pp30) REVERT: C 66 GLU cc_start: 0.9270 (mm-30) cc_final: 0.8929 (tp30) REVERT: C 132 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8069 (mp0) REVERT: C 136 LYS cc_start: 0.9108 (mttt) cc_final: 0.8829 (mttm) REVERT: C 161 GLU cc_start: 0.7931 (pm20) cc_final: 0.7725 (pm20) outliers start: 19 outliers final: 12 residues processed: 112 average time/residue: 1.0456 time to fit residues: 125.9145 Evaluate side-chains 108 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 721 GLU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 132 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 74 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.111426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.071907 restraints weight = 35764.453| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.89 r_work: 0.2914 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7500 Z= 0.128 Angle : 0.565 8.979 10205 Z= 0.275 Chirality : 0.044 0.381 1193 Planarity : 0.004 0.058 1347 Dihedral : 4.670 59.720 1037 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.73 % Allowed : 18.27 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.08 (0.27), residues: 961 helix: 2.61 (0.33), residues: 260 sheet: 0.21 (0.48), residues: 106 loop : -0.01 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 410 TYR 0.010 0.001 TYR C 91 PHE 0.007 0.001 PHE B 368 TRP 0.004 0.001 TRP C 58 HIS 0.005 0.001 HIS B 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 7500) covalent geometry : angle 0.56507 / 0.27 (10205) hydrogen bonds : bond 0.03201 / 2.09 ( 280) hydrogen bonds : angle 4.81013 / 3.30 ( 774) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 LYS cc_start: 0.8858 (ptmt) cc_final: 0.8519 (pmtt) REVERT: A 376 TYR cc_start: 0.8374 (m-80) cc_final: 0.8146 (m-80) REVERT: A 410 ARG cc_start: 0.8198 (mtp-110) cc_final: 0.7888 (mtp85) REVERT: B 394 GLN cc_start: 0.8530 (mt0) cc_final: 0.8121 (mm-40) REVERT: B 401 GLN cc_start: 0.8595 (pt0) cc_final: 0.7992 (pp30) REVERT: B 684 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8057 (mp0) REVERT: C 63 GLU cc_start: 0.9223 (pm20) cc_final: 0.8970 (pm20) REVERT: C 66 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8938 (tp30) REVERT: C 132 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: C 136 LYS cc_start: 0.9105 (mttt) cc_final: 0.8822 (mttm) REVERT: C 161 GLU cc_start: 0.7882 (pm20) cc_final: 0.7673 (pm20) REVERT: C 165 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7604 (mm-30) outliers start: 14 outliers final: 10 residues processed: 107 average time/residue: 1.0692 time to fit residues: 122.4348 Evaluate side-chains 110 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 721 GLU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 132 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 35 optimal weight: 0.9990 chunk 45 optimal weight: 0.0670 chunk 64 optimal weight: 0.5980 chunk 53 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.111867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.072449 restraints weight = 35876.750| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.87 r_work: 0.2921 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7500 Z= 0.122 Angle : 0.579 9.391 10205 Z= 0.281 Chirality : 0.044 0.380 1193 Planarity : 0.004 0.056 1347 Dihedral : 4.626 59.983 1037 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.73 % Allowed : 18.77 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.12 (0.27), residues: 961 helix: 2.61 (0.33), residues: 260 sheet: 0.23 (0.48), residues: 106 loop : 0.03 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 410 TYR 0.010 0.001 TYR C 91 PHE 0.007 0.001 PHE A 368 TRP 0.004 0.001 TRP C 58 HIS 0.005 0.001 HIS B 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 ( 7500) covalent geometry : angle 0.57880 / 0.28 (10205) hydrogen bonds : bond 0.03113 / 2.03 ( 280) hydrogen bonds : angle 4.72793 / 3.24 ( 774) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.7780 (mpp) cc_final: 0.7365 (mpp) REVERT: A 373 LYS cc_start: 0.8856 (ptmt) cc_final: 0.8513 (pmtt) REVERT: A 376 TYR cc_start: 0.8372 (m-80) cc_final: 0.8144 (m-80) REVERT: A 410 ARG cc_start: 0.8184 (mtp-110) cc_final: 0.7864 (mtp85) REVERT: B 394 GLN cc_start: 0.8526 (mt0) cc_final: 0.8116 (mm-40) REVERT: B 401 GLN cc_start: 0.8593 (pt0) cc_final: 0.7989 (pp30) REVERT: B 684 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8050 (mp0) REVERT: C 66 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8942 (tp30) REVERT: C 132 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8041 (mp0) outliers start: 14 outliers final: 9 residues processed: 108 average time/residue: 0.9730 time to fit residues: 112.2695 Evaluate side-chains 105 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 721 GLU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 132 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.111503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.071809 restraints weight = 35718.546| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.89 r_work: 0.2911 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7500 Z= 0.144 Angle : 0.600 10.334 10205 Z= 0.291 Chirality : 0.044 0.381 1193 Planarity : 0.004 0.053 1347 Dihedral : 4.640 59.919 1037 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.36 % Allowed : 19.63 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.07 (0.27), residues: 961 helix: 2.55 (0.32), residues: 260 sheet: 0.20 (0.48), residues: 106 loop : 0.01 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 410 TYR 0.010 0.001 TYR C 91 PHE 0.008 0.001 PHE A 388 TRP 0.004 0.001 TRP C 58 HIS 0.005 0.001 HIS B 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 ( 7500) covalent geometry : angle 0.59969 / 0.29 (10205) hydrogen bonds : bond 0.03224 / 2.11 ( 280) hydrogen bonds : angle 4.71558 / 3.23 ( 774) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.7804 (mpp) cc_final: 0.7400 (mpp) REVERT: A 373 LYS cc_start: 0.8854 (ptmt) cc_final: 0.8518 (pmtt) REVERT: A 376 TYR cc_start: 0.8359 (m-80) cc_final: 0.8132 (m-80) REVERT: A 410 ARG cc_start: 0.8199 (mtp-110) cc_final: 0.7869 (mtp85) REVERT: A 683 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8304 (mm110) REVERT: B 394 GLN cc_start: 0.8544 (mt0) cc_final: 0.8134 (mm-40) REVERT: B 401 GLN cc_start: 0.8599 (pt0) cc_final: 0.7959 (pp30) REVERT: B 666 LYS cc_start: 0.7046 (mmmt) cc_final: 0.6761 (mmmt) REVERT: B 684 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8065 (mp0) REVERT: C 66 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8941 (tp30) REVERT: C 132 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8019 (mp0) outliers start: 11 outliers final: 9 residues processed: 105 average time/residue: 1.1294 time to fit residues: 126.9005 Evaluate side-chains 104 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 132 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 14 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 30 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.112174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.072645 restraints weight = 35769.321| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.88 r_work: 0.2931 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7500 Z= 0.118 Angle : 0.601 10.300 10205 Z= 0.290 Chirality : 0.044 0.380 1193 Planarity : 0.004 0.051 1347 Dihedral : 4.598 59.870 1037 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.73 % Allowed : 19.38 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.27), residues: 961 helix: 2.57 (0.33), residues: 260 sheet: 0.25 (0.48), residues: 110 loop : 0.07 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 410 TYR 0.009 0.001 TYR C 91 PHE 0.006 0.001 PHE B 368 TRP 0.004 0.001 TRP C 58 HIS 0.005 0.001 HIS B 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 7500) covalent geometry : angle 0.60095 / 0.29 (10205) hydrogen bonds : bond 0.03004 / 1.97 ( 280) hydrogen bonds : angle 4.65100 / 3.19 ( 774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6233.02 seconds wall clock time: 105 minutes 48.83 seconds (6348.83 seconds total)