Starting phenix.real_space_refine on Thu Jul 2 17:08:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x0z_32930/07_2026/7x0z_32930.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x0z_32930/07_2026/7x0z_32930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x0z_32930/07_2026/7x0z_32930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x0z_32930/07_2026/7x0z_32930.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7x0z_32930/07_2026/7x0z_32930.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x0z_32930/07_2026/7x0z_32930.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x0z_32930/07_2026/7x0z_32930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x0z_32930/07_2026/7x0z_32930.map" } resolution = 2.96 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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 5946 2.51 5 N 1638 2.21 5 O 1649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9285 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4597 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 22, 'TRANS': 553} Chain breaks: 2 Chain: "B" Number of atoms: 4624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4624 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 22, 'TRANS': 557} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.95, per 1000 atoms: 0.21 Number of scatterers: 9285 At special positions: 0 Unit cell: (83.83, 78.85, 131.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 6 15.00 Mg 2 11.99 O 1649 8.00 N 1638 7.00 C 5946 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 328.6 milliseconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 4 sheets defined 69.1% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 68 through 83 removed outlier: 3.544A pdb=" N LEU A 72 " --> pdb=" O ASN A 68 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 81 " --> pdb=" O TRP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 124 Processing helix chain 'A' and resid 128 through 175 removed outlier: 3.929A pdb=" N LEU A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Proline residue: A 143 - end of helix Processing helix chain 'A' and resid 178 through 186 removed outlier: 4.040A pdb=" N SER A 184 " --> pdb=" O TYR A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 236 removed outlier: 4.049A pdb=" N ASP A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N VAL A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Proline residue: A 218 - end of helix removed outlier: 3.743A pdb=" N ARG A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 262 removed outlier: 4.031A pdb=" N ALA A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 246 " --> pdb=" O TRP A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 289 Processing helix chain 'A' and resid 289 through 297 Processing helix chain 'A' and resid 298 through 335 removed outlier: 3.614A pdb=" N GLN A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 346 Processing helix chain 'A' and resid 380 through 404 Processing helix chain 'A' and resid 405 through 431 removed outlier: 3.579A pdb=" N GLU A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 521 removed outlier: 3.572A pdb=" N PHE A 517 " --> pdb=" O LYS A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 558 Processing helix chain 'A' and resid 562 through 569 removed outlier: 3.534A pdb=" N LYS A 569 " --> pdb=" O ASP A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 581 removed outlier: 3.518A pdb=" N LEU A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 591 removed outlier: 3.744A pdb=" N GLN A 590 " --> pdb=" O HIS A 586 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 586 through 591' Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 606 through 621 removed outlier: 3.832A pdb=" N GLN A 611 " --> pdb=" O GLY A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 650 Processing helix chain 'A' and resid 660 through 667 removed outlier: 4.154A pdb=" N LYS A 665 " --> pdb=" O SER A 662 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR A 666 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS A 667 " --> pdb=" O TRP A 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 83 Processing helix chain 'B' and resid 88 through 123 removed outlier: 3.978A pdb=" N VAL B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 140 removed outlier: 3.507A pdb=" N ILE B 140 " --> pdb=" O GLN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 175 removed outlier: 3.607A pdb=" N THR B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 186 removed outlier: 4.184A pdb=" N SER B 184 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 235 removed outlier: 3.717A pdb=" N ASP B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N VAL B 201 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Proline residue: B 218 - end of helix Processing helix chain 'B' and resid 240 through 262 Processing helix chain 'B' and resid 264 through 289 Processing helix chain 'B' and resid 289 through 297 Processing helix chain 'B' and resid 298 through 335 Processing helix chain 'B' and resid 337 through 347 removed outlier: 3.741A pdb=" N VAL B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 404 Processing helix chain 'B' and resid 405 through 431 removed outlier: 3.536A pdb=" N ARG B 431 " --> pdb=" O GLU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 521 removed outlier: 3.542A pdb=" N LEU B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 517 " --> pdb=" O LYS B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 558 Processing helix chain 'B' and resid 562 through 569 removed outlier: 3.787A pdb=" N LYS B 569 " --> pdb=" O ASP B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 583 removed outlier: 3.548A pdb=" N LEU B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 591 removed outlier: 3.621A pdb=" N ARG B 591 " --> pdb=" O ILE B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 605 Processing helix chain 'B' and resid 608 through 621 Processing helix chain 'B' and resid 636 through 650 Processing helix chain 'B' and resid 660 through 667 removed outlier: 4.323A pdb=" N LYS B 665 " --> pdb=" O SER B 662 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR B 666 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS B 667 " --> pdb=" O TRP B 664 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 469 removed outlier: 6.827A pdb=" N GLN A 466 " --> pdb=" O LEU A 531 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LYS A 533 " --> pdb=" O GLN A 466 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL A 468 " --> pdb=" O LYS A 533 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU A 493 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ALA A 491 " --> pdb=" O PRO A 480 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL A 482 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL A 489 " --> pdb=" O VAL A 482 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 503 through 504 removed outlier: 6.862A pdb=" N LEU A 503 " --> pdb=" O SER A 656 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA A 626 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE A 657 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU A 628 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE A 540 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP A 629 " --> pdb=" O PHE A 540 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE A 542 " --> pdb=" O ASP A 629 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 467 through 469 removed outlier: 6.203A pdb=" N VAL B 468 " --> pdb=" O LYS B 533 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE B 475 " --> pdb=" O ILE B 495 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE B 495 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU B 477 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU B 493 " --> pdb=" O GLU B 477 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE B 479 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ALA B 491 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE B 481 " --> pdb=" O VAL B 489 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 503 through 504 removed outlier: 6.990A pdb=" N LEU B 503 " --> pdb=" O SER B 656 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA B 626 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE B 657 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B 628 " --> pdb=" O ILE B 657 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE B 540 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ASP B 629 " --> pdb=" O PHE B 540 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE B 542 " --> pdb=" O ASP B 629 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 592 hydrogen bonds defined for protein. 1749 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.44 Time building geometry restraints manager: 1.18 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: 3022 1.34 - 1.46: 1449 1.46 - 1.57: 4935 1.57 - 1.69: 13 1.69 - 1.81: 74 Bond restraints: 9493 Sorted by residual: bond pdb=" C3' ATP A 802 " pdb=" C4' ATP A 802 " ideal model delta sigma weight residual 1.526 1.306 0.220 1.10e-02 8.26e+03 3.99e+02 bond pdb=" C3' ATP B 802 " pdb=" C4' ATP B 802 " ideal model delta sigma weight residual 1.526 1.309 0.217 1.10e-02 8.26e+03 3.89e+02 bond pdb=" C1' ATP A 802 " pdb=" C2' ATP A 802 " ideal model delta sigma weight residual 1.531 1.335 0.196 1.20e-02 6.94e+03 2.68e+02 bond pdb=" C1' ATP B 802 " pdb=" C2' ATP B 802 " ideal model delta sigma weight residual 1.531 1.336 0.195 1.20e-02 6.94e+03 2.63e+02 bond pdb=" C4' ATP B 802 " pdb=" O4' ATP B 802 " ideal model delta sigma weight residual 1.444 1.577 -0.133 1.10e-02 8.26e+03 1.46e+02 ... (remaining 9488 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.07: 12804 4.07 - 8.15: 53 8.15 - 12.22: 11 12.22 - 16.29: 3 16.29 - 20.36: 1 Bond angle restraints: 12872 Sorted by residual: angle pdb=" PA ATP A 802 " pdb=" O3A ATP A 802 " pdb=" PB ATP A 802 " ideal model delta sigma weight residual 136.83 116.47 20.36 1.00e+00 1.00e+00 4.15e+02 angle pdb=" PB ATP A 802 " pdb=" O3B ATP A 802 " pdb=" PG ATP A 802 " ideal model delta sigma weight residual 139.87 124.27 15.60 1.00e+00 1.00e+00 2.43e+02 angle pdb=" PB ATP B 802 " pdb=" O3B ATP B 802 " pdb=" PG ATP B 802 " ideal model delta sigma weight residual 139.87 125.96 13.91 1.00e+00 1.00e+00 1.93e+02 angle pdb=" PA ATP B 802 " pdb=" O3A ATP B 802 " pdb=" PB ATP B 802 " ideal model delta sigma weight residual 136.83 125.53 11.30 1.00e+00 1.00e+00 1.28e+02 angle pdb=" C5 ATP B 802 " pdb=" C4 ATP B 802 " pdb=" N3 ATP B 802 " ideal model delta sigma weight residual 126.80 118.06 8.74 1.00e+00 1.00e+00 7.65e+01 ... (remaining 12867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5079 17.99 - 35.98: 470 35.98 - 53.97: 56 53.97 - 71.96: 14 71.96 - 89.95: 11 Dihedral angle restraints: 5630 sinusoidal: 2276 harmonic: 3354 Sorted by residual: dihedral pdb=" CA ILE B 558 " pdb=" C ILE B 558 " pdb=" N TYR B 559 " pdb=" CA TYR B 559 " ideal model delta harmonic sigma weight residual -180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ILE A 558 " pdb=" C ILE A 558 " pdb=" N TYR A 559 " pdb=" CA TYR A 559 " ideal model delta harmonic sigma weight residual 180.00 -158.81 -21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA HIS A 669 " pdb=" C HIS A 669 " pdb=" N LEU A 670 " pdb=" CA LEU A 670 " ideal model delta harmonic sigma weight residual 180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 5627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1114 0.047 - 0.094: 250 0.094 - 0.141: 61 0.141 - 0.188: 3 0.188 - 0.235: 3 Chirality restraints: 1431 Sorted by residual: chirality pdb=" C2' ATP A 802 " pdb=" C1' ATP A 802 " pdb=" C3' ATP A 802 " pdb=" O2' ATP A 802 " both_signs ideal model delta sigma weight residual False -2.68 -2.44 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C3' ATP A 802 " pdb=" C2' ATP A 802 " pdb=" C4' ATP A 802 " pdb=" O3' ATP A 802 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE A 505 " pdb=" CA ILE A 505 " pdb=" CG1 ILE A 505 " pdb=" CG2 ILE A 505 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 1428 not shown) Planarity restraints: 1622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 535 " -0.055 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO A 536 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 536 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 536 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 507 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO A 508 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 508 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 508 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 106 " 0.014 2.00e-02 2.50e+03 1.13e-02 2.23e+00 pdb=" CG PHE A 106 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 106 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 106 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 106 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 106 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 106 " 0.005 2.00e-02 2.50e+03 ... (remaining 1619 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 56 2.56 - 3.14: 7320 3.14 - 3.73: 14915 3.73 - 4.31: 20506 4.31 - 4.90: 34928 Nonbonded interactions: 77725 Sorted by model distance: nonbonded pdb=" OG SER A 514 " pdb="MG MG A 801 " model vdw 1.974 2.170 nonbonded pdb=" OG SER B 514 " pdb="MG MG B 801 " model vdw 2.050 2.170 nonbonded pdb=" OE1 GLN B 544 " pdb="MG MG B 801 " model vdw 2.074 2.170 nonbonded pdb=" O MET A 548 " pdb=" NH2 ARG B 285 " model vdw 2.180 3.120 nonbonded pdb=" O THR B 632 " pdb=" NH1 ARG B 660 " model vdw 2.190 3.120 ... (remaining 77720 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 64 through 351 or resid 379 through 802)) } 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: 4.040 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.100 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 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 : 0.007 0.220 9493 Z= 0.529 Angle : 0.792 20.362 12872 Z= 0.533 Chirality : 0.042 0.235 1431 Planarity : 0.004 0.083 1622 Dihedral : 14.145 89.948 3474 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.25), residues: 1144 helix: 1.50 (0.19), residues: 737 sheet: -0.80 (0.70), residues: 60 loop : -2.21 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 163 TYR 0.025 0.002 TYR A 110 PHE 0.025 0.001 PHE A 106 TRP 0.018 0.001 TRP B 326 HIS 0.008 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.53 ( 9493) covalent geometry : angle 0.79202 / 0.53 (12872) hydrogen bonds : bond 0.10432 / 7.16 ( 592) hydrogen bonds : angle 4.74923 / 3.59 ( 1749) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.274 Fit side-chains REVERT: A 72 LEU cc_start: 0.8671 (tp) cc_final: 0.8471 (tp) REVERT: A 89 ARG cc_start: 0.7158 (ttm-80) cc_final: 0.6940 (ttt180) REVERT: A 598 MET cc_start: 0.7980 (mtt) cc_final: 0.7734 (mtp) REVERT: B 421 GLU cc_start: 0.7681 (tp30) cc_final: 0.7280 (pt0) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.6387 time to fit residues: 86.5501 Evaluate side-chains 105 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.0170 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 HIS A 586 HIS B 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.166297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.132709 restraints weight = 9295.676| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.60 r_work: 0.3284 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9493 Z= 0.149 Angle : 0.555 10.088 12872 Z= 0.283 Chirality : 0.040 0.155 1431 Planarity : 0.004 0.066 1622 Dihedral : 5.849 85.910 1296 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.64 % Allowed : 8.43 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.25), residues: 1144 helix: 1.90 (0.19), residues: 738 sheet: -1.15 (0.63), residues: 67 loop : -2.22 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 436 TYR 0.015 0.001 TYR B 310 PHE 0.019 0.001 PHE A 106 TRP 0.014 0.001 TRP B 326 HIS 0.007 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 9493) covalent geometry : angle 0.55527 / 0.28 (12872) hydrogen bonds : bond 0.05056 / 3.27 ( 592) hydrogen bonds : angle 3.90811 / 2.93 ( 1749) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.274 Fit side-chains REVERT: A 69 ARG cc_start: 0.7507 (ttm170) cc_final: 0.7243 (tpp80) REVERT: A 72 LEU cc_start: 0.8535 (tp) cc_final: 0.8320 (tp) REVERT: A 272 GLU cc_start: 0.8174 (tt0) cc_final: 0.7928 (tt0) REVERT: A 498 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: A 598 MET cc_start: 0.8466 (mtt) cc_final: 0.8139 (mtp) REVERT: B 421 GLU cc_start: 0.8268 (tp30) cc_final: 0.7218 (pt0) outliers start: 16 outliers final: 4 residues processed: 119 average time/residue: 0.7050 time to fit residues: 88.5649 Evaluate side-chains 108 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 506 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 77 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 100 optimal weight: 0.0570 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 HIS A 210 HIS A 586 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.167368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.133330 restraints weight = 9290.704| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.66 r_work: 0.3332 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9493 Z= 0.144 Angle : 0.533 9.757 12872 Z= 0.270 Chirality : 0.040 0.155 1431 Planarity : 0.004 0.059 1622 Dihedral : 5.641 89.223 1296 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.54 % Allowed : 11.00 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.25), residues: 1144 helix: 2.05 (0.18), residues: 738 sheet: -2.05 (0.59), residues: 69 loop : -2.09 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 660 TYR 0.014 0.001 TYR B 310 PHE 0.013 0.001 PHE A 106 TRP 0.013 0.001 TRP B 326 HIS 0.007 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 9493) covalent geometry : angle 0.53278 / 0.27 (12872) hydrogen bonds : bond 0.04926 / 3.17 ( 592) hydrogen bonds : angle 3.79044 / 2.84 ( 1749) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.344 Fit side-chains REVERT: A 72 LEU cc_start: 0.8664 (tp) cc_final: 0.8460 (tp) REVERT: A 155 GLU cc_start: 0.8175 (tt0) cc_final: 0.7881 (tt0) REVERT: A 272 GLU cc_start: 0.8347 (tt0) cc_final: 0.8077 (tt0) REVERT: A 598 MET cc_start: 0.8539 (mtt) cc_final: 0.8245 (mtp) REVERT: B 421 GLU cc_start: 0.8361 (tp30) cc_final: 0.7442 (pt0) outliers start: 15 outliers final: 6 residues processed: 120 average time/residue: 0.6845 time to fit residues: 87.0700 Evaluate side-chains 108 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 672 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 76 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 93 optimal weight: 0.0670 chunk 30 optimal weight: 0.9980 chunk 102 optimal weight: 0.0870 chunk 110 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 HIS A 210 HIS A 586 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.168223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.134290 restraints weight = 9332.441| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.75 r_work: 0.3320 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9493 Z= 0.135 Angle : 0.515 9.511 12872 Z= 0.260 Chirality : 0.039 0.154 1431 Planarity : 0.004 0.055 1622 Dihedral : 5.400 89.476 1296 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.85 % Allowed : 12.13 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.25), residues: 1144 helix: 2.18 (0.18), residues: 739 sheet: -2.04 (0.59), residues: 69 loop : -2.05 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 660 TYR 0.014 0.001 TYR B 310 PHE 0.011 0.001 PHE A 252 TRP 0.013 0.001 TRP B 326 HIS 0.006 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 9493) covalent geometry : angle 0.51482 / 0.26 (12872) hydrogen bonds : bond 0.04739 / 3.05 ( 592) hydrogen bonds : angle 3.72686 / 2.79 ( 1749) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.345 Fit side-chains REVERT: A 89 ARG cc_start: 0.7431 (ttm-80) cc_final: 0.7201 (ttt180) REVERT: A 155 GLU cc_start: 0.8172 (tt0) cc_final: 0.7897 (tt0) REVERT: A 272 GLU cc_start: 0.8383 (tt0) cc_final: 0.8075 (tt0) REVERT: A 335 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7203 (mmm) REVERT: A 403 MET cc_start: 0.8742 (ttm) cc_final: 0.8465 (mtt) REVERT: A 598 MET cc_start: 0.8591 (mtt) cc_final: 0.8286 (mtp) REVERT: B 421 GLU cc_start: 0.8355 (tp30) cc_final: 0.7420 (pt0) REVERT: B 435 LYS cc_start: 0.8004 (mttp) cc_final: 0.7588 (mttp) outliers start: 18 outliers final: 6 residues processed: 126 average time/residue: 0.6981 time to fit residues: 93.2181 Evaluate side-chains 111 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 672 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 99 optimal weight: 0.5980 chunk 111 optimal weight: 0.1980 chunk 87 optimal weight: 1.9990 chunk 104 optimal weight: 0.3980 chunk 114 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 0.0370 chunk 77 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 86 optimal weight: 0.0770 overall best weight: 0.2616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 HIS A 210 HIS A 586 HIS B 502 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.171829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.138313 restraints weight = 9397.338| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.67 r_work: 0.3371 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 9493 Z= 0.112 Angle : 0.487 8.954 12872 Z= 0.246 Chirality : 0.038 0.154 1431 Planarity : 0.004 0.051 1622 Dihedral : 5.030 82.419 1296 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.36 % Allowed : 13.16 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.25), residues: 1144 helix: 2.39 (0.18), residues: 736 sheet: -1.97 (0.60), residues: 70 loop : -1.99 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 172 TYR 0.012 0.001 TYR B 310 PHE 0.010 0.001 PHE A 252 TRP 0.013 0.001 TRP B 326 HIS 0.007 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 9493) covalent geometry : angle 0.48744 / 0.25 (12872) hydrogen bonds : bond 0.04396 / 2.83 ( 592) hydrogen bonds : angle 3.60166 / 2.69 ( 1749) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.351 Fit side-chains REVERT: A 89 ARG cc_start: 0.7408 (ttm-80) cc_final: 0.7184 (ttt180) REVERT: A 155 GLU cc_start: 0.8013 (tt0) cc_final: 0.7786 (tt0) REVERT: A 272 GLU cc_start: 0.8334 (tt0) cc_final: 0.7982 (tt0) REVERT: A 312 ASP cc_start: 0.8099 (m-30) cc_final: 0.7623 (m-30) REVERT: A 335 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7065 (mmm) REVERT: A 427 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7706 (mp0) REVERT: A 501 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7785 (ttm) REVERT: A 598 MET cc_start: 0.8508 (mtt) cc_final: 0.8205 (mtp) REVERT: B 421 GLU cc_start: 0.8300 (tp30) cc_final: 0.7297 (pt0) REVERT: B 487 GLU cc_start: 0.6275 (tt0) cc_final: 0.6003 (tt0) outliers start: 23 outliers final: 6 residues processed: 128 average time/residue: 0.6399 time to fit residues: 87.1789 Evaluate side-chains 114 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 523 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 54 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 103 optimal weight: 0.0270 chunk 112 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 HIS A 210 HIS A 586 HIS B 502 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.169306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.135544 restraints weight = 9351.619| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.59 r_work: 0.3371 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9493 Z= 0.135 Angle : 0.513 9.935 12872 Z= 0.257 Chirality : 0.039 0.183 1431 Planarity : 0.004 0.051 1622 Dihedral : 4.979 75.583 1296 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.47 % Allowed : 14.08 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.25), residues: 1144 helix: 2.32 (0.18), residues: 740 sheet: -2.00 (0.59), residues: 70 loop : -1.98 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 152 TYR 0.014 0.001 TYR A 310 PHE 0.006 0.001 PHE A 106 TRP 0.011 0.001 TRP B 326 HIS 0.006 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 9493) covalent geometry : angle 0.51257 / 0.26 (12872) hydrogen bonds : bond 0.04651 / 2.99 ( 592) hydrogen bonds : angle 3.63967 / 2.72 ( 1749) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.339 Fit side-chains REVERT: A 89 ARG cc_start: 0.7446 (ttm-80) cc_final: 0.7219 (ttt180) REVERT: A 155 GLU cc_start: 0.8091 (tt0) cc_final: 0.7780 (tt0) REVERT: A 272 GLU cc_start: 0.8394 (tt0) cc_final: 0.8032 (tt0) REVERT: A 335 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7198 (mmm) REVERT: A 427 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7742 (mp0) REVERT: A 501 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7860 (mtt) REVERT: A 598 MET cc_start: 0.8537 (mtt) cc_final: 0.8228 (mtp) REVERT: A 684 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7197 (tp) REVERT: B 421 GLU cc_start: 0.8372 (tp30) cc_final: 0.7389 (pt0) REVERT: B 487 GLU cc_start: 0.6293 (tt0) cc_final: 0.6028 (tt0) REVERT: B 659 HIS cc_start: 0.7337 (OUTLIER) cc_final: 0.6560 (p90) outliers start: 24 outliers final: 10 residues processed: 125 average time/residue: 0.6878 time to fit residues: 91.2539 Evaluate side-chains 114 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 659 HIS Chi-restraints excluded: chain B residue 668 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 26 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 23 optimal weight: 0.0970 chunk 67 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 HIS A 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.171212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.137681 restraints weight = 9412.075| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.51 r_work: 0.3394 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9493 Z= 0.120 Angle : 0.512 9.893 12872 Z= 0.256 Chirality : 0.039 0.211 1431 Planarity : 0.004 0.050 1622 Dihedral : 4.730 63.234 1296 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.36 % Allowed : 15.31 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.25), residues: 1144 helix: 2.43 (0.18), residues: 738 sheet: -1.97 (0.59), residues: 70 loop : -1.99 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 152 TYR 0.012 0.001 TYR B 310 PHE 0.007 0.001 PHE A 106 TRP 0.013 0.001 TRP B 326 HIS 0.006 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 9493) covalent geometry : angle 0.51212 / 0.26 (12872) hydrogen bonds : bond 0.04427 / 2.85 ( 592) hydrogen bonds : angle 3.58204 / 2.68 ( 1749) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.344 Fit side-chains REVERT: A 89 ARG cc_start: 0.7363 (ttm-80) cc_final: 0.7136 (ttt180) REVERT: A 155 GLU cc_start: 0.8013 (tt0) cc_final: 0.7725 (tt0) REVERT: A 272 GLU cc_start: 0.8340 (tt0) cc_final: 0.7993 (tt0) REVERT: A 335 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7126 (mmm) REVERT: A 427 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7601 (mp0) REVERT: A 470 VAL cc_start: 0.8562 (m) cc_final: 0.8332 (p) REVERT: A 501 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7729 (ttt) REVERT: A 574 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6978 (mp10) REVERT: A 598 MET cc_start: 0.8448 (mtt) cc_final: 0.8126 (mtp) REVERT: B 421 GLU cc_start: 0.8332 (tp30) cc_final: 0.7273 (pt0) REVERT: B 487 GLU cc_start: 0.6085 (tt0) cc_final: 0.5820 (tt0) REVERT: B 659 HIS cc_start: 0.7233 (OUTLIER) cc_final: 0.6462 (p90) outliers start: 23 outliers final: 10 residues processed: 123 average time/residue: 0.6276 time to fit residues: 82.2034 Evaluate side-chains 120 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 659 HIS Chi-restraints excluded: chain B residue 668 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 38 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 40 optimal weight: 0.0980 chunk 5 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 HIS A 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.168203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.134314 restraints weight = 9354.031| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.65 r_work: 0.3316 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9493 Z= 0.150 Angle : 0.548 10.810 12872 Z= 0.273 Chirality : 0.040 0.223 1431 Planarity : 0.004 0.051 1622 Dihedral : 4.701 58.595 1296 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.98 % Allowed : 14.80 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.25), residues: 1144 helix: 2.28 (0.18), residues: 746 sheet: -1.97 (0.60), residues: 70 loop : -2.18 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 163 TYR 0.015 0.001 TYR B 310 PHE 0.007 0.001 PHE B 673 TRP 0.010 0.001 TRP B 326 HIS 0.005 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 9493) covalent geometry : angle 0.54847 / 0.27 (12872) hydrogen bonds : bond 0.04755 / 3.06 ( 592) hydrogen bonds : angle 3.68299 / 2.75 ( 1749) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.364 Fit side-chains REVERT: A 89 ARG cc_start: 0.7504 (ttm-80) cc_final: 0.7284 (ttt180) REVERT: A 155 GLU cc_start: 0.8172 (tt0) cc_final: 0.7948 (tt0) REVERT: A 272 GLU cc_start: 0.8412 (tt0) cc_final: 0.8059 (tt0) REVERT: A 311 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.6874 (tp40) REVERT: A 335 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.7292 (mmm) REVERT: A 427 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7800 (mp0) REVERT: A 501 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7768 (ttm) REVERT: A 574 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7175 (mp10) REVERT: A 598 MET cc_start: 0.8557 (mtt) cc_final: 0.8258 (mtp) REVERT: B 421 GLU cc_start: 0.8390 (tp30) cc_final: 0.7460 (pt0) REVERT: B 487 GLU cc_start: 0.6241 (tt0) cc_final: 0.5935 (tt0) outliers start: 29 outliers final: 11 residues processed: 125 average time/residue: 0.6412 time to fit residues: 85.3134 Evaluate side-chains 118 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 668 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 40 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 99 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 HIS A 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.168305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.134159 restraints weight = 9310.364| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.74 r_work: 0.3273 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9493 Z= 0.149 Angle : 0.545 10.927 12872 Z= 0.272 Chirality : 0.040 0.226 1431 Planarity : 0.004 0.051 1622 Dihedral : 4.656 57.414 1296 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.47 % Allowed : 15.52 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.25), residues: 1144 helix: 2.27 (0.18), residues: 744 sheet: -1.97 (0.60), residues: 70 loop : -2.19 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 324 TYR 0.014 0.001 TYR B 310 PHE 0.006 0.001 PHE B 673 TRP 0.011 0.001 TRP B 326 HIS 0.007 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 9493) covalent geometry : angle 0.54503 / 0.27 (12872) hydrogen bonds : bond 0.04745 / 3.05 ( 592) hydrogen bonds : angle 3.69357 / 2.76 ( 1749) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.354 Fit side-chains REVERT: A 89 ARG cc_start: 0.7480 (ttm-80) cc_final: 0.7258 (ttt180) REVERT: A 155 GLU cc_start: 0.8158 (tt0) cc_final: 0.7939 (tt0) REVERT: A 272 GLU cc_start: 0.8401 (tt0) cc_final: 0.8022 (tt0) REVERT: A 311 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.6775 (tp40) REVERT: A 335 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.7215 (mmm) REVERT: A 427 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7784 (mp0) REVERT: A 501 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7768 (ttm) REVERT: A 574 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7186 (mp10) REVERT: A 598 MET cc_start: 0.8544 (mtt) cc_final: 0.8233 (mtp) REVERT: B 421 GLU cc_start: 0.8391 (tp30) cc_final: 0.7420 (pt0) REVERT: B 487 GLU cc_start: 0.6243 (tt0) cc_final: 0.6017 (tt0) outliers start: 24 outliers final: 11 residues processed: 118 average time/residue: 0.6897 time to fit residues: 86.3309 Evaluate side-chains 116 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 668 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 107 optimal weight: 0.0040 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 26 optimal weight: 0.0980 chunk 63 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.170401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.136286 restraints weight = 9307.964| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.71 r_work: 0.3267 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9493 Z= 0.125 Angle : 0.524 10.444 12872 Z= 0.261 Chirality : 0.039 0.231 1431 Planarity : 0.004 0.050 1622 Dihedral : 4.519 56.077 1296 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.54 % Allowed : 16.34 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.25), residues: 1144 helix: 2.36 (0.18), residues: 746 sheet: -1.91 (0.61), residues: 70 loop : -2.14 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 518 TYR 0.013 0.001 TYR B 310 PHE 0.006 0.001 PHE A 333 TRP 0.014 0.001 TRP B 326 HIS 0.008 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 9493) covalent geometry : angle 0.52424 / 0.26 (12872) hydrogen bonds : bond 0.04498 / 2.89 ( 592) hydrogen bonds : angle 3.63114 / 2.71 ( 1749) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.350 Fit side-chains REVERT: A 89 ARG cc_start: 0.7368 (ttm-80) cc_final: 0.7149 (ttt180) REVERT: A 155 GLU cc_start: 0.8083 (tt0) cc_final: 0.7804 (tt0) REVERT: A 272 GLU cc_start: 0.8372 (tt0) cc_final: 0.7998 (tt0) REVERT: A 335 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7166 (mmm) REVERT: A 427 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7679 (mp0) REVERT: A 501 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7622 (ttm) REVERT: A 598 MET cc_start: 0.8487 (mtt) cc_final: 0.8166 (mtp) REVERT: B 421 GLU cc_start: 0.8352 (tp30) cc_final: 0.7322 (pt0) REVERT: B 487 GLU cc_start: 0.6176 (tt0) cc_final: 0.5960 (tt0) outliers start: 15 outliers final: 11 residues processed: 117 average time/residue: 0.6563 time to fit residues: 81.6056 Evaluate side-chains 117 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 668 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 94 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 76 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 108 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.169398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.135436 restraints weight = 9294.868| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.72 r_work: 0.3365 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9493 Z= 0.137 Angle : 0.535 10.627 12872 Z= 0.267 Chirality : 0.040 0.219 1431 Planarity : 0.004 0.050 1622 Dihedral : 4.546 55.216 1296 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.64 % Allowed : 16.65 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.25), residues: 1144 helix: 2.34 (0.18), residues: 746 sheet: -1.94 (0.61), residues: 70 loop : -2.17 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 518 TYR 0.013 0.001 TYR B 310 PHE 0.006 0.001 PHE A 333 TRP 0.011 0.001 TRP B 326 HIS 0.008 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 9493) covalent geometry : angle 0.53517 / 0.27 (12872) hydrogen bonds : bond 0.04602 / 2.95 ( 592) hydrogen bonds : angle 3.64553 / 2.73 ( 1749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3161.63 seconds wall clock time: 54 minutes 50.81 seconds (3290.81 seconds total)