Starting phenix.real_space_refine on Tue Mar 3 19:17:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ehl_31142/03_2026/7ehl_31142.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ehl_31142/03_2026/7ehl_31142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ehl_31142/03_2026/7ehl_31142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ehl_31142/03_2026/7ehl_31142.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ehl_31142/03_2026/7ehl_31142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ehl_31142/03_2026/7ehl_31142.map" } resolution = 4.1 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= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 180 atoms to isotropic. 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 34 5.16 5 C 5104 2.51 5 N 1400 2.21 5 O 1502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8048 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 3936 Classifications: {'peptide': 563} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 14, 'TRANS': 548} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'PHE:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 6, 'TYR:plan': 1, 'ARG:plan': 16, 'ASP:plan': 4, 'GLU:plan': 10} Unresolved non-hydrogen planarities: 184 Chain: "B" Number of atoms: 3936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 3936 Classifications: {'peptide': 563} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 14, 'TRANS': 548} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'PHE:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 6, 'TYR:plan': 1, 'ARG:plan': 16, 'ASP:plan': 4, 'GLU:plan': 10} Unresolved non-hydrogen planarities: 184 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Unusual residues: {' MG': 1, 'ANP': 1, 'CLR': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Unusual residues: {' MG': 1, 'ANP': 1, 'CLR': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.37, per 1000 atoms: 0.29 Number of scatterers: 8048 At special positions: 0 Unit cell: (100.386, 92.274, 136.89, 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 34 16.00 P 6 15.00 Mg 2 11.99 O 1502 8.00 N 1400 7.00 C 5104 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: 0.75 Conformation dependent library (CDL) restraints added in 284.9 milliseconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2036 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 6 sheets defined 70.1% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 134 through 142 Processing helix chain 'A' and resid 144 through 182 Proline residue: A 166 - end of helix Processing helix chain 'A' and resid 190 through 236 removed outlier: 3.826A pdb=" N LEU A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 246 removed outlier: 3.838A pdb=" N PHE A 243 " --> pdb=" O ASP A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 290 removed outlier: 3.915A pdb=" N ASP A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 331 Proline residue: A 303 - end of helix removed outlier: 4.081A pdb=" N MET A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 340 removed outlier: 3.649A pdb=" N ASN A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 347 removed outlier: 3.680A pdb=" N VAL A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 403 removed outlier: 4.091A pdb=" N GLY A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 450 removed outlier: 4.132A pdb=" N VAL A 416 " --> pdb=" O MET A 412 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER A 418 " --> pdb=" O PHE A 414 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLN A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 542 through 550 Processing helix chain 'A' and resid 564 through 570 removed outlier: 3.613A pdb=" N ARG A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 588 removed outlier: 3.729A pdb=" N TYR A 582 " --> pdb=" O ASP A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 595 removed outlier: 3.590A pdb=" N THR A 595 " --> pdb=" O HIS A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 627 removed outlier: 3.510A pdb=" N ALA A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 658 removed outlier: 3.513A pdb=" N GLU A 647 " --> pdb=" O ASP A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 673 removed outlier: 3.518A pdb=" N THR A 672 " --> pdb=" O ARG A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 700 removed outlier: 3.814A pdb=" N LYS A 698 " --> pdb=" O GLU A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 711 removed outlier: 3.654A pdb=" N GLU A 705 " --> pdb=" O GLY A 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 144 through 182 Proline residue: B 166 - end of helix Processing helix chain 'B' and resid 190 through 236 removed outlier: 3.826A pdb=" N LEU B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 246 removed outlier: 3.838A pdb=" N PHE B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 290 removed outlier: 3.915A pdb=" N ASP B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 331 Proline residue: B 303 - end of helix removed outlier: 4.081A pdb=" N MET B 312 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.649A pdb=" N ASN B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 347 removed outlier: 3.680A pdb=" N VAL B 344 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 403 removed outlier: 4.091A pdb=" N GLY B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 450 removed outlier: 4.132A pdb=" N VAL B 416 " --> pdb=" O MET B 412 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA B 417 " --> pdb=" O SER B 413 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER B 418 " --> pdb=" O PHE B 414 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLN B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR B 420 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY B 433 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA B 450 " --> pdb=" O PHE B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 518 Processing helix chain 'B' and resid 542 through 550 Processing helix chain 'B' and resid 564 through 570 removed outlier: 3.613A pdb=" N ARG B 570 " --> pdb=" O MET B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 588 removed outlier: 3.729A pdb=" N TYR B 582 " --> pdb=" O ASP B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 595 removed outlier: 3.590A pdb=" N THR B 595 " --> pdb=" O HIS B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 628 removed outlier: 3.718A pdb=" N ARG B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS B 628 " --> pdb=" O ARG B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 658 removed outlier: 3.513A pdb=" N GLU B 647 " --> pdb=" O ASP B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 673 removed outlier: 3.518A pdb=" N THR B 672 " --> pdb=" O ARG B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 700 removed outlier: 3.814A pdb=" N LYS B 698 " --> pdb=" O GLU B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 711 removed outlier: 3.654A pdb=" N GLU B 705 " --> pdb=" O GLY B 701 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 496 through 497 removed outlier: 3.694A pdb=" N VAL A 472 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL A 477 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA A 528 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 502 through 505 removed outlier: 6.440A pdb=" N LEU A 633 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE A 666 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU A 635 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 678 through 682 Processing sheet with id=AA4, first strand: chain 'B' and resid 496 through 497 removed outlier: 3.694A pdb=" N VAL B 472 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL B 477 " --> pdb=" O ALA B 528 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 528 " --> pdb=" O VAL B 477 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 502 through 505 removed outlier: 6.440A pdb=" N LEU B 633 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE B 666 " --> pdb=" O LEU B 633 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU B 635 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 678 through 682 602 hydrogen bonds defined for protein. 1794 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: 1.20 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2712 1.35 - 1.46: 1768 1.46 - 1.58: 3604 1.58 - 1.70: 30 1.70 - 1.81: 58 Bond restraints: 8172 Sorted by residual: bond pdb=" C5 CLR A 903 " pdb=" C6 CLR A 903 " ideal model delta sigma weight residual 1.332 1.558 -0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C5 CLR B1001 " pdb=" C6 CLR B1001 " ideal model delta sigma weight residual 1.332 1.558 -0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C5 CLR B1002 " pdb=" C6 CLR B1002 " ideal model delta sigma weight residual 1.332 1.557 -0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C5 CLR A 901 " pdb=" C6 CLR A 901 " ideal model delta sigma weight residual 1.332 1.557 -0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C3' ANP B1003 " pdb=" C4' ANP B1003 " ideal model delta sigma weight residual 1.532 1.339 0.193 2.00e-02 2.50e+03 9.29e+01 ... (remaining 8167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 10821 2.48 - 4.97: 238 4.97 - 7.45: 67 7.45 - 9.94: 14 9.94 - 12.42: 18 Bond angle restraints: 11158 Sorted by residual: angle pdb=" C5 CLR A 903 " pdb=" C6 CLR A 903 " pdb=" C7 CLR A 903 " ideal model delta sigma weight residual 125.11 112.69 12.42 3.00e+00 1.11e-01 1.71e+01 angle pdb=" C5 CLR B1001 " pdb=" C6 CLR B1001 " pdb=" C7 CLR B1001 " ideal model delta sigma weight residual 125.11 112.69 12.42 3.00e+00 1.11e-01 1.71e+01 angle pdb=" C5 CLR B1002 " pdb=" C6 CLR B1002 " pdb=" C7 CLR B1002 " ideal model delta sigma weight residual 125.11 112.82 12.29 3.00e+00 1.11e-01 1.68e+01 angle pdb=" C5 CLR A 901 " pdb=" C6 CLR A 901 " pdb=" C7 CLR A 901 " ideal model delta sigma weight residual 125.11 112.82 12.29 3.00e+00 1.11e-01 1.68e+01 angle pdb=" N ALA B 348 " pdb=" CA ALA B 348 " pdb=" C ALA B 348 " ideal model delta sigma weight residual 113.29 121.00 -7.71 2.00e+00 2.50e-01 1.48e+01 ... (remaining 11153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 4535 17.38 - 34.75: 353 34.75 - 52.13: 91 52.13 - 69.51: 3 69.51 - 86.88: 18 Dihedral angle restraints: 5000 sinusoidal: 1832 harmonic: 3168 Sorted by residual: dihedral pdb=" CA PHE B 347 " pdb=" C PHE B 347 " pdb=" N ALA B 348 " pdb=" CA ALA B 348 " ideal model delta harmonic sigma weight residual 180.00 163.60 16.40 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA PHE A 347 " pdb=" C PHE A 347 " pdb=" N ALA A 348 " pdb=" CA ALA A 348 " ideal model delta harmonic sigma weight residual 180.00 163.61 16.39 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB GLU B 580 " pdb=" CG GLU B 580 " pdb=" CD GLU B 580 " pdb=" OE1 GLU B 580 " ideal model delta sinusoidal sigma weight residual 0.00 82.62 -82.62 1 3.00e+01 1.11e-03 9.30e+00 ... (remaining 4997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1278 0.099 - 0.197: 62 0.197 - 0.296: 12 0.296 - 0.394: 2 0.394 - 0.492: 6 Chirality restraints: 1360 Sorted by residual: chirality pdb=" C13 CLR B1002 " pdb=" C12 CLR B1002 " pdb=" C14 CLR B1002 " pdb=" C17 CLR B1002 " both_signs ideal model delta sigma weight residual False -2.93 -2.44 -0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" C13 CLR A 901 " pdb=" C12 CLR A 901 " pdb=" C14 CLR A 901 " pdb=" C17 CLR A 901 " both_signs ideal model delta sigma weight residual False -2.93 -2.44 -0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" C13 CLR A 903 " pdb=" C12 CLR A 903 " pdb=" C14 CLR A 903 " pdb=" C17 CLR A 903 " both_signs ideal model delta sigma weight residual False -2.93 -2.45 -0.48 2.00e-01 2.50e+01 5.77e+00 ... (remaining 1357 not shown) Planarity restraints: 1418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 619 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C ARG A 619 " 0.031 2.00e-02 2.50e+03 pdb=" O ARG A 619 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 620 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 347 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.83e+00 pdb=" C PHE A 347 " -0.029 2.00e-02 2.50e+03 pdb=" O PHE A 347 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA A 348 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 347 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" C PHE B 347 " -0.029 2.00e-02 2.50e+03 pdb=" O PHE B 347 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA B 348 " 0.010 2.00e-02 2.50e+03 ... (remaining 1415 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 23 2.35 - 2.98: 4081 2.98 - 3.62: 12767 3.62 - 4.26: 16186 4.26 - 4.90: 27147 Nonbonded interactions: 60204 Sorted by model distance: nonbonded pdb=" OD1 ASN B 568 " pdb=" NH2 ARG B 624 " model vdw 1.708 3.120 nonbonded pdb=" CG2 THR B 514 " pdb="MG MG B1004 " model vdw 1.970 2.590 nonbonded pdb=" CG2 THR A 514 " pdb="MG MG A 904 " model vdw 1.972 2.590 nonbonded pdb=" O2B ANP A 902 " pdb="MG MG A 904 " model vdw 2.062 2.170 nonbonded pdb=" O2B ANP B1003 " pdb="MG MG B1004 " model vdw 2.066 2.170 ... (remaining 60199 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 132 through 901 or resid 904)) selection = (chain 'B' and (resid 132 through 1001 or resid 1004)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.610 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 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 : 0.012 0.226 8172 Z= 0.592 Angle : 0.997 12.422 11158 Z= 0.457 Chirality : 0.059 0.492 1360 Planarity : 0.003 0.030 1418 Dihedral : 14.295 86.881 2964 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.19 (0.26), residues: 1102 helix: 2.50 (0.19), residues: 758 sheet: 0.76 (0.67), residues: 60 loop : -1.44 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 367 TYR 0.016 0.002 TYR B 202 PHE 0.015 0.001 PHE A 571 TRP 0.004 0.001 TRP A 138 HIS 0.004 0.001 HIS B 668 Details of bonding type rmsd covalent geometry : bond 0.01155 ( 8172) covalent geometry : angle 0.99726 (11158) hydrogen bonds : bond 0.10763 ( 602) hydrogen bonds : angle 4.74829 ( 1794) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 LEU cc_start: 0.8160 (tp) cc_final: 0.7881 (tp) REVERT: A 223 MET cc_start: 0.8921 (tpt) cc_final: 0.8669 (tpp) REVERT: A 427 ASN cc_start: 0.9546 (m-40) cc_final: 0.9076 (m-40) REVERT: A 491 LYS cc_start: 0.8792 (tttt) cc_final: 0.8590 (tppt) REVERT: A 493 PHE cc_start: 0.8276 (t80) cc_final: 0.8034 (t80) REVERT: A 636 ASP cc_start: 0.8174 (t70) cc_final: 0.7923 (t70) REVERT: B 148 LEU cc_start: 0.8150 (tp) cc_final: 0.7930 (tp) REVERT: B 216 LEU cc_start: 0.8976 (tp) cc_final: 0.8574 (tp) REVERT: B 366 CYS cc_start: 0.8679 (m) cc_final: 0.8459 (m) REVERT: B 371 LEU cc_start: 0.9601 (tt) cc_final: 0.9299 (pp) REVERT: B 427 ASN cc_start: 0.9507 (m-40) cc_final: 0.8989 (m-40) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.0693 time to fit residues: 23.8368 Evaluate side-chains 201 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.0670 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.112325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.099990 restraints weight = 25410.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.102574 restraints weight = 15008.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.104411 restraints weight = 9944.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.105746 restraints weight = 7118.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.106653 restraints weight = 5381.468| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8172 Z= 0.120 Angle : 0.567 8.083 11158 Z= 0.284 Chirality : 0.039 0.153 1360 Planarity : 0.003 0.034 1418 Dihedral : 7.419 80.646 1504 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.28 % Allowed : 3.09 % Favored : 96.63 % 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: 2.45 (0.26), residues: 1102 helix: 2.60 (0.19), residues: 764 sheet: 0.97 (0.65), residues: 62 loop : -1.17 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 356 TYR 0.012 0.002 TYR B 582 PHE 0.019 0.001 PHE A 553 TRP 0.006 0.001 TRP A 138 HIS 0.003 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8172) covalent geometry : angle 0.56693 (11158) hydrogen bonds : bond 0.04210 ( 602) hydrogen bonds : angle 3.94934 ( 1794) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 242 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LEU cc_start: 0.8108 (tp) cc_final: 0.7830 (tp) REVERT: A 216 LEU cc_start: 0.9071 (tp) cc_final: 0.8744 (tp) REVERT: A 223 MET cc_start: 0.8816 (tpt) cc_final: 0.8592 (tpp) REVERT: A 355 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7699 (pm20) REVERT: A 427 ASN cc_start: 0.9578 (m-40) cc_final: 0.9142 (m-40) REVERT: A 553 PHE cc_start: 0.8604 (t80) cc_final: 0.8275 (t80) REVERT: A 636 ASP cc_start: 0.8221 (t70) cc_final: 0.8008 (t0) REVERT: A 655 ASP cc_start: 0.8556 (m-30) cc_final: 0.8292 (t70) REVERT: B 142 HIS cc_start: 0.8326 (t70) cc_final: 0.8085 (t70) REVERT: B 148 LEU cc_start: 0.8098 (tp) cc_final: 0.7894 (tp) REVERT: B 216 LEU cc_start: 0.9020 (tp) cc_final: 0.8701 (tp) REVERT: B 356 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.8166 (mtm-85) REVERT: B 366 CYS cc_start: 0.8688 (m) cc_final: 0.7957 (m) REVERT: B 367 ARG cc_start: 0.8941 (mmp80) cc_final: 0.8412 (mmp80) REVERT: B 371 LEU cc_start: 0.9619 (tt) cc_final: 0.9354 (pp) REVERT: B 427 ASN cc_start: 0.9545 (m-40) cc_final: 0.9058 (m-40) outliers start: 2 outliers final: 1 residues processed: 244 average time/residue: 0.0720 time to fit residues: 24.9616 Evaluate side-chains 201 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 199 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 87 optimal weight: 0.0070 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 ASN A 422 GLN B 383 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.111397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.099230 restraints weight = 25216.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.101824 restraints weight = 14779.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.103629 restraints weight = 9708.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.104887 restraints weight = 6912.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.105811 restraints weight = 5247.730| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8172 Z= 0.123 Angle : 0.552 7.978 11158 Z= 0.283 Chirality : 0.039 0.151 1360 Planarity : 0.003 0.034 1418 Dihedral : 7.263 78.465 1504 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.56 % Allowed : 3.09 % Favored : 96.35 % 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: 2.51 (0.26), residues: 1102 helix: 2.68 (0.19), residues: 752 sheet: 1.21 (0.66), residues: 62 loop : -1.14 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 367 TYR 0.012 0.002 TYR B 703 PHE 0.029 0.001 PHE A 571 TRP 0.008 0.001 TRP A 138 HIS 0.003 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8172) covalent geometry : angle 0.55197 (11158) hydrogen bonds : bond 0.04275 ( 602) hydrogen bonds : angle 3.87174 ( 1794) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 235 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LEU cc_start: 0.8139 (tp) cc_final: 0.7861 (tp) REVERT: A 216 LEU cc_start: 0.9095 (tp) cc_final: 0.8796 (tp) REVERT: A 355 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7751 (pm20) REVERT: A 383 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7631 (t0) REVERT: A 427 ASN cc_start: 0.9586 (m-40) cc_final: 0.9126 (m-40) REVERT: A 434 GLN cc_start: 0.8616 (mp10) cc_final: 0.8395 (mp10) REVERT: A 553 PHE cc_start: 0.8646 (t80) cc_final: 0.8311 (t80) REVERT: A 655 ASP cc_start: 0.8583 (m-30) cc_final: 0.8318 (t70) REVERT: B 142 HIS cc_start: 0.8323 (t70) cc_final: 0.8066 (t70) REVERT: B 148 LEU cc_start: 0.8155 (tp) cc_final: 0.7929 (tp) REVERT: B 216 LEU cc_start: 0.9038 (tp) cc_final: 0.8743 (tp) REVERT: B 366 CYS cc_start: 0.8767 (m) cc_final: 0.8382 (m) REVERT: B 383 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.7533 (t0) REVERT: B 434 GLN cc_start: 0.8547 (mp10) cc_final: 0.8262 (mp10) outliers start: 4 outliers final: 1 residues processed: 239 average time/residue: 0.0711 time to fit residues: 24.5149 Evaluate side-chains 201 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 197 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.104910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.092724 restraints weight = 25735.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.095297 restraints weight = 14612.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.097067 restraints weight = 9469.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.098265 restraints weight = 6693.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.099152 restraints weight = 5083.352| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8172 Z= 0.205 Angle : 0.628 7.275 11158 Z= 0.333 Chirality : 0.041 0.148 1360 Planarity : 0.004 0.038 1418 Dihedral : 7.051 77.576 1504 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % 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: 2.32 (0.26), residues: 1102 helix: 2.49 (0.19), residues: 766 sheet: 0.93 (0.67), residues: 62 loop : -1.22 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 365 TYR 0.012 0.002 TYR B 202 PHE 0.020 0.002 PHE B 553 TRP 0.005 0.001 TRP A 138 HIS 0.005 0.001 HIS B 591 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 8172) covalent geometry : angle 0.62840 (11158) hydrogen bonds : bond 0.04862 ( 602) hydrogen bonds : angle 3.94770 ( 1794) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LEU cc_start: 0.8311 (tp) cc_final: 0.8009 (tp) REVERT: A 216 LEU cc_start: 0.9103 (tp) cc_final: 0.8864 (tp) REVERT: A 223 MET cc_start: 0.8960 (tpt) cc_final: 0.8634 (tpt) REVERT: A 226 ASP cc_start: 0.8246 (t0) cc_final: 0.7997 (t0) REVERT: A 356 ARG cc_start: 0.8270 (mtm-85) cc_final: 0.7992 (mtm-85) REVERT: A 414 PHE cc_start: 0.7585 (t80) cc_final: 0.7323 (t80) REVERT: B 148 LEU cc_start: 0.8307 (tp) cc_final: 0.8096 (tp) REVERT: B 216 LEU cc_start: 0.9064 (tp) cc_final: 0.8828 (tp) REVERT: B 356 ARG cc_start: 0.8318 (mtm-85) cc_final: 0.8095 (mtm-85) REVERT: B 366 CYS cc_start: 0.8771 (m) cc_final: 0.8389 (m) REVERT: B 434 GLN cc_start: 0.8568 (mp10) cc_final: 0.8290 (mp10) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.0694 time to fit residues: 21.9566 Evaluate side-chains 185 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 49 optimal weight: 0.0050 chunk 99 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.108849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.096681 restraints weight = 25178.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.099324 restraints weight = 14377.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.101154 restraints weight = 9339.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.102438 restraints weight = 6580.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.103360 restraints weight = 4951.250| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8172 Z= 0.123 Angle : 0.580 7.927 11158 Z= 0.294 Chirality : 0.039 0.149 1360 Planarity : 0.003 0.035 1418 Dihedral : 7.081 77.043 1504 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.61 (0.26), residues: 1102 helix: 2.70 (0.19), residues: 754 sheet: 1.09 (0.66), residues: 62 loop : -0.90 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 356 TYR 0.012 0.002 TYR B 703 PHE 0.022 0.002 PHE B 266 TRP 0.008 0.001 TRP A 138 HIS 0.003 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8172) covalent geometry : angle 0.58006 (11158) hydrogen bonds : bond 0.04724 ( 602) hydrogen bonds : angle 3.79341 ( 1794) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 LEU cc_start: 0.8786 (tp) cc_final: 0.8396 (tp) REVERT: A 148 LEU cc_start: 0.8197 (tp) cc_final: 0.7903 (tp) REVERT: A 226 ASP cc_start: 0.8191 (t0) cc_final: 0.7989 (t0) REVERT: A 356 ARG cc_start: 0.8310 (mtm-85) cc_final: 0.8020 (mtm-85) REVERT: A 491 LYS cc_start: 0.9282 (tppt) cc_final: 0.9002 (mmtt) REVERT: A 655 ASP cc_start: 0.8620 (m-30) cc_final: 0.8352 (t70) REVERT: B 223 MET cc_start: 0.8688 (tpt) cc_final: 0.8466 (tpt) REVERT: B 356 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.8179 (mtm-85) REVERT: B 434 GLN cc_start: 0.8630 (mp10) cc_final: 0.8365 (mp10) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.0734 time to fit residues: 23.3034 Evaluate side-chains 185 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 37 optimal weight: 0.0370 chunk 74 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 overall best weight: 1.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.108399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.096448 restraints weight = 24950.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.099039 restraints weight = 14337.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.100800 restraints weight = 9307.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.102032 restraints weight = 6570.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.102930 restraints weight = 4940.386| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8172 Z= 0.124 Angle : 0.565 7.225 11158 Z= 0.285 Chirality : 0.039 0.140 1360 Planarity : 0.003 0.035 1418 Dihedral : 6.656 75.344 1504 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.28 % Allowed : 2.25 % Favored : 97.47 % 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: 2.62 (0.26), residues: 1102 helix: 2.71 (0.19), residues: 754 sheet: 1.14 (0.65), residues: 62 loop : -0.93 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 365 TYR 0.017 0.002 TYR B 703 PHE 0.018 0.001 PHE B 266 TRP 0.004 0.001 TRP A 138 HIS 0.004 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8172) covalent geometry : angle 0.56492 (11158) hydrogen bonds : bond 0.04618 ( 602) hydrogen bonds : angle 3.75361 ( 1794) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 226 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 LEU cc_start: 0.8139 (tp) cc_final: 0.7864 (tp) REVERT: A 226 ASP cc_start: 0.8242 (t0) cc_final: 0.8001 (t0) REVERT: A 356 ARG cc_start: 0.8307 (mtm-85) cc_final: 0.8073 (mtm-85) REVERT: A 491 LYS cc_start: 0.9268 (tppt) cc_final: 0.8952 (mmtm) REVERT: A 655 ASP cc_start: 0.8592 (m-30) cc_final: 0.8328 (t70) REVERT: B 136 LEU cc_start: 0.8967 (tp) cc_final: 0.8526 (tp) REVERT: B 148 LEU cc_start: 0.8110 (tp) cc_final: 0.7838 (tp) REVERT: B 356 ARG cc_start: 0.8338 (mtm-85) cc_final: 0.8080 (mtm-85) REVERT: B 365 ARG cc_start: 0.7897 (ttt-90) cc_final: 0.7370 (ttt-90) REVERT: B 427 ASN cc_start: 0.9563 (m-40) cc_final: 0.9048 (m-40) REVERT: B 434 GLN cc_start: 0.8591 (mp10) cc_final: 0.8257 (mp10) REVERT: B 538 LEU cc_start: 0.9111 (mp) cc_final: 0.8670 (tp) outliers start: 2 outliers final: 0 residues processed: 228 average time/residue: 0.0680 time to fit residues: 22.4323 Evaluate side-chains 193 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 81 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 37 optimal weight: 0.0980 chunk 108 optimal weight: 5.9990 chunk 95 optimal weight: 0.0670 chunk 63 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.109536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.097300 restraints weight = 25249.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.099955 restraints weight = 14523.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.101764 restraints weight = 9413.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.103045 restraints weight = 6660.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.103971 restraints weight = 5010.950| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8172 Z= 0.120 Angle : 0.572 7.243 11158 Z= 0.291 Chirality : 0.039 0.157 1360 Planarity : 0.003 0.034 1418 Dihedral : 6.772 74.481 1504 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.26), residues: 1102 helix: 2.66 (0.19), residues: 754 sheet: 1.24 (0.65), residues: 62 loop : -0.97 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 356 TYR 0.013 0.002 TYR B 202 PHE 0.022 0.001 PHE B 266 TRP 0.005 0.001 TRP B 138 HIS 0.003 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8172) covalent geometry : angle 0.57236 (11158) hydrogen bonds : bond 0.04618 ( 602) hydrogen bonds : angle 3.78436 ( 1794) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 LEU cc_start: 0.8816 (tp) cc_final: 0.8492 (tp) REVERT: A 148 LEU cc_start: 0.8121 (tp) cc_final: 0.7840 (tp) REVERT: A 226 ASP cc_start: 0.8230 (t0) cc_final: 0.8003 (t0) REVERT: A 356 ARG cc_start: 0.8331 (mtm-85) cc_final: 0.8078 (mtm-85) REVERT: A 427 ASN cc_start: 0.9602 (m-40) cc_final: 0.9138 (m-40) REVERT: A 434 GLN cc_start: 0.8719 (mp10) cc_final: 0.8394 (mp10) REVERT: A 491 LYS cc_start: 0.9261 (tppt) cc_final: 0.8961 (mmtm) REVERT: A 655 ASP cc_start: 0.8572 (m-30) cc_final: 0.8291 (t70) REVERT: B 136 LEU cc_start: 0.8951 (tp) cc_final: 0.8587 (tp) REVERT: B 223 MET cc_start: 0.8880 (tpt) cc_final: 0.8601 (tpt) REVERT: B 356 ARG cc_start: 0.8379 (mtm-85) cc_final: 0.8145 (mtm-85) REVERT: B 365 ARG cc_start: 0.7794 (ttt-90) cc_final: 0.7357 (ttt-90) REVERT: B 427 ASN cc_start: 0.9546 (m-40) cc_final: 0.9021 (m-40) REVERT: B 487 PHE cc_start: 0.7053 (t80) cc_final: 0.6831 (t80) REVERT: B 491 LYS cc_start: 0.9339 (tppt) cc_final: 0.8986 (mmtm) REVERT: B 538 LEU cc_start: 0.9100 (mp) cc_final: 0.8635 (tp) REVERT: B 655 ASP cc_start: 0.8395 (m-30) cc_final: 0.8070 (t70) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.0726 time to fit residues: 24.1323 Evaluate side-chains 194 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 94 optimal weight: 0.0870 chunk 99 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 73 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN B 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.109625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.097547 restraints weight = 25023.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.100191 restraints weight = 14373.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.101982 restraints weight = 9325.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.103238 restraints weight = 6584.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.104143 restraints weight = 4951.771| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8172 Z= 0.120 Angle : 0.566 7.271 11158 Z= 0.289 Chirality : 0.039 0.155 1360 Planarity : 0.003 0.034 1418 Dihedral : 6.740 73.598 1504 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: 2.58 (0.26), residues: 1102 helix: 2.67 (0.19), residues: 754 sheet: 1.32 (0.65), residues: 62 loop : -0.94 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 367 TYR 0.009 0.001 TYR A 202 PHE 0.020 0.001 PHE A 553 TRP 0.004 0.001 TRP B 138 HIS 0.003 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8172) covalent geometry : angle 0.56650 (11158) hydrogen bonds : bond 0.04554 ( 602) hydrogen bonds : angle 3.79502 ( 1794) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 LEU cc_start: 0.8822 (tp) cc_final: 0.8488 (tp) REVERT: A 148 LEU cc_start: 0.8126 (tp) cc_final: 0.7855 (tp) REVERT: A 226 ASP cc_start: 0.8229 (t0) cc_final: 0.7996 (t0) REVERT: A 349 MET cc_start: 0.7547 (mmm) cc_final: 0.7312 (tpt) REVERT: A 491 LYS cc_start: 0.9274 (tppt) cc_final: 0.8988 (mmtm) REVERT: A 553 PHE cc_start: 0.8589 (t80) cc_final: 0.8297 (t80) REVERT: A 655 ASP cc_start: 0.8572 (m-30) cc_final: 0.8291 (t70) REVERT: B 136 LEU cc_start: 0.8960 (tp) cc_final: 0.8601 (tp) REVERT: B 356 ARG cc_start: 0.8389 (mtm-85) cc_final: 0.8145 (mtm-85) REVERT: B 365 ARG cc_start: 0.7896 (ttt-90) cc_final: 0.7434 (ttt-90) REVERT: B 370 GLU cc_start: 0.8532 (mp0) cc_final: 0.8226 (mt-10) REVERT: B 434 GLN cc_start: 0.8662 (mp10) cc_final: 0.8376 (mp10) REVERT: B 487 PHE cc_start: 0.7040 (t80) cc_final: 0.6830 (t80) REVERT: B 538 LEU cc_start: 0.9104 (mp) cc_final: 0.8647 (tp) REVERT: B 655 ASP cc_start: 0.8358 (m-30) cc_final: 0.8055 (t70) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.0751 time to fit residues: 24.8898 Evaluate side-chains 196 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.0060 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 20.0000 chunk 94 optimal weight: 0.0470 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 93 optimal weight: 0.0870 chunk 106 optimal weight: 1.9990 overall best weight: 0.4074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.110441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.098263 restraints weight = 24935.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.100903 restraints weight = 14399.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.102739 restraints weight = 9354.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.104007 restraints weight = 6594.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.104917 restraints weight = 4963.684| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8172 Z= 0.124 Angle : 0.597 7.421 11158 Z= 0.307 Chirality : 0.039 0.158 1360 Planarity : 0.003 0.033 1418 Dihedral : 6.716 72.789 1504 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 2.57 (0.26), residues: 1102 helix: 2.62 (0.19), residues: 754 sheet: 1.46 (0.65), residues: 62 loop : -0.86 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 356 TYR 0.010 0.001 TYR A 202 PHE 0.022 0.002 PHE B 266 TRP 0.006 0.001 TRP B 138 HIS 0.003 0.001 HIS B 668 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8172) covalent geometry : angle 0.59745 (11158) hydrogen bonds : bond 0.04524 ( 602) hydrogen bonds : angle 3.87582 ( 1794) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 LEU cc_start: 0.8814 (tp) cc_final: 0.8484 (tp) REVERT: A 148 LEU cc_start: 0.8126 (tp) cc_final: 0.7844 (tp) REVERT: A 226 ASP cc_start: 0.8203 (t0) cc_final: 0.7975 (t0) REVERT: A 427 ASN cc_start: 0.9600 (m-40) cc_final: 0.9136 (m-40) REVERT: A 491 LYS cc_start: 0.9274 (tppt) cc_final: 0.8976 (mmtm) REVERT: A 553 PHE cc_start: 0.8573 (t80) cc_final: 0.8288 (t80) REVERT: A 655 ASP cc_start: 0.8519 (m-30) cc_final: 0.8246 (t70) REVERT: B 136 LEU cc_start: 0.8951 (tp) cc_final: 0.8591 (tp) REVERT: B 223 MET cc_start: 0.8781 (tpt) cc_final: 0.8579 (tpt) REVERT: B 356 ARG cc_start: 0.8428 (mtm-85) cc_final: 0.8203 (mtm-85) REVERT: B 365 ARG cc_start: 0.7815 (ttt-90) cc_final: 0.7084 (ttt-90) REVERT: B 427 ASN cc_start: 0.9539 (m-40) cc_final: 0.9012 (m-40) REVERT: B 434 GLN cc_start: 0.8544 (mp10) cc_final: 0.8178 (mp10) REVERT: B 487 PHE cc_start: 0.7095 (t80) cc_final: 0.6877 (t80) REVERT: B 491 LYS cc_start: 0.9275 (tppt) cc_final: 0.8936 (mmtt) REVERT: B 538 LEU cc_start: 0.9113 (mp) cc_final: 0.8663 (tp) REVERT: B 557 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8808 (pt0) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.0727 time to fit residues: 24.6604 Evaluate side-chains 198 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN B 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.109139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.096988 restraints weight = 24929.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.099610 restraints weight = 14393.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.101398 restraints weight = 9352.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.102658 restraints weight = 6612.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.103573 restraints weight = 4976.020| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8172 Z= 0.130 Angle : 0.582 7.230 11158 Z= 0.301 Chirality : 0.040 0.160 1360 Planarity : 0.003 0.034 1418 Dihedral : 6.697 72.870 1504 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: 2.62 (0.26), residues: 1102 helix: 2.67 (0.19), residues: 754 sheet: 1.43 (0.65), residues: 62 loop : -0.87 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 367 TYR 0.012 0.002 TYR B 202 PHE 0.019 0.002 PHE A 266 TRP 0.004 0.001 TRP A 688 HIS 0.003 0.001 HIS B 668 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8172) covalent geometry : angle 0.58231 (11158) hydrogen bonds : bond 0.04535 ( 602) hydrogen bonds : angle 3.87692 ( 1794) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 LEU cc_start: 0.8820 (tp) cc_final: 0.8487 (tp) REVERT: A 148 LEU cc_start: 0.8127 (tp) cc_final: 0.7829 (tp) REVERT: A 226 ASP cc_start: 0.8230 (t0) cc_final: 0.8018 (t0) REVERT: A 387 ASN cc_start: 0.8521 (m-40) cc_final: 0.8316 (m-40) REVERT: A 427 ASN cc_start: 0.9594 (m-40) cc_final: 0.9137 (m-40) REVERT: A 491 LYS cc_start: 0.9340 (tppt) cc_final: 0.9045 (tppt) REVERT: B 136 LEU cc_start: 0.8973 (tp) cc_final: 0.8733 (tp) REVERT: B 148 LEU cc_start: 0.8032 (tp) cc_final: 0.7787 (tp) REVERT: B 356 ARG cc_start: 0.8420 (mtm-85) cc_final: 0.8149 (mtm-85) REVERT: B 365 ARG cc_start: 0.7794 (ttt-90) cc_final: 0.7559 (ttt180) REVERT: B 487 PHE cc_start: 0.7065 (t80) cc_final: 0.6849 (t80) REVERT: B 491 LYS cc_start: 0.9278 (tppt) cc_final: 0.8897 (mmtt) REVERT: B 538 LEU cc_start: 0.9112 (mp) cc_final: 0.8642 (tp) REVERT: B 557 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8816 (pt0) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.0677 time to fit residues: 22.1566 Evaluate side-chains 189 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 89 optimal weight: 0.1980 chunk 66 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.109279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.097122 restraints weight = 25184.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.099746 restraints weight = 14566.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.101562 restraints weight = 9492.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.102787 restraints weight = 6727.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.103725 restraints weight = 5098.692| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8172 Z= 0.127 Angle : 0.587 7.429 11158 Z= 0.305 Chirality : 0.039 0.165 1360 Planarity : 0.003 0.033 1418 Dihedral : 6.748 73.453 1504 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: 2.60 (0.26), residues: 1102 helix: 2.65 (0.19), residues: 754 sheet: 1.44 (0.65), residues: 62 loop : -0.87 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 367 TYR 0.012 0.002 TYR B 202 PHE 0.020 0.001 PHE B 266 TRP 0.004 0.001 TRP B 138 HIS 0.003 0.001 HIS B 668 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8172) covalent geometry : angle 0.58728 (11158) hydrogen bonds : bond 0.04559 ( 602) hydrogen bonds : angle 3.88394 ( 1794) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1268.21 seconds wall clock time: 22 minutes 28.37 seconds (1348.37 seconds total)