Starting phenix.real_space_refine on Fri Oct 23 01:55:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sf9_54817/10_2026/9sf9_54817.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sf9_54817/10_2026/9sf9_54817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sf9_54817/10_2026/9sf9_54817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sf9_54817/10_2026/9sf9_54817.map" model { file = "/net/cci-nas-00/data/ceres_data/9sf9_54817/10_2026/9sf9_54817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sf9_54817/10_2026/9sf9_54817.cif" } resolution = 2.8 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= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 4815 2.51 5 N 1308 2.21 5 O 1416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7560 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3712 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 524, 3707 Classifications: {'peptide': 524} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 99} Link IDs: {'PTRANS': 25, 'TRANS': 498} Chain breaks: 17 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 385 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLU:plan': 17, 'TYR:plan': 1, 'ASP:plan': 22, 'ASN:plan1': 7, 'ARG:plan': 10, 'PHE:plan': 2, 'GLN:plan1': 9, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 244 Conformer: "B" Number of residues, atoms: 524, 3707 Classifications: {'peptide': 524} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 99} Link IDs: {'PTRANS': 25, 'TRANS': 498} Chain breaks: 17 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 385 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLU:plan': 17, 'TYR:plan': 1, 'ASP:plan': 22, 'ASN:plan1': 7, 'ARG:plan': 10, 'PHE:plan': 2, 'GLN:plan1': 9, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 244 bond proxies already assigned to first conformer: 3763 Chain: "B" Number of atoms: 3848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 3848 Classifications: {'peptide': 551} Incomplete info: {'backbone_only': 4, 'n_c_alpha_c_only': 5, 'truncation_to_alanine': 111} Link IDs: {'PTRANS': 25, 'TRANS': 525} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 10 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 444 Unresolved non-hydrogen angles: 549 Unresolved non-hydrogen dihedrals: 335 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLU:plan': 21, 'GLN:plan1': 9, 'ASP:plan': 21, 'ASN:plan1': 9, 'ARG:plan': 9, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 247 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 318 " occ=0.51 ... (8 atoms not shown) pdb=" CB BTYR A 318 " occ=0.49 Time building chain proxies: 2.10, per 1000 atoms: 0.28 Number of scatterers: 7560 At special positions: 0 Unit cell: (68.4, 96.9, 112.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 1416 8.00 N 1308 7.00 C 4815 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: 0.55 Conformation dependent library (CDL) restraints added in 523.2 milliseconds 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1970 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 15 sheets defined 16.5% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 291 through 297 Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 427 through 434 Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 607 through 621 Processing helix chain 'A' and resid 689 through 693 Processing helix chain 'A' and resid 736 through 753 removed outlier: 4.151A pdb=" N ARG A 740 " --> pdb=" O LYS A 736 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 743 " --> pdb=" O GLN A 739 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 750 " --> pdb=" O ASN A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 782 removed outlier: 3.506A pdb=" N GLN A 778 " --> pdb=" O THR A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 797 removed outlier: 3.936A pdb=" N ARG A 797 " --> pdb=" O ILE A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 819 No H-bonds generated for 'chain 'A' and resid 817 through 819' Processing helix chain 'A' and resid 834 through 838 removed outlier: 3.665A pdb=" N GLY A 838 " --> pdb=" O GLU A 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 Processing helix chain 'B' and resid 373 through 378 Processing helix chain 'B' and resid 427 through 434 Processing helix chain 'B' and resid 567 through 580 Processing helix chain 'B' and resid 607 through 621 removed outlier: 3.540A pdb=" N ALA B 611 " --> pdb=" O ALA B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 757 removed outlier: 3.542A pdb=" N ARG B 741 " --> pdb=" O SER B 737 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 751 " --> pdb=" O MET B 747 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 752 " --> pdb=" O LEU B 748 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU B 754 " --> pdb=" O GLN B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 781 Processing helix chain 'B' and resid 817 through 820 removed outlier: 3.926A pdb=" N ASP B 820 " --> pdb=" O HIS B 817 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 817 through 820' Processing sheet with id=AA1, first strand: chain 'A' and resid 315 through 318 removed outlier: 6.602A pdb=" N TYR A 326 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N THR A 382 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG A 343 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 401 through 402 removed outlier: 6.119A pdb=" N LEU A 401 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ASP A 443 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 504 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS A 446 " --> pdb=" O TYR A 502 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N TYR A 502 " --> pdb=" O LYS A 446 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 401 through 402 removed outlier: 6.119A pdb=" N LEU A 401 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ASP A 443 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL A 521 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEU A 488 " --> pdb=" O VAL A 521 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 627 through 629 removed outlier: 6.878A pdb=" N GLY A 649 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ILE A 591 " --> pdb=" O GLY A 649 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU A 651 " --> pdb=" O GLY A 589 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N GLY A 589 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ILE A 588 " --> pdb=" O SER A 553 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N ASN A 555 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N LEU A 590 " --> pdb=" O ASN A 555 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N GLU A 557 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLU A 592 " --> pdb=" O GLU A 557 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 658 through 659 Processing sheet with id=AA6, first strand: chain 'A' and resid 658 through 659 removed outlier: 5.419A pdb=" N LYS A 697 " --> pdb=" O HIS A 716 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N HIS A 716 " --> pdb=" O LYS A 697 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN A 761 " --> pdb=" O LYS A 709 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE A 762 " --> pdb=" O SER A 815 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 800 through 802 Processing sheet with id=AA8, first strand: chain 'B' and resid 356 through 357 removed outlier: 6.563A pdb=" N TYR B 326 " --> pdb=" O THR B 317 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N GLY B 341 " --> pdb=" O THR B 382 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N ILE B 384 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG B 343 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN B 383 " --> pdb=" O GLU B 364 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 401 through 402 removed outlier: 5.841A pdb=" N LEU B 401 " --> pdb=" O ALA B 441 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ASP B 443 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N VAL B 521 " --> pdb=" O PRO B 486 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU B 488 " --> pdb=" O VAL B 521 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 473 through 474 removed outlier: 6.203A pdb=" N VAL B 473 " --> pdb=" O ASN B 806 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 501 through 503 Processing sheet with id=AB3, first strand: chain 'B' and resid 627 through 629 removed outlier: 6.863A pdb=" N GLY B 649 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE B 591 " --> pdb=" O GLY B 649 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU B 651 " --> pdb=" O GLY B 589 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLY B 589 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL B 593 " --> pdb=" O ILE B 556 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN B 558 " --> pdb=" O VAL B 593 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 658 through 659 Processing sheet with id=AB5, first strand: chain 'B' and resid 658 through 659 removed outlier: 7.107A pdb=" N LYS B 709 " --> pdb=" O ASN B 761 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N VAL B 763 " --> pdb=" O LYS B 709 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL B 711 " --> pdb=" O VAL B 763 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU B 765 " --> pdb=" O VAL B 711 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL B 713 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ASP B 767 " --> pdb=" O VAL B 713 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASN B 715 " --> pdb=" O ASP B 767 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 762 " --> pdb=" O SER B 815 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 673 through 674 246 hydrogen bonds defined for protein. 624 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: 1.36 Time building geometry restraints manager: 0.77 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: 2511 1.34 - 1.46: 1176 1.46 - 1.58: 3969 1.58 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 7696 Sorted by residual: bond pdb=" N GLY B 728 " pdb=" CA GLY B 728 " ideal model delta sigma weight residual 1.444 1.477 -0.033 9.10e-03 1.21e+04 1.32e+01 bond pdb=" N VAL B 363 " pdb=" CA VAL B 363 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.21e+01 bond pdb=" N VAL B 351 " pdb=" CA VAL B 351 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.36e+00 bond pdb=" N ILE B 456 " pdb=" CA ILE B 456 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.08e-02 8.57e+03 9.36e+00 bond pdb=" N VAL B 421 " pdb=" CA VAL B 421 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.30e+00 ... (remaining 7691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 10099 2.89 - 5.78: 355 5.78 - 8.66: 26 8.66 - 11.55: 2 11.55 - 14.44: 1 Bond angle restraints: 10483 Sorted by residual: angle pdb=" N PRO B 732 " pdb=" CA PRO B 732 " pdb=" C PRO B 732 " ideal model delta sigma weight residual 114.80 100.36 14.44 1.42e+00 4.96e-01 1.03e+02 angle pdb=" N PHE B 366 " pdb=" CA PHE B 366 " pdb=" CB PHE B 366 " ideal model delta sigma weight residual 110.38 100.37 10.01 1.37e+00 5.33e-01 5.33e+01 angle pdb=" N PRO B 303 " pdb=" CA PRO B 303 " pdb=" C PRO B 303 " ideal model delta sigma weight residual 113.78 104.48 9.30 1.62e+00 3.81e-01 3.30e+01 angle pdb=" N PRO A 732 " pdb=" CA PRO A 732 " pdb=" CB PRO A 732 " ideal model delta sigma weight residual 103.00 96.71 6.29 1.10e+00 8.26e-01 3.27e+01 angle pdb=" N THR A 464 " pdb=" CA THR A 464 " pdb=" C THR A 464 " ideal model delta sigma weight residual 112.72 106.24 6.48 1.14e+00 7.69e-01 3.23e+01 ... (remaining 10478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4007 17.95 - 35.90: 371 35.90 - 53.85: 110 53.85 - 71.80: 23 71.80 - 89.75: 4 Dihedral angle restraints: 4515 sinusoidal: 1459 harmonic: 3056 Sorted by residual: dihedral pdb=" CA ASN B 416 " pdb=" C ASN B 416 " pdb=" N ASP B 417 " pdb=" CA ASP B 417 " ideal model delta harmonic sigma weight residual -180.00 -157.12 -22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ALA B 690 " pdb=" C ALA B 690 " pdb=" N ALA B 691 " pdb=" CA ALA B 691 " ideal model delta harmonic sigma weight residual 180.00 157.44 22.56 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" N PHE B 366 " pdb=" C PHE B 366 " pdb=" CA PHE B 366 " pdb=" CB PHE B 366 " ideal model delta harmonic sigma weight residual 122.80 113.10 9.70 0 2.50e+00 1.60e-01 1.50e+01 ... (remaining 4512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 927 0.066 - 0.133: 234 0.133 - 0.199: 61 0.199 - 0.266: 14 0.266 - 0.332: 2 Chirality restraints: 1238 Sorted by residual: chirality pdb=" CB VAL B 789 " pdb=" CA VAL B 789 " pdb=" CG1 VAL B 789 " pdb=" CG2 VAL B 789 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA ILE B 812 " pdb=" N ILE B 812 " pdb=" C ILE B 812 " pdb=" CB ILE B 812 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA VAL B 730 " pdb=" N VAL B 730 " pdb=" C VAL B 730 " pdb=" CB VAL B 730 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 1235 not shown) Planarity restraints: 1366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 791 " -0.493 9.50e-02 1.11e+02 2.21e-01 2.98e+01 pdb=" NE ARG A 791 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 791 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 791 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 791 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 791 " 0.437 9.50e-02 1.11e+02 1.96e-01 2.35e+01 pdb=" NE ARG B 791 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG B 791 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 791 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 791 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 658 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C SER A 658 " -0.059 2.00e-02 2.50e+03 pdb=" O SER A 658 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU A 659 " 0.020 2.00e-02 2.50e+03 ... (remaining 1363 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 245 2.67 - 3.23: 7026 3.23 - 3.79: 12019 3.79 - 4.34: 17505 4.34 - 4.90: 27663 Nonbonded interactions: 64458 Sorted by model distance: nonbonded pdb=" O ASN B 689 " pdb=" OD1 ASN B 689 " model vdw 2.117 3.040 nonbonded pdb=" OH TYR A 512 " pdb=" O TYR A 727 " model vdw 2.223 3.040 nonbonded pdb=" ND2 ASN A 469 " pdb=" OD1 ASP A 796 " model vdw 2.240 3.120 nonbonded pdb=" O PRO B 410 " pdb=" OG1 THR B 482 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR A 628 " pdb=" OD2 ASP A 630 " model vdw 2.292 3.040 ... (remaining 64453 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' and (resid 291 through 292 or (resid 293 and (name N or name CA or na \ me C )) or resid 294 through 301 or (resid 302 and (name N or name CA or name C \ or name O or name CB )) or resid 303 through 304 or (resid 305 and (name N or na \ me CA or name C or name O )) or (resid 306 and (name N or name CA or name C )) o \ r resid 307 or (resid 308 and (name N or name CA or name C or name O )) or resid \ 310 through 317 or resid 321 or resid 323 through 328 or (resid 329 through 331 \ and (name N or name CA or name C or name O or name CB )) or resid 332 through 3 \ 33 or (resid 335 through 337 and (name N or name CA or name C or name O or name \ CB )) or resid 338 through 355 or (resid 356 and (name N or name CA or name C or \ name O or name CB or name CG1)) or resid 357 through 364 or (resid 365 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD )) or resid \ 366 through 374 or (resid 375 through 376 and (name N or name CA or name C or na \ me O or name CB )) or resid 377 through 383 or (resid 384 and (name N or name CA \ or name C or name O or name CB )) or (resid 385 and (name N or name CA or name \ C )) or (resid 386 and (name N or name CA or name C or name O )) or resid 397 th \ rough 406 or (resid 407 through 409 and (name N or name CA or name C or name O o \ r name CB )) or resid 410 through 419 or (resid 421 and (name N or name CA or na \ me C or name CB )) or resid 422 or (resid 423 and (name N or name CA or name C o \ r name O )) or resid 424 through 432 or (resid 433 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1)) or resid 434 throug \ h 435 or (resid 436 and (name N or name CA or name C or name O or name CB )) or \ resid 437 through 461 or (resid 462 and (name N or name CA or name C or name O o \ r name CB )) or resid 463 through 468 or (resid 469 and (name N or name CA or na \ me C or name O or name CB )) or resid 470 through 517 or (resid 518 and (name N \ or name CA or name C or name O or name CB )) or resid 519 through 523 or (resid \ 524 and (name N or name CA or name C or name O or name CB )) or resid 527 throug \ h 530 or (resid 531 through 532 and (name N or name CA or name C or name O or na \ me CB )) or resid 533 through 535 or (resid 536 and (name N or name CA or name C \ or name O or name CB )) or resid 537 through 575 or (resid 576 and (name N or n \ ame CA or name C or name O or name CB )) or resid 577 through 600 or (resid 601 \ through 602 and (name N or name CA or name C or name O or name CB )) or resid 60 \ 3 through 608 or (resid 609 and (name N or name CA or name C or name O or name C \ B )) or resid 610 through 626 or (resid 627 and (name N or name CA or name C or \ name O or name CB )) or resid 628 through 630 or (resid 631 through 632 and (nam \ e N or name CA or name C or name O or name CB )) or resid 633 or (resid 634 and \ (name N or name CA or name C or name O or name CB )) or resid 635 through 636 or \ (resid 637 through 638 and (name N or name CA or name C or name O or name CB )) \ or resid 639 through 696 or (resid 697 and (name N or name CA or name C or name \ O or name CB )) or resid 698 through 701 or (resid 702 and (name N or name CA o \ r name C or name O or name CB )) or resid 703 through 722 or (resid 723 through \ 725 and (name N or name CA or name C or name O or name CB )) or resid 726 throug \ h 730 or (resid 731 and (name N or name CA or name C or name O or name CB )) or \ resid 732 or (resid 735 through 736 and (name N or name CA or name C or name O o \ r name CB )) or resid 737 through 739 or (resid 740 and (name N or name CA or na \ me C or name O or name CB )) or resid 741 through 742 or (resid 743 and (name N \ or name CA or name C or name O or name CB )) or resid 744 through 761 or (resid \ 762 and (name N or name CA or name C or name O or name CB )) or resid 763 throug \ h 766 or (resid 767 and (name N or name CA or name C or name O or name CB )) or \ resid 768 through 774 or (resid 775 and (name N or name CA or name C or name O o \ r name CB )) or resid 776 through 780 or (resid 781 and (name N or name CA or na \ me C or name O or name CB )) or resid 784 through 793 or (resid 794 and (name N \ or name CA or name C or name O or name CB )) or resid 795 through 809 or (resid \ 810 and (name N or name CA or name C or name O or name CB )) or resid 811 throug \ h 819 or (resid 820 and (name N or name CA or name C or name O or name CB )) or \ resid 821 through 834 or (resid 835 through 836 and (name N or name CA or name C \ or name O or name CB )) or resid 837 through 841 or (resid 842 and (name N or n \ ame CA or name C or name O or name CB or name CG or name OD2)) or resid 843 thro \ ugh 852)) selection = (chain 'B' and (resid 291 through 298 or (resid 299 and (name N or name CA or na \ me C or name O or name CB )) or resid 300 through 306 or (resid 307 and (name N \ or name CA or name C or name O or name CB )) or resid 308 or (resid 310 through \ 312 and (name N or name CA or name C or name O or name CB )) or resid 314 or (re \ sid 315 and (name N or name CA or name C or name O or name CB )) or resid 316 th \ rough 317 or resid 320 or resid 323 through 342 or (resid 343 and (name N or nam \ e CA or name C or name O or name CB )) or resid 344 or (resid 345 through 346 an \ d (name N or name CA or name C or name O or name CB )) or resid 352 through 353 \ or resid 355 through 357 or resid 362 through 363 or (resid 364 and (name N or n \ ame CA or name C or name O or name CB )) or resid 365 or (resid 366 and (name N \ or name CA or name C or name O or name CB )) or resid 367 through 386 or (resid \ 397 and (name N or name CA or name C or name O or name CB )) or resid 398 throug \ h 405 or (resid 406 through 409 and (name N or name CA or name C or name O or na \ me CB )) or resid 410 through 411 or (resid 412 and (name N or name CA or name C \ or name O or name CB )) or resid 413 or resid 415 through 419 or resid 421 thro \ ugh 442 or (resid 443 through 445 and (name N or name CA or name C or name O or \ name CB )) or resid 446 through 464 or (resid 465 and (name N or name CA or name \ C or name O or name CB )) or resid 466 through 492 or (resid 494 and (name N or \ name CA or name C or name O or name CB or name CG or name CD )) or (resid 495 a \ nd (name N or name CA or name C or name O or name CB )) or resid 496 through 504 \ or (resid 505 and (name N or name CA or name C or name O or name CB )) or resid \ 506 through 521 or (resid 522 through 524 and (name N or name CA or name C or n \ ame O or name CB )) or resid 527 through 528 or resid 530 through 531 or (resid \ 532 and (name N or name CA or name C or name O or name CB )) or resid 533 throug \ h 544 or (resid 545 and (name N or name CA or name C or name O or name CB )) or \ resid 546 or (resid 547 through 548 and (name N or name CA or name C or name O o \ r name CB )) or resid 549 through 563 or (resid 564 and (name N or name CA or na \ me C or name O or name CB )) or resid 565 through 567 or (resid 568 through 569 \ and (name N or name CA or name C or name O or name CB )) or resid 570 through 60 \ 1 or (resid 602 and (name N or name CA or name C or name O or name CB )) or resi \ d 603 through 615 or (resid 616 through 617 and (name N or name CA or name C or \ name O or name CB )) or resid 618 or (resid 619 through 620 and (name N or name \ CA or name C or name O or name CB )) or resid 621 through 624 or (resid 625 and \ (name N or name CA or name C or name O or name CB )) or resid 626 through 640 or \ (resid 641 and (name N or name CA or name C or name CB or name CG or name CD or \ name OE1)) or resid 642 through 657 or (resid 658 and (name N or name CA or nam \ e C or name O or name CB )) or resid 659 through 660 or (resid 662 through 663 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD )) or \ resid 664 through 668 or (resid 669 through 670 and (name N or name CA or name \ C or name O or name CB )) or resid 671 through 673 or resid 677 through 678 or ( \ resid 679 and (name N or name CA or name C or name O or name CB )) or resid 680 \ through 687 or (resid 688 through 689 and (name N or name CA or name C or name O \ or name CB )) or (resid 690 and (name N or name CA or name C or name O )) or re \ sid 691 through 707 or (resid 708 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name NE or name CZ )) or resid 709 through 732 \ or (resid 735 through 736 and (name N or name CA or name C or name O or name CB \ )) or resid 737 through 752 or (resid 753 and (name N or name CA or name C or na \ me CB )) or resid 754 through 756 or resid 759 through 792 or (resid 793 through \ 794 and (name N or name CA or name C or name O or name CB )) or resid 795 throu \ gh 816 or (resid 817 and (name N or name CA or name C or name O or name CB )) or \ resid 818 through 852)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.920 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 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 : 0.008 0.054 7696 Z= 0.525 Angle : 1.131 14.439 10483 Z= 0.773 Chirality : 0.067 0.332 1238 Planarity : 0.009 0.221 1366 Dihedral : 16.208 89.745 2545 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 1.07 % Allowed : 6.45 % Favored : 92.48 % Rotamer: Outliers : 7.01 % Allowed : 19.27 % Favored : 73.72 % Cbeta Deviations : 0.10 % 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: -2.08 (0.24), residues: 1025 helix: -0.67 (0.44), residues: 140 sheet: -1.18 (0.31), residues: 222 loop : -1.68 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 740 TYR 0.018 0.002 TYR B 800 PHE 0.014 0.002 PHE A 559 TRP 0.006 0.001 TRP B 692 HIS 0.004 0.001 HIS B 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00755 / 0.52 ( 7696) covalent geometry : angle 1.13143 / 0.77 (10483) hydrogen bonds : bond 0.14819 / 10.05 ( 242) hydrogen bonds : angle 6.95636 / 4.86 ( 624) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 105 time to evaluate : 0.218 Fit side-chains TARDY: cannot create tardy model for: "GLN A 641 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP B 321 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 435 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7214 (ttp) REVERT: B 315 VAL cc_start: 0.8005 (OUTLIER) cc_final: 0.7791 (p) REVERT: B 532 ASP cc_start: 0.7452 (t0) cc_final: 0.6903 (m-30) REVERT: B 557 GLU cc_start: 0.7547 (tt0) cc_final: 0.7314 (mt-10) REVERT: B 796 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.7065 (t0) REVERT: B 806 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.7420 (m110) outliers start: 48 outliers final: 25 residues processed: 139 average time/residue: 0.3071 time to fit residues: 46.8289 Evaluate side-chains 124 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 469 ASN Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 641 GLN Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 729 CYS Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 729 CYS Chi-restraints excluded: chain B residue 730 VAL Chi-restraints excluded: chain B residue 737 SER Chi-restraints excluded: chain B residue 795 SER Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 806 ASN Chi-restraints excluded: chain B residue 827 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 100, 106, 38] chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 GLN A 597 ASN B 689 ASN B 792 HIS ** B 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.164119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.133150 restraints weight = 8429.216| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.81 r_work: 0.3493 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7696 Z= 0.121 Angle : 0.558 6.734 10483 Z= 0.295 Chirality : 0.045 0.143 1238 Planarity : 0.004 0.034 1366 Dihedral : 7.031 73.589 1154 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.71 % Favored : 96.00 % Rotamer: Outliers : 4.96 % Allowed : 18.83 % Favored : 76.20 % 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: -1.55 (0.25), residues: 1025 helix: -0.20 (0.44), residues: 145 sheet: -1.24 (0.32), residues: 221 loop : -1.16 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 407 TYR 0.014 0.001 TYR B 800 PHE 0.013 0.001 PHE B 366 TRP 0.006 0.001 TRP A 692 HIS 0.006 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 7696) covalent geometry : angle 0.55814 / 0.29 (10483) hydrogen bonds : bond 0.03919 / 2.86 ( 242) hydrogen bonds : angle 5.18203 / 3.59 ( 624) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.178 Fit side-chains REVERT: A 415 ASP cc_start: 0.6526 (OUTLIER) cc_final: 0.6070 (p0) REVERT: B 455 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7342 (tt0) REVERT: B 557 GLU cc_start: 0.7199 (tt0) cc_final: 0.6812 (tp30) REVERT: B 592 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7636 (mt-10) REVERT: B 608 THR cc_start: 0.7547 (m) cc_final: 0.7176 (m) REVERT: B 796 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.7160 (t0) REVERT: B 811 ASN cc_start: 0.7580 (m-40) cc_final: 0.7376 (m-40) REVERT: B 822 TYR cc_start: 0.8387 (p90) cc_final: 0.8162 (p90) outliers start: 34 outliers final: 14 residues processed: 122 average time/residue: 0.3184 time to fit residues: 42.6186 Evaluate side-chains 105 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 729 CYS Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 795 SER Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 829 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [13, 10, 43, 53, 68, 39, 83, 27, 63, 59, 22] chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 GLN A 469 ASN A 724 ASN A 787 ASN A 811 ASN A 821 HIS B 689 ASN B 787 ASN B 805 ASN ** B 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.158418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.127554 restraints weight = 8596.147| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.80 r_work: 0.3429 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 7696 Z= 0.379 Angle : 0.766 7.402 10483 Z= 0.403 Chirality : 0.053 0.172 1238 Planarity : 0.006 0.045 1366 Dihedral : 6.386 51.782 1126 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.66 % Favored : 94.04 % Rotamer: Outliers : 6.86 % Allowed : 18.25 % Favored : 74.89 % 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: -1.99 (0.24), residues: 1025 helix: -0.96 (0.40), residues: 144 sheet: -1.57 (0.31), residues: 229 loop : -1.32 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 407 TYR 0.019 0.003 TYR A 512 PHE 0.030 0.003 PHE B 366 TRP 0.008 0.002 TRP B 432 HIS 0.012 0.002 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00907 / 0.38 ( 7696) covalent geometry : angle 0.76619 / 0.40 (10483) hydrogen bonds : bond 0.04836 / 3.55 ( 242) hydrogen bonds : angle 5.43577 / 3.79 ( 624) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 84 time to evaluate : 0.275 Fit side-chains REVERT: B 726 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7124 (mt) REVERT: B 785 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.7809 (mmm) REVERT: B 791 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7767 (mtp85) REVERT: B 793 ASP cc_start: 0.7053 (t0) cc_final: 0.6638 (m-30) REVERT: B 796 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7266 (t0) REVERT: B 806 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.7503 (m110) REVERT: B 822 TYR cc_start: 0.8673 (p90) cc_final: 0.8244 (p90) outliers start: 47 outliers final: 33 residues processed: 115 average time/residue: 0.3586 time to fit residues: 44.9161 Evaluate side-chains 115 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 78 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 469 ASN Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 696 ARG Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 729 CYS Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 795 SER Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 806 ASN Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [40, 56, 32, 105, 101, 99, 100, 2, 28, 73, 52] chunk 40 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 GLN ** B 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 ASN ** B 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.163042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.132260 restraints weight = 8558.529| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.82 r_work: 0.3450 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7696 Z= 0.172 Angle : 0.587 7.036 10483 Z= 0.309 Chirality : 0.046 0.149 1238 Planarity : 0.004 0.039 1366 Dihedral : 5.780 51.193 1126 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.81 % Favored : 96.00 % Rotamer: Outliers : 5.11 % Allowed : 19.85 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.25), residues: 1025 helix: -0.42 (0.42), residues: 145 sheet: -1.52 (0.32), residues: 219 loop : -1.05 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 407 TYR 0.015 0.002 TYR B 800 PHE 0.013 0.002 PHE B 366 TRP 0.006 0.001 TRP A 692 HIS 0.007 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 7696) covalent geometry : angle 0.58706 / 0.31 (10483) hydrogen bonds : bond 0.03868 / 2.86 ( 242) hydrogen bonds : angle 5.05606 / 3.51 ( 624) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 88 time to evaluate : 0.199 Fit side-chains TARDY: cannot create tardy model for: "ASP B 321 " (corrupted residue). Skipping it. REVERT: A 544 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.7091 (tppt) REVERT: A 839 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.6760 (ttt180) REVERT: B 557 GLU cc_start: 0.7215 (tt0) cc_final: 0.6987 (tp30) REVERT: B 595 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7581 (p0) REVERT: B 726 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6841 (mt) REVERT: B 791 ARG cc_start: 0.7942 (mtp85) cc_final: 0.7737 (mtp85) REVERT: B 793 ASP cc_start: 0.6967 (t0) cc_final: 0.6634 (m-30) REVERT: B 796 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.7177 (t0) REVERT: B 822 TYR cc_start: 0.8612 (p90) cc_final: 0.8256 (p90) REVERT: B 826 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7560 (mtt) outliers start: 35 outliers final: 21 residues processed: 109 average time/residue: 0.3625 time to fit residues: 42.9077 Evaluate side-chains 108 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 469 ASN Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 729 CYS Chi-restraints excluded: chain A residue 839 ARG Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 729 CYS Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [98, 70, 48, 16, 84, 27, 71, 59, 68, 58, 92] chunk 98 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 16 optimal weight: 0.0870 chunk 84 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 GLN A 469 ASN ** B 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 689 ASN B 787 ASN ** B 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.161398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.130479 restraints weight = 8518.244| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.82 r_work: 0.3463 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7696 Z= 0.222 Angle : 0.614 6.483 10483 Z= 0.323 Chirality : 0.047 0.153 1238 Planarity : 0.004 0.041 1366 Dihedral : 5.744 50.194 1125 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.39 % Favored : 95.41 % Rotamer: Outliers : 6.86 % Allowed : 18.98 % Favored : 74.16 % 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: -1.57 (0.25), residues: 1025 helix: -0.36 (0.41), residues: 145 sheet: -1.48 (0.33), residues: 217 loop : -1.04 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 407 TYR 0.016 0.002 TYR B 800 PHE 0.015 0.002 PHE B 366 TRP 0.005 0.001 TRP B 432 HIS 0.008 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.22 ( 7696) covalent geometry : angle 0.61410 / 0.32 (10483) hydrogen bonds : bond 0.04008 / 2.98 ( 242) hydrogen bonds : angle 5.08591 / 3.53 ( 624) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 82 time to evaluate : 0.278 Fit side-chains REVERT: A 469 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8436 (m-40) REVERT: A 544 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.7100 (tppt) REVERT: A 696 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.6842 (mpp-170) REVERT: A 839 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.6877 (ttt180) REVERT: B 544 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.6338 (tptt) REVERT: B 680 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8754 (mt) REVERT: B 726 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6768 (mt) REVERT: B 793 ASP cc_start: 0.7066 (t0) cc_final: 0.6636 (m-30) REVERT: B 796 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7280 (t0) REVERT: B 806 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.7587 (m110) REVERT: B 822 TYR cc_start: 0.8633 (p90) cc_final: 0.8249 (p90) outliers start: 47 outliers final: 25 residues processed: 115 average time/residue: 0.3820 time to fit residues: 47.4877 Evaluate side-chains 113 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 469 ASN Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 696 ARG Chi-restraints excluded: chain A residue 729 CYS Chi-restraints excluded: chain A residue 839 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 729 CYS Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 806 ASN Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [85, 15, 73, 51, 49, 67, 77, 50, 12, 25, 35] chunk 85 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 GLN ** B 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.163096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.132247 restraints weight = 8520.375| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.73 r_work: 0.3492 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7696 Z= 0.110 Angle : 0.522 5.823 10483 Z= 0.274 Chirality : 0.044 0.138 1238 Planarity : 0.004 0.050 1366 Dihedral : 5.215 50.591 1125 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.42 % Favored : 96.39 % Rotamer: Outliers : 4.67 % Allowed : 21.46 % Favored : 73.87 % 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: -1.19 (0.26), residues: 1025 helix: 0.30 (0.43), residues: 145 sheet: -1.36 (0.33), residues: 216 loop : -0.82 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 407 TYR 0.011 0.001 TYR B 800 PHE 0.009 0.001 PHE A 650 TRP 0.006 0.001 TRP A 692 HIS 0.004 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 7696) covalent geometry : angle 0.52150 / 0.27 (10483) hydrogen bonds : bond 0.03376 / 2.50 ( 242) hydrogen bonds : angle 4.83931 / 3.35 ( 624) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.243 Fit side-chains TARDY: cannot create tardy model for: "ASP B 321 " (corrupted residue). Skipping it. REVERT: A 544 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6922 (tppt) REVERT: A 723 ASP cc_start: 0.7736 (m-30) cc_final: 0.7454 (m-30) REVERT: A 839 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.6713 (ttt180) REVERT: B 544 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.6420 (tptt) REVERT: B 594 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.6946 (tt0) REVERT: B 726 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6666 (mt) REVERT: B 793 ASP cc_start: 0.7070 (t0) cc_final: 0.6777 (m-30) REVERT: B 796 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7269 (t0) REVERT: B 822 TYR cc_start: 0.8567 (p90) cc_final: 0.8310 (p90) outliers start: 32 outliers final: 17 residues processed: 106 average time/residue: 0.4017 time to fit residues: 45.9081 Evaluate side-chains 102 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 469 ASN Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 839 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 594 GLN Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [95, 0, 43, 92, 39, 3, 25, 64, 84, 11, 16] chunk 95 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 GLN B 594 GLN B 596 ASN B 689 ASN ** B 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.163845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.135141 restraints weight = 8490.320| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.70 r_work: 0.3512 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7696 Z= 0.195 Angle : 0.580 6.011 10483 Z= 0.306 Chirality : 0.046 0.147 1238 Planarity : 0.004 0.050 1366 Dihedral : 5.293 50.429 1122 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.91 % Favored : 95.90 % Rotamer: Outliers : 5.40 % Allowed : 20.44 % Favored : 74.16 % 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: -1.27 (0.25), residues: 1025 helix: 0.08 (0.42), residues: 145 sheet: -1.34 (0.33), residues: 217 loop : -0.86 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 407 TYR 0.014 0.002 TYR B 800 PHE 0.014 0.002 PHE B 751 TRP 0.006 0.001 TRP B 692 HIS 0.007 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 ( 7696) covalent geometry : angle 0.57988 / 0.31 (10483) hydrogen bonds : bond 0.03794 / 2.84 ( 242) hydrogen bonds : angle 4.93231 / 3.43 ( 624) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 81 time to evaluate : 0.259 Fit side-chains REVERT: A 544 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6959 (tppt) REVERT: A 723 ASP cc_start: 0.7803 (m-30) cc_final: 0.7321 (m-30) REVERT: A 839 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.6835 (ttt180) REVERT: B 544 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.6470 (tptt) REVERT: B 680 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8730 (mt) REVERT: B 726 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6782 (mt) REVERT: B 793 ASP cc_start: 0.7061 (t0) cc_final: 0.6705 (m-30) REVERT: B 796 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7246 (t0) REVERT: B 822 TYR cc_start: 0.8581 (p90) cc_final: 0.8270 (p90) outliers start: 37 outliers final: 21 residues processed: 110 average time/residue: 0.3759 time to fit residues: 44.8194 Evaluate side-chains 105 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 469 ASN Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 839 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 594 GLN Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 729 CYS Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [56, 89, 27, 102, 25, 77, 82, 94, 63, 96, 12] chunk 56 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 102 optimal weight: 0.0980 chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 GLN A 469 ASN B 594 GLN ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 689 ASN ** B 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.157196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.125943 restraints weight = 8674.469| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.83 r_work: 0.3447 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 7696 Z= 0.259 Angle : 0.638 6.140 10483 Z= 0.336 Chirality : 0.048 0.164 1238 Planarity : 0.005 0.052 1366 Dihedral : 5.534 48.914 1122 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.10 % Favored : 95.70 % Rotamer: Outliers : 5.26 % Allowed : 20.73 % Favored : 74.01 % 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: -1.43 (0.25), residues: 1025 helix: -0.21 (0.41), residues: 145 sheet: -1.45 (0.33), residues: 215 loop : -0.93 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 407 TYR 0.013 0.002 TYR A 512 PHE 0.016 0.002 PHE B 751 TRP 0.006 0.001 TRP B 432 HIS 0.008 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.26 ( 7696) covalent geometry : angle 0.63761 / 0.34 (10483) hydrogen bonds : bond 0.04076 / 3.05 ( 242) hydrogen bonds : angle 5.08492 / 3.53 ( 624) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.227 Fit side-chains REVERT: A 544 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.7090 (tppt) REVERT: A 839 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.6900 (ttt180) REVERT: B 544 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.6340 (tptt) REVERT: B 680 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8757 (mt) REVERT: B 726 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6657 (mt) REVERT: B 793 ASP cc_start: 0.7185 (t0) cc_final: 0.6558 (m-30) REVERT: B 796 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7463 (t0) REVERT: B 806 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.7553 (m110) outliers start: 36 outliers final: 25 residues processed: 109 average time/residue: 0.3839 time to fit residues: 45.1850 Evaluate side-chains 111 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 469 ASN Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 839 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 594 GLN Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 689 ASN Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 720 LYS Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 729 CYS Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 806 ASN Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [33, 58, 37, 21, 3, 99, 4, 28, 17, 15, 2] chunk 33 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 37 optimal weight: 0.0570 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 GLN ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 689 ASN ** B 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.166738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.138152 restraints weight = 8451.180| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.73 r_work: 0.3556 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7696 Z= 0.109 Angle : 0.527 6.555 10483 Z= 0.279 Chirality : 0.044 0.137 1238 Planarity : 0.004 0.040 1366 Dihedral : 5.036 49.402 1122 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.12 % Favored : 96.68 % Rotamer: Outliers : 3.94 % Allowed : 21.75 % Favored : 74.31 % 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: -1.05 (0.26), residues: 1025 helix: 0.35 (0.43), residues: 145 sheet: -1.15 (0.34), residues: 215 loop : -0.75 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 407 TYR 0.010 0.001 TYR B 800 PHE 0.015 0.001 PHE A 325 TRP 0.010 0.001 TRP B 692 HIS 0.004 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 7696) covalent geometry : angle 0.52715 / 0.28 (10483) hydrogen bonds : bond 0.03402 / 2.54 ( 242) hydrogen bonds : angle 4.82812 / 3.34 ( 624) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.257 Fit side-chains REVERT: A 544 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.6918 (tppt) REVERT: A 723 ASP cc_start: 0.7773 (m-30) cc_final: 0.7304 (m-30) REVERT: A 839 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.6640 (ttt180) REVERT: B 726 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6711 (mt) REVERT: B 793 ASP cc_start: 0.7003 (t0) cc_final: 0.6726 (m-30) outliers start: 27 outliers final: 18 residues processed: 103 average time/residue: 0.3634 time to fit residues: 40.5795 Evaluate side-chains 103 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 839 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 720 LYS Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 729 CYS Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [68, 64, 37, 49, 72, 69, 80, 53, 61, 45, 74] chunk 68 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 0.0970 chunk 69 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.0170 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 GLN ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.168181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.137470 restraints weight = 8446.924| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.73 r_work: 0.3546 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7696 Z= 0.105 Angle : 0.524 7.048 10483 Z= 0.275 Chirality : 0.044 0.134 1238 Planarity : 0.003 0.041 1366 Dihedral : 4.633 39.953 1120 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.12 % Favored : 96.68 % Rotamer: Outliers : 2.77 % Allowed : 22.77 % Favored : 74.45 % 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: -0.89 (0.26), residues: 1025 helix: 0.66 (0.44), residues: 144 sheet: -1.07 (0.33), residues: 222 loop : -0.67 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 407 TYR 0.009 0.001 TYR B 800 PHE 0.015 0.001 PHE A 325 TRP 0.006 0.001 TRP A 692 HIS 0.004 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 ( 7696) covalent geometry : angle 0.52389 / 0.27 (10483) hydrogen bonds : bond 0.03287 / 2.45 ( 242) hydrogen bonds : angle 4.79004 / 3.30 ( 624) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.301 Fit side-chains REVERT: A 415 ASP cc_start: 0.6805 (OUTLIER) cc_final: 0.6581 (p0) REVERT: A 544 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6864 (tppt) REVERT: A 723 ASP cc_start: 0.7714 (m-30) cc_final: 0.7242 (m-30) REVERT: A 839 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.6707 (ttt180) REVERT: B 406 ASP cc_start: 0.7757 (m-30) cc_final: 0.7395 (m-30) REVERT: B 544 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.6395 (tptt) REVERT: B 726 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6708 (mt) REVERT: B 793 ASP cc_start: 0.6970 (t0) cc_final: 0.6724 (m-30) outliers start: 19 outliers final: 12 residues processed: 104 average time/residue: 0.3662 time to fit residues: 41.3679 Evaluate side-chains 100 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 839 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 729 CYS Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 827 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [2, 58, 84, 31, 90, 52, 6, 27, 94, 24, 60] chunk 2 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 GLN B 679 ASN ** B 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.163172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.134326 restraints weight = 8470.155| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.73 r_work: 0.3493 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 7696 Z= 0.241 Angle : 0.623 6.950 10483 Z= 0.328 Chirality : 0.048 0.146 1238 Planarity : 0.005 0.058 1366 Dihedral : 4.950 34.027 1118 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.30 % Favored : 95.51 % Rotamer: Outliers : 3.50 % Allowed : 22.19 % Favored : 74.31 % 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: -1.25 (0.25), residues: 1025 helix: 0.06 (0.41), residues: 145 sheet: -1.39 (0.33), residues: 215 loop : -0.81 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 407 TYR 0.013 0.002 TYR A 512 PHE 0.016 0.002 PHE B 751 TRP 0.007 0.001 TRP A 692 HIS 0.008 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.24 ( 7696) covalent geometry : angle 0.62297 / 0.33 (10483) hydrogen bonds : bond 0.03892 / 2.92 ( 242) hydrogen bonds : angle 4.97755 / 3.45 ( 624) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2527.85 seconds wall clock time: 43 minutes 54.90 seconds (2634.90 seconds total)