Starting phenix.real_space_refine on Mon Aug 5 02:12:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bh7_44535/08_2024/9bh7_44535.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bh7_44535/08_2024/9bh7_44535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bh7_44535/08_2024/9bh7_44535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bh7_44535/08_2024/9bh7_44535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bh7_44535/08_2024/9bh7_44535.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bh7_44535/08_2024/9bh7_44535.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.032 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 80 5.16 5 C 7776 2.51 5 N 2112 2.21 5 O 2198 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 12166 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6083 Classifications: {'peptide': 772} Link IDs: {'PTRANS': 22, 'TRANS': 749} Chain breaks: 5 Chain: "B" Number of atoms: 6083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6083 Classifications: {'peptide': 772} Link IDs: {'PTRANS': 22, 'TRANS': 749} Chain breaks: 5 Time building chain proxies: 7.07, per 1000 atoms: 0.58 Number of scatterers: 12166 At special positions: 0 Unit cell: (117.453, 150.773, 89.964, 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 80 16.00 O 2198 8.00 N 2112 7.00 C 7776 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 - 3.50 Amino acid : False - 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: 4.60 Conformation dependent library (CDL) restraints added in 2.0 seconds 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 9 sheets defined 63.1% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 93 through 102 Processing helix chain 'A' and resid 120 through 136 removed outlier: 4.360A pdb=" N VAL A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 3.976A pdb=" N GLU A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 204 Processing helix chain 'A' and resid 205 through 208 removed outlier: 4.591A pdb=" N ASP A 208 " --> pdb=" O ASN A 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 205 through 208' Processing helix chain 'A' and resid 217 through 223 removed outlier: 3.896A pdb=" N GLY A 222 " --> pdb=" O HIS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 247 removed outlier: 3.508A pdb=" N LEU A 229 " --> pdb=" O HIS A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 325 through 335 removed outlier: 4.363A pdb=" N THR A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 368 Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 402 through 412 removed outlier: 3.691A pdb=" N LYS A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Proline residue: A 410 - end of helix Processing helix chain 'A' and resid 421 through 435 Processing helix chain 'A' and resid 444 through 449 removed outlier: 3.806A pdb=" N SER A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 528 through 542 Processing helix chain 'A' and resid 546 through 557 Processing helix chain 'A' and resid 557 through 564 Processing helix chain 'A' and resid 578 through 592 Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 624 through 640 removed outlier: 3.990A pdb=" N ASP A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A 640 " --> pdb=" O GLN A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 655 Processing helix chain 'A' and resid 665 through 676 removed outlier: 3.522A pdb=" N LYS A 675 " --> pdb=" O CYS A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 688 Processing helix chain 'A' and resid 690 through 700 removed outlier: 4.172A pdb=" N ARG A 696 " --> pdb=" O GLY A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 729 Processing helix chain 'A' and resid 733 through 742 Processing helix chain 'A' and resid 744 through 770 Processing helix chain 'A' and resid 771 through 780 removed outlier: 4.220A pdb=" N GLN A 780 " --> pdb=" O LEU A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 788 Processing helix chain 'A' and resid 790 through 794 removed outlier: 3.508A pdb=" N CYS A 794 " --> pdb=" O ARG A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 803 through 814 Processing helix chain 'A' and resid 817 through 824 Processing helix chain 'A' and resid 825 through 835 Processing helix chain 'A' and resid 871 through 892 Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.619A pdb=" N TRP B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.683A pdb=" N LYS B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 102 Processing helix chain 'B' and resid 120 through 136 removed outlier: 4.155A pdb=" N VAL B 124 " --> pdb=" O GLY B 120 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 162 Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 219 through 224 removed outlier: 4.308A pdb=" N ASP B 223 " --> pdb=" O HIS B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 247 removed outlier: 3.535A pdb=" N GLU B 231 " --> pdb=" O GLY B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 325 through 335 removed outlier: 4.562A pdb=" N THR B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 368 Processing helix chain 'B' and resid 383 through 396 removed outlier: 3.923A pdb=" N LEU B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 removed outlier: 3.610A pdb=" N LYS B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 435 Processing helix chain 'B' and resid 443 through 450 removed outlier: 4.324A pdb=" N SER B 447 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 479 Processing helix chain 'B' and resid 500 through 510 Processing helix chain 'B' and resid 528 through 542 Processing helix chain 'B' and resid 546 through 557 Processing helix chain 'B' and resid 557 through 564 Processing helix chain 'B' and resid 578 through 592 Processing helix chain 'B' and resid 612 through 622 Processing helix chain 'B' and resid 624 through 640 removed outlier: 4.010A pdb=" N ASP B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 655 Processing helix chain 'B' and resid 665 through 676 removed outlier: 3.527A pdb=" N LYS B 675 " --> pdb=" O CYS B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 688 Processing helix chain 'B' and resid 690 through 700 Processing helix chain 'B' and resid 706 through 730 Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 744 through 770 Processing helix chain 'B' and resid 771 through 788 removed outlier: 3.613A pdb=" N LEU B 776 " --> pdb=" O HIS B 772 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLN B 780 " --> pdb=" O LEU B 776 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE B 781 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN B 782 " --> pdb=" O LEU B 778 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS B 783 " --> pdb=" O SER B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 796 removed outlier: 4.161A pdb=" N ASP B 795 " --> pdb=" O GLU B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 814 Processing helix chain 'B' and resid 817 through 824 Processing helix chain 'B' and resid 825 through 836 Processing helix chain 'B' and resid 871 through 892 Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171 removed outlier: 6.645A pdb=" N ALA A 140 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N CYS A 189 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N PHE A 142 " --> pdb=" O CYS A 189 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS A 139 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL A 213 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU A 141 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL A 215 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE A 143 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA3, first strand: chain 'A' and resid 292 through 293 removed outlier: 6.504A pdb=" N VAL A 457 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE A 495 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A 459 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU A 341 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 340 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ALA A 442 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU A 342 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA A 414 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 463 through 464 Processing sheet with id=AA5, first strand: chain 'A' and resid 595 through 598 Processing sheet with id=AA6, first strand: chain 'B' and resid 168 through 171 removed outlier: 6.702A pdb=" N ALA B 140 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N CYS B 189 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE B 142 " --> pdb=" O CYS B 189 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS B 139 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL B 213 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B 141 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL B 215 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE B 143 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLY B 211 " --> pdb=" O GLN B 260 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL B 262 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 213 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N MET B 264 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL B 215 " --> pdb=" O MET B 264 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 309 through 312 removed outlier: 7.216A pdb=" N ILE B 302 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL B 457 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE B 495 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE B 459 " --> pdb=" O ILE B 495 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL B 340 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ALA B 442 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU B 342 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA B 414 " --> pdb=" O ALA B 441 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 463 through 464 Processing sheet with id=AA9, first strand: chain 'B' and resid 595 through 598 698 hydrogen bonds defined for protein. 2025 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: 4.40 Time building geometry restraints manager: 5.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3976 1.34 - 1.46: 2107 1.46 - 1.58: 6165 1.58 - 1.69: 0 1.69 - 1.81: 126 Bond restraints: 12374 Sorted by residual: bond pdb=" CB CYS B 496 " pdb=" SG CYS B 496 " ideal model delta sigma weight residual 1.808 1.770 0.038 3.30e-02 9.18e+02 1.35e+00 bond pdb=" CB CYS A 496 " pdb=" SG CYS A 496 " ideal model delta sigma weight residual 1.808 1.772 0.036 3.30e-02 9.18e+02 1.17e+00 bond pdb=" CA VAL A 797 " pdb=" CB VAL A 797 " ideal model delta sigma weight residual 1.540 1.552 -0.012 1.36e-02 5.41e+03 7.40e-01 bond pdb=" CB VAL A 340 " pdb=" CG2 VAL A 340 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.91e-01 bond pdb=" CG LEU A 778 " pdb=" CD2 LEU A 778 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.49e-01 ... (remaining 12369 not shown) Histogram of bond angle deviations from ideal: 99.60 - 106.49: 285 106.49 - 113.38: 6962 113.38 - 120.27: 4485 120.27 - 127.16: 4852 127.16 - 134.05: 124 Bond angle restraints: 16708 Sorted by residual: angle pdb=" N PHE B 781 " pdb=" CA PHE B 781 " pdb=" C PHE B 781 " ideal model delta sigma weight residual 111.71 115.49 -3.78 1.15e+00 7.56e-01 1.08e+01 angle pdb=" N PHE A 781 " pdb=" CA PHE A 781 " pdb=" C PHE A 781 " ideal model delta sigma weight residual 112.54 116.32 -3.78 1.22e+00 6.72e-01 9.59e+00 angle pdb=" N THR A 408 " pdb=" CA THR A 408 " pdb=" C THR A 408 " ideal model delta sigma weight residual 111.36 114.45 -3.09 1.09e+00 8.42e-01 8.05e+00 angle pdb=" CB ARG A 460 " pdb=" CG ARG A 460 " pdb=" CD ARG A 460 " ideal model delta sigma weight residual 111.30 117.69 -6.39 2.30e+00 1.89e-01 7.73e+00 angle pdb=" CA ARG A 460 " pdb=" CB ARG A 460 " pdb=" CG ARG A 460 " ideal model delta sigma weight residual 114.10 108.59 5.51 2.00e+00 2.50e-01 7.59e+00 ... (remaining 16703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 6997 17.73 - 35.45: 416 35.45 - 53.18: 56 53.18 - 70.91: 26 70.91 - 88.63: 9 Dihedral angle restraints: 7504 sinusoidal: 3038 harmonic: 4466 Sorted by residual: dihedral pdb=" CA LEU A 101 " pdb=" C LEU A 101 " pdb=" N LEU A 102 " pdb=" CA LEU A 102 " ideal model delta harmonic sigma weight residual -180.00 -151.98 -28.02 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA THR B 662 " pdb=" C THR B 662 " pdb=" N THR B 663 " pdb=" CA THR B 663 " ideal model delta harmonic sigma weight residual 180.00 152.46 27.54 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA ARG B 311 " pdb=" C ARG B 311 " pdb=" N GLU B 312 " pdb=" CA GLU B 312 " ideal model delta harmonic sigma weight residual 180.00 152.85 27.15 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 7501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1158 0.033 - 0.066: 551 0.066 - 0.099: 153 0.099 - 0.132: 73 0.132 - 0.165: 13 Chirality restraints: 1948 Sorted by residual: chirality pdb=" CA VAL A 409 " pdb=" N VAL A 409 " pdb=" C VAL A 409 " pdb=" CB VAL A 409 " both_signs ideal model delta sigma weight residual False 2.44 2.28 0.17 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CA LYS B 206 " pdb=" N LYS B 206 " pdb=" C LYS B 206 " pdb=" CB LYS B 206 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" CA ILE A 459 " pdb=" N ILE A 459 " pdb=" C ILE A 459 " pdb=" CB ILE A 459 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.96e-01 ... (remaining 1945 not shown) Planarity restraints: 2096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 758 " 0.012 2.00e-02 2.50e+03 1.74e-02 6.04e+00 pdb=" CG TYR A 758 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 758 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A 758 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 758 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR A 758 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 758 " -0.024 2.00e-02 2.50e+03 pdb=" OH TYR A 758 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 784 " 0.190 9.50e-02 1.11e+02 8.57e-02 5.13e+00 pdb=" NE ARG B 784 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 784 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 784 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 784 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 745 " 0.160 9.50e-02 1.11e+02 7.26e-02 4.32e+00 pdb=" NE ARG B 745 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 745 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG B 745 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 745 " -0.000 2.00e-02 2.50e+03 ... (remaining 2093 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 4169 2.88 - 3.38: 12043 3.38 - 3.89: 19128 3.89 - 4.39: 22610 4.39 - 4.90: 38202 Nonbonded interactions: 96152 Sorted by model distance: nonbonded pdb=" O LEU B 317 " pdb=" OG SER B 328 " model vdw 2.370 3.040 nonbonded pdb=" NZ LYS B 121 " pdb=" O SER B 265 " model vdw 2.387 3.120 nonbonded pdb=" OH TYR B 84 " pdb=" OE1 GLU B 126 " model vdw 2.404 3.040 nonbonded pdb=" OD1 ASN B 337 " pdb=" NH2 ARG B 438 " model vdw 2.405 3.120 nonbonded pdb=" NZ LYS A 83 " pdb=" OE1 GLU A 163 " model vdw 2.409 3.120 ... (remaining 96147 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 34.540 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 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 : 0.003 0.038 12374 Z= 0.194 Angle : 0.635 6.393 16708 Z= 0.389 Chirality : 0.045 0.165 1948 Planarity : 0.007 0.086 2096 Dihedral : 12.657 88.633 4608 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 0.66 % Favored : 99.21 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.19), residues: 1520 helix: -0.99 (0.14), residues: 868 sheet: 0.36 (0.38), residues: 158 loop : -0.33 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 863 HIS 0.006 0.001 HIS B 710 PHE 0.015 0.002 PHE B 632 TYR 0.026 0.004 TYR A 758 ARG 0.019 0.003 ARG B 745 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6345 (mt-10) REVERT: A 151 LYS cc_start: 0.8708 (mttt) cc_final: 0.8407 (mttp) REVERT: A 557 THR cc_start: 0.8053 (m) cc_final: 0.7692 (p) REVERT: B 126 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6505 (mt-10) REVERT: B 151 LYS cc_start: 0.8800 (mttt) cc_final: 0.8511 (mttp) REVERT: B 531 MET cc_start: 0.7282 (tpp) cc_final: 0.7028 (tpt) REVERT: B 802 LEU cc_start: 0.8595 (tp) cc_final: 0.8372 (mp) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.3327 time to fit residues: 136.5358 Evaluate side-chains 172 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 46 optimal weight: 0.0060 chunk 73 optimal weight: 0.0980 chunk 89 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 416 HIS A 434 GLN A 592 ASN A 716 HIS B 110 ASN B 219 HIS B 416 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12374 Z= 0.192 Angle : 0.592 10.379 16708 Z= 0.318 Chirality : 0.041 0.138 1948 Planarity : 0.004 0.043 2096 Dihedral : 5.299 20.150 1662 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 2.70 % Allowed : 6.37 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.21), residues: 1520 helix: 0.77 (0.16), residues: 890 sheet: 0.52 (0.39), residues: 160 loop : 0.44 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 95 HIS 0.009 0.001 HIS A 85 PHE 0.023 0.002 PHE A 313 TYR 0.024 0.002 TYR A 228 ARG 0.005 0.001 ARG B 784 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 197 time to evaluate : 1.337 Fit side-chains revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8693 (tt) REVERT: A 151 LYS cc_start: 0.8602 (mttt) cc_final: 0.8371 (mttp) REVERT: A 154 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8240 (ttmm) REVERT: A 167 LYS cc_start: 0.7898 (tppt) cc_final: 0.7535 (mmtm) REVERT: A 331 TYR cc_start: 0.6636 (t80) cc_final: 0.6398 (t80) REVERT: A 587 MET cc_start: 0.8177 (tpp) cc_final: 0.7828 (tpp) REVERT: B 802 LEU cc_start: 0.8593 (tp) cc_final: 0.8378 (mp) outliers start: 36 outliers final: 16 residues processed: 213 average time/residue: 0.2629 time to fit residues: 78.5686 Evaluate side-chains 176 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 886 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN A 325 HIS B 610 HIS B 716 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 12374 Z= 0.461 Angle : 0.700 12.027 16708 Z= 0.365 Chirality : 0.046 0.138 1948 Planarity : 0.004 0.048 2096 Dihedral : 5.276 20.380 1662 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.62 % Allowed : 10.57 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1520 helix: 0.74 (0.16), residues: 874 sheet: -0.04 (0.39), residues: 166 loop : 0.26 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 863 HIS 0.010 0.002 HIS A 416 PHE 0.022 0.003 PHE A 765 TYR 0.018 0.002 TYR A 228 ARG 0.009 0.001 ARG B 784 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 177 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ILE cc_start: 0.8232 (mm) cc_final: 0.7818 (mt) REVERT: A 167 LYS cc_start: 0.8048 (tppt) cc_final: 0.7783 (mmtm) REVERT: A 531 MET cc_start: 0.7093 (tpt) cc_final: 0.6782 (tpt) REVERT: A 649 HIS cc_start: 0.8789 (OUTLIER) cc_final: 0.7707 (t-170) REVERT: B 172 MET cc_start: 0.7875 (mtt) cc_final: 0.7625 (mtt) REVERT: B 802 LEU cc_start: 0.8610 (tp) cc_final: 0.8354 (mp) outliers start: 35 outliers final: 26 residues processed: 199 average time/residue: 0.2355 time to fit residues: 67.6316 Evaluate side-chains 184 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 649 HIS Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 886 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 73 optimal weight: 0.0870 chunk 133 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 180 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12374 Z= 0.182 Angle : 0.519 8.556 16708 Z= 0.276 Chirality : 0.039 0.132 1948 Planarity : 0.004 0.040 2096 Dihedral : 4.667 17.669 1662 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.32 % Allowed : 12.44 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.21), residues: 1520 helix: 1.42 (0.17), residues: 866 sheet: 0.28 (0.40), residues: 156 loop : 0.47 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 661 HIS 0.005 0.001 HIS B 710 PHE 0.019 0.001 PHE A 313 TYR 0.017 0.002 TYR A 553 ARG 0.006 0.000 ARG A 823 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 174 time to evaluate : 1.548 Fit side-chains REVERT: A 166 ILE cc_start: 0.8058 (mm) cc_final: 0.7681 (mt) REVERT: A 167 LYS cc_start: 0.8084 (tppt) cc_final: 0.7828 (mmtm) REVERT: A 200 ARG cc_start: 0.7742 (ttp80) cc_final: 0.7540 (ttp80) REVERT: B 130 LEU cc_start: 0.9104 (tp) cc_final: 0.8858 (tp) REVERT: B 172 MET cc_start: 0.7825 (mtt) cc_final: 0.7614 (mtt) REVERT: B 587 MET cc_start: 0.8268 (tpp) cc_final: 0.7948 (tpp) REVERT: B 649 HIS cc_start: 0.8549 (OUTLIER) cc_final: 0.7079 (t-170) outliers start: 31 outliers final: 22 residues processed: 192 average time/residue: 0.2405 time to fit residues: 66.6238 Evaluate side-chains 177 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 649 HIS Chi-restraints excluded: chain B residue 886 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 2 optimal weight: 0.0030 chunk 110 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12374 Z= 0.168 Angle : 0.517 7.970 16708 Z= 0.270 Chirality : 0.039 0.130 1948 Planarity : 0.004 0.039 2096 Dihedral : 4.416 16.916 1662 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.40 % Allowed : 14.02 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.22), residues: 1520 helix: 1.67 (0.17), residues: 866 sheet: 0.34 (0.40), residues: 156 loop : 0.50 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 95 HIS 0.005 0.001 HIS A 85 PHE 0.019 0.001 PHE A 313 TYR 0.022 0.002 TYR B 667 ARG 0.005 0.000 ARG A 823 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 172 time to evaluate : 1.390 Fit side-chains REVERT: A 167 LYS cc_start: 0.8135 (tppt) cc_final: 0.7916 (mmtm) REVERT: A 587 MET cc_start: 0.8129 (tpp) cc_final: 0.7834 (tpp) REVERT: A 649 HIS cc_start: 0.8660 (OUTLIER) cc_final: 0.7507 (t-170) REVERT: B 130 LEU cc_start: 0.9134 (tp) cc_final: 0.8812 (tp) REVERT: B 172 MET cc_start: 0.7810 (mtt) cc_final: 0.7591 (mtt) REVERT: B 587 MET cc_start: 0.8257 (tpp) cc_final: 0.7958 (tpp) REVERT: B 649 HIS cc_start: 0.8534 (OUTLIER) cc_final: 0.7022 (t-170) REVERT: B 699 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7861 (tmtt) outliers start: 32 outliers final: 20 residues processed: 189 average time/residue: 0.2370 time to fit residues: 65.5119 Evaluate side-chains 180 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 157 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 649 HIS Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 649 HIS Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 886 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12374 Z= 0.212 Angle : 0.522 8.554 16708 Z= 0.272 Chirality : 0.039 0.138 1948 Planarity : 0.004 0.040 2096 Dihedral : 4.335 16.585 1662 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.85 % Allowed : 14.69 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.22), residues: 1520 helix: 1.77 (0.17), residues: 864 sheet: 0.26 (0.40), residues: 156 loop : 0.42 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 863 HIS 0.007 0.001 HIS A 219 PHE 0.015 0.001 PHE A 765 TYR 0.017 0.002 TYR B 667 ARG 0.006 0.000 ARG A 823 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 163 time to evaluate : 1.412 Fit side-chains REVERT: A 587 MET cc_start: 0.8125 (tpp) cc_final: 0.7814 (tpp) REVERT: A 649 HIS cc_start: 0.8662 (OUTLIER) cc_final: 0.7589 (t-170) REVERT: B 166 ILE cc_start: 0.8493 (mm) cc_final: 0.8289 (mp) REVERT: B 172 MET cc_start: 0.7890 (mtt) cc_final: 0.7675 (mtt) REVERT: B 587 MET cc_start: 0.8259 (tpp) cc_final: 0.7949 (tpp) REVERT: B 649 HIS cc_start: 0.8565 (OUTLIER) cc_final: 0.7002 (t-170) outliers start: 38 outliers final: 27 residues processed: 184 average time/residue: 0.2470 time to fit residues: 65.6705 Evaluate side-chains 183 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 649 HIS Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 649 HIS Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 886 ILE Chi-restraints excluded: chain B residue 887 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12374 Z= 0.204 Angle : 0.524 8.442 16708 Z= 0.272 Chirality : 0.039 0.144 1948 Planarity : 0.003 0.042 2096 Dihedral : 4.246 16.552 1662 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.85 % Allowed : 14.99 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.22), residues: 1520 helix: 1.84 (0.17), residues: 864 sheet: 0.18 (0.40), residues: 156 loop : 0.40 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 863 HIS 0.006 0.001 HIS A 219 PHE 0.018 0.001 PHE A 313 TYR 0.017 0.002 TYR B 667 ARG 0.007 0.000 ARG A 823 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 161 time to evaluate : 1.308 Fit side-chains REVERT: A 587 MET cc_start: 0.8105 (tpp) cc_final: 0.7801 (tpp) REVERT: A 649 HIS cc_start: 0.8657 (OUTLIER) cc_final: 0.7566 (t-170) REVERT: B 172 MET cc_start: 0.7859 (mtt) cc_final: 0.7653 (mtt) REVERT: B 587 MET cc_start: 0.8240 (tpp) cc_final: 0.7949 (tpp) REVERT: B 649 HIS cc_start: 0.8563 (OUTLIER) cc_final: 0.6035 (t-170) outliers start: 38 outliers final: 27 residues processed: 178 average time/residue: 0.2354 time to fit residues: 62.2599 Evaluate side-chains 184 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 649 HIS Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 649 HIS Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 886 ILE Chi-restraints excluded: chain B residue 887 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 0.2980 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 116 optimal weight: 0.5980 chunk 135 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12374 Z= 0.174 Angle : 0.504 7.786 16708 Z= 0.263 Chirality : 0.038 0.142 1948 Planarity : 0.003 0.040 2096 Dihedral : 4.135 16.597 1662 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.55 % Allowed : 15.44 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.22), residues: 1520 helix: 1.97 (0.17), residues: 864 sheet: 0.25 (0.40), residues: 156 loop : 0.43 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 863 HIS 0.006 0.001 HIS A 85 PHE 0.014 0.001 PHE A 313 TYR 0.017 0.002 TYR B 667 ARG 0.007 0.000 ARG A 823 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 165 time to evaluate : 1.351 Fit side-chains REVERT: A 587 MET cc_start: 0.8113 (tpp) cc_final: 0.7835 (tpp) REVERT: A 649 HIS cc_start: 0.8625 (OUTLIER) cc_final: 0.7539 (t-170) REVERT: B 587 MET cc_start: 0.8221 (tpp) cc_final: 0.7946 (tpp) REVERT: B 649 HIS cc_start: 0.8568 (OUTLIER) cc_final: 0.6117 (t-170) outliers start: 34 outliers final: 26 residues processed: 182 average time/residue: 0.2510 time to fit residues: 66.1355 Evaluate side-chains 185 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 157 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 649 HIS Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 649 HIS Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 886 ILE Chi-restraints excluded: chain B residue 887 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 83 optimal weight: 0.1980 chunk 60 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12374 Z= 0.176 Angle : 0.531 7.906 16708 Z= 0.276 Chirality : 0.039 0.170 1948 Planarity : 0.004 0.040 2096 Dihedral : 4.121 18.325 1662 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.55 % Allowed : 15.97 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.22), residues: 1520 helix: 1.96 (0.17), residues: 868 sheet: 0.49 (0.41), residues: 152 loop : 0.32 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 863 HIS 0.008 0.001 HIS B 338 PHE 0.031 0.001 PHE A 693 TYR 0.017 0.001 TYR B 667 ARG 0.007 0.000 ARG B 823 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 165 time to evaluate : 1.479 Fit side-chains REVERT: A 587 MET cc_start: 0.8106 (tpp) cc_final: 0.7836 (tpp) REVERT: A 649 HIS cc_start: 0.8641 (OUTLIER) cc_final: 0.7553 (t-170) REVERT: A 885 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7551 (tmm) REVERT: B 172 MET cc_start: 0.7672 (mtt) cc_final: 0.7441 (mtt) REVERT: B 587 MET cc_start: 0.8212 (tpp) cc_final: 0.7937 (tpp) REVERT: B 649 HIS cc_start: 0.8573 (OUTLIER) cc_final: 0.6124 (t-170) outliers start: 34 outliers final: 24 residues processed: 184 average time/residue: 0.2432 time to fit residues: 64.7324 Evaluate side-chains 189 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 649 HIS Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 649 HIS Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 886 ILE Chi-restraints excluded: chain B residue 887 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 97 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 780 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12374 Z= 0.185 Angle : 0.540 8.114 16708 Z= 0.280 Chirality : 0.039 0.167 1948 Planarity : 0.004 0.040 2096 Dihedral : 4.116 28.216 1662 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.40 % Allowed : 16.57 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.22), residues: 1520 helix: 1.97 (0.17), residues: 868 sheet: 0.50 (0.41), residues: 152 loop : 0.28 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 863 HIS 0.006 0.001 HIS A 85 PHE 0.030 0.001 PHE A 693 TYR 0.022 0.002 TYR B 553 ARG 0.008 0.000 ARG A 823 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 160 time to evaluate : 1.392 Fit side-chains REVERT: A 587 MET cc_start: 0.8101 (tpp) cc_final: 0.7822 (tpp) REVERT: A 649 HIS cc_start: 0.8639 (OUTLIER) cc_final: 0.7557 (t-170) REVERT: A 885 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7557 (tmm) REVERT: B 587 MET cc_start: 0.8211 (tpp) cc_final: 0.7932 (tpp) REVERT: B 649 HIS cc_start: 0.8579 (OUTLIER) cc_final: 0.6034 (t-170) outliers start: 32 outliers final: 27 residues processed: 176 average time/residue: 0.2408 time to fit residues: 61.2844 Evaluate side-chains 187 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 157 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 649 HIS Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 649 HIS Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 886 ILE Chi-restraints excluded: chain B residue 887 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 51 optimal weight: 0.0870 chunk 125 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.121598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.099115 restraints weight = 22007.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.103156 restraints weight = 19212.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.103383 restraints weight = 14868.164| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12374 Z= 0.173 Angle : 0.534 9.381 16708 Z= 0.278 Chirality : 0.039 0.170 1948 Planarity : 0.004 0.041 2096 Dihedral : 4.106 31.448 1662 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.55 % Allowed : 16.42 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.22), residues: 1520 helix: 2.05 (0.17), residues: 866 sheet: 0.58 (0.41), residues: 152 loop : 0.31 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 863 HIS 0.007 0.001 HIS A 85 PHE 0.029 0.001 PHE A 693 TYR 0.019 0.002 TYR B 667 ARG 0.008 0.000 ARG B 823 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2467.30 seconds wall clock time: 44 minutes 55.56 seconds (2695.56 seconds total)