Starting phenix.real_space_refine on Sun Aug 24 17:12:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jgk_36237/08_2025/8jgk_36237_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jgk_36237/08_2025/8jgk_36237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jgk_36237/08_2025/8jgk_36237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jgk_36237/08_2025/8jgk_36237.map" model { file = "/net/cci-nas-00/data/ceres_data/8jgk_36237/08_2025/8jgk_36237_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jgk_36237/08_2025/8jgk_36237_trim.cif" } resolution = 4.04 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 72 5.16 5 C 7060 2.51 5 N 1780 2.21 5 O 1884 1.98 5 H 10850 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21650 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 10798 Classifications: {'peptide': 684} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 655} Chain breaks: 4 Chain: "B" Number of atoms: 10798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 10798 Classifications: {'peptide': 684} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 655} Chain breaks: 4 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.27, per 1000 atoms: 0.15 Number of scatterers: 21650 At special positions: 0 Unit cell: (101.37, 101.37, 106.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 P 4 15.00 O 1884 8.00 N 1780 7.00 C 7060 6.00 H 10850 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 161 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS A 463 " - pdb=" SG CYS A 472 " distance=2.03 Simple disulfide: pdb=" SG CYS A 562 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 161 " - pdb=" SG CYS B 172 " distance=2.03 Simple disulfide: pdb=" SG CYS B 463 " - pdb=" SG CYS B 472 " distance=2.03 Simple disulfide: pdb=" SG CYS B 562 " - pdb=" SG CYS B 568 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 520.8 milliseconds Enol-peptide restraints added in 1.4 microseconds 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 7 sheets defined 68.4% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 92 through 110 removed outlier: 3.653A pdb=" N GLU A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 157 removed outlier: 4.160A pdb=" N GLY A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TRP A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 175 Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 203 through 233 Processing helix chain 'A' and resid 234 through 237 removed outlier: 4.132A pdb=" N CYS A 237 " --> pdb=" O PRO A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 237' Processing helix chain 'A' and resid 240 through 250 removed outlier: 3.589A pdb=" N GLY A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 258 removed outlier: 4.088A pdb=" N LEU A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 275 removed outlier: 3.576A pdb=" N ILE A 264 " --> pdb=" O TRP A 260 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 298 removed outlier: 3.644A pdb=" N VAL A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 306 through 327 Processing helix chain 'A' and resid 328 through 340 removed outlier: 3.530A pdb=" N LEU A 337 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 366 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 418 removed outlier: 4.400A pdb=" N PHE A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 420 No H-bonds generated for 'chain 'A' and resid 419 through 420' Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 426 through 441 Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.987A pdb=" N LEU A 450 " --> pdb=" O PRO A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 494 through 518 removed outlier: 3.872A pdb=" N SER A 498 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 515 " --> pdb=" O ILE A 511 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE A 516 " --> pdb=" O ILE A 512 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 517 " --> pdb=" O MET A 513 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE A 518 " --> pdb=" O THR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 552 Processing helix chain 'A' and resid 555 through 560 removed outlier: 3.886A pdb=" N GLU A 560 " --> pdb=" O PHE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 588 Processing helix chain 'A' and resid 590 through 600 removed outlier: 3.738A pdb=" N VAL A 594 " --> pdb=" O THR A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 605 No H-bonds generated for 'chain 'A' and resid 603 through 605' Processing helix chain 'A' and resid 606 through 623 removed outlier: 3.843A pdb=" N LEU A 610 " --> pdb=" O TYR A 606 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 623 " --> pdb=" O TRP A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 653 through 657 Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 709 through 722 Processing helix chain 'A' and resid 767 through 779 removed outlier: 3.639A pdb=" N VAL A 771 " --> pdb=" O PRO A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 805 Processing helix chain 'B' and resid 92 through 110 removed outlier: 3.679A pdb=" N GLU B 96 " --> pdb=" O ASP B 92 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS B 110 " --> pdb=" O ARG B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 157 removed outlier: 4.119A pdb=" N GLY B 128 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TRP B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B 157 " --> pdb=" O MET B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 203 through 233 Processing helix chain 'B' and resid 234 through 237 removed outlier: 4.087A pdb=" N CYS B 237 " --> pdb=" O PRO B 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 234 through 237' Processing helix chain 'B' and resid 240 through 250 removed outlier: 3.714A pdb=" N GLY B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 removed outlier: 4.096A pdb=" N LEU B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 275 removed outlier: 3.579A pdb=" N ILE B 264 " --> pdb=" O TRP B 260 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 298 removed outlier: 3.667A pdb=" N VAL B 288 " --> pdb=" O PRO B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 306 removed outlier: 3.521A pdb=" N SER B 304 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 327 removed outlier: 3.503A pdb=" N ALA B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 340 Processing helix chain 'B' and resid 348 through 366 Processing helix chain 'B' and resid 389 through 418 removed outlier: 4.268A pdb=" N PHE B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 395 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 420 No H-bonds generated for 'chain 'B' and resid 419 through 420' Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 426 through 441 Processing helix chain 'B' and resid 445 through 450 removed outlier: 3.918A pdb=" N LEU B 450 " --> pdb=" O PRO B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'B' and resid 494 through 518 removed outlier: 3.998A pdb=" N SER B 498 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 512 " --> pdb=" O ILE B 508 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL B 515 " --> pdb=" O ILE B 511 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE B 516 " --> pdb=" O ILE B 512 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 517 " --> pdb=" O MET B 513 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 552 Processing helix chain 'B' and resid 555 through 560 removed outlier: 3.981A pdb=" N GLU B 560 " --> pdb=" O PHE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 588 Processing helix chain 'B' and resid 591 through 601 Processing helix chain 'B' and resid 603 through 605 No H-bonds generated for 'chain 'B' and resid 603 through 605' Processing helix chain 'B' and resid 606 through 623 removed outlier: 3.670A pdb=" N ALA B 623 " --> pdb=" O TRP B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 638 Processing helix chain 'B' and resid 653 through 657 Processing helix chain 'B' and resid 676 through 687 Processing helix chain 'B' and resid 709 through 722 Processing helix chain 'B' and resid 767 through 779 removed outlier: 3.594A pdb=" N VAL B 771 " --> pdb=" O PRO B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 805 Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 379 through 380 removed outlier: 7.603A pdb=" N VAL A 379 " --> pdb=" O GLY A 602 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 691 through 695 Processing sheet with id=AA4, first strand: chain 'A' and resid 782 through 787 removed outlier: 6.590A pdb=" N CYS A 783 " --> pdb=" O ILE A 794 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE A 794 " --> pdb=" O CYS A 783 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL A 785 " --> pdb=" O LEU A 792 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA6, first strand: chain 'B' and resid 691 through 695 Processing sheet with id=AA7, first strand: chain 'B' and resid 782 through 787 removed outlier: 6.599A pdb=" N CYS B 783 " --> pdb=" O ILE B 794 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE B 794 " --> pdb=" O CYS B 783 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 785 " --> pdb=" O LEU B 792 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1860 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.84 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10826 1.03 - 1.23: 25 1.23 - 1.42: 4665 1.42 - 1.62: 6308 1.62 - 1.81: 108 Bond restraints: 21932 Sorted by residual: bond pdb=" CB PRO A 666 " pdb=" CG PRO A 666 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.35e+00 bond pdb=" SD MET B 213 " pdb=" CE MET B 213 " ideal model delta sigma weight residual 1.791 1.754 0.037 2.50e-02 1.60e+03 2.21e+00 bond pdb=" N HIS A 633 " pdb=" CA HIS A 633 " ideal model delta sigma weight residual 1.459 1.476 -0.017 1.23e-02 6.61e+03 1.94e+00 bond pdb=" CA MET B 213 " pdb=" CB MET B 213 " ideal model delta sigma weight residual 1.529 1.511 0.018 1.55e-02 4.16e+03 1.36e+00 bond pdb=" N HIS B 633 " pdb=" CA HIS B 633 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.23e-02 6.61e+03 1.33e+00 ... (remaining 21927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 38767 1.45 - 2.90: 779 2.90 - 4.35: 75 4.35 - 5.80: 16 5.80 - 7.26: 7 Bond angle restraints: 39644 Sorted by residual: angle pdb=" CA PRO A 666 " pdb=" N PRO A 666 " pdb=" CD PRO A 666 " ideal model delta sigma weight residual 112.00 106.09 5.91 1.40e+00 5.10e-01 1.78e+01 angle pdb=" C MET B 213 " pdb=" CA MET B 213 " pdb=" CB MET B 213 " ideal model delta sigma weight residual 110.88 105.76 5.12 1.57e+00 4.06e-01 1.06e+01 angle pdb=" CA ARG B 710 " pdb=" CB ARG B 710 " pdb=" CG ARG B 710 " ideal model delta sigma weight residual 114.10 120.24 -6.14 2.00e+00 2.50e-01 9.42e+00 angle pdb=" C ILE B 716 " pdb=" N GLU B 717 " pdb=" CA GLU B 717 " ideal model delta sigma weight residual 120.72 116.07 4.65 1.67e+00 3.59e-01 7.76e+00 angle pdb=" CA TRP A 152 " pdb=" CB TRP A 152 " pdb=" CG TRP A 152 " ideal model delta sigma weight residual 113.60 118.34 -4.74 1.90e+00 2.77e-01 6.23e+00 ... (remaining 39639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.52: 9858 30.52 - 61.04: 417 61.04 - 91.55: 23 91.55 - 122.07: 4 122.07 - 152.59: 2 Dihedral angle restraints: 10304 sinusoidal: 5472 harmonic: 4832 Sorted by residual: dihedral pdb=" C5' ADP A 901 " pdb=" O5' ADP A 901 " pdb=" PA ADP A 901 " pdb=" O2A ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 92.59 -152.59 1 2.00e+01 2.50e-03 4.53e+01 dihedral pdb=" C5' ADP B 901 " pdb=" O5' ADP B 901 " pdb=" PA ADP B 901 " pdb=" O2A ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 90.07 -150.07 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" O1B ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PB ADP A 901 " pdb=" PA ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 57.15 -117.15 1 2.00e+01 2.50e-03 3.50e+01 ... (remaining 10301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1275 0.036 - 0.073: 301 0.073 - 0.109: 104 0.109 - 0.146: 14 0.146 - 0.182: 4 Chirality restraints: 1698 Sorted by residual: chirality pdb=" CA ARG B 710 " pdb=" N ARG B 710 " pdb=" C ARG B 710 " pdb=" CB ARG B 710 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CA PRO B 392 " pdb=" N PRO B 392 " pdb=" C PRO B 392 " pdb=" CB PRO B 392 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA GLU B 717 " pdb=" N GLU B 717 " pdb=" C GLU B 717 " pdb=" CB GLU B 717 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 1695 not shown) Planarity restraints: 3144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 665 " -0.062 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO A 666 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 666 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 666 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 193 " 0.017 2.00e-02 2.50e+03 1.07e-02 4.61e+00 pdb=" CG TRP B 193 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP B 193 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP B 193 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 193 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 193 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 193 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 193 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 193 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 193 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP B 193 " 0.007 2.00e-02 2.50e+03 pdb=" HE1 TRP B 193 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP B 193 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 193 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 193 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP B 193 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 213 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C MET B 213 " 0.036 2.00e-02 2.50e+03 pdb=" O MET B 213 " -0.013 2.00e-02 2.50e+03 pdb=" N TYR B 214 " -0.012 2.00e-02 2.50e+03 ... (remaining 3141 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1153 2.18 - 2.79: 44020 2.79 - 3.39: 60813 3.39 - 4.00: 74905 4.00 - 4.60: 117230 Nonbonded interactions: 298121 Sorted by model distance: nonbonded pdb=" O PRO B 234 " pdb=" HZ1 LYS B 521 " model vdw 1.580 2.450 nonbonded pdb=" O PRO A 234 " pdb=" HZ1 LYS A 521 " model vdw 1.584 2.450 nonbonded pdb=" O PHE A 251 " pdb="HH21 ARG A 311 " model vdw 1.594 2.450 nonbonded pdb="HH12 ARG B 588 " pdb=" O GLY B 625 " model vdw 1.599 2.450 nonbonded pdb=" O ILE A 684 " pdb="HH22 ARG A 709 " model vdw 1.608 2.450 ... (remaining 298116 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: 0.03 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: 0.880 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: 0.080 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.110 Find NCS groups from input model: 0.250 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 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 0.091 11088 Z= 0.129 Angle : 0.559 7.255 15064 Z= 0.297 Chirality : 0.037 0.182 1698 Planarity : 0.005 0.091 1844 Dihedral : 14.396 152.591 3920 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.73 (0.23), residues: 1348 helix: 1.47 (0.18), residues: 820 sheet: -1.55 (1.07), residues: 20 loop : -1.07 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 710 TYR 0.016 0.001 TYR A 211 PHE 0.016 0.001 PHE B 393 TRP 0.037 0.001 TRP B 193 HIS 0.004 0.001 HIS B 553 Details of bonding type rmsd covalent geometry : bond 0.00278 (11082) covalent geometry : angle 0.55871 (15052) SS BOND : bond 0.00175 ( 6) SS BOND : angle 0.46908 ( 12) hydrogen bonds : bond 0.15362 ( 636) hydrogen bonds : angle 6.39389 ( 1860) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 TYR cc_start: 0.6738 (t80) cc_final: 0.6491 (t80) REVERT: B 298 TYR cc_start: 0.6756 (t80) cc_final: 0.6418 (t80) REVERT: B 350 TRP cc_start: 0.4598 (p-90) cc_final: 0.3521 (m100) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2029 time to fit residues: 62.0186 Evaluate side-chains 186 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 0.0970 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 HIS ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.216934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.182922 restraints weight = 48273.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.189121 restraints weight = 24760.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.192985 restraints weight = 16432.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.195153 restraints weight = 12677.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.196884 restraints weight = 10862.998| |-----------------------------------------------------------------------------| r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11088 Z= 0.129 Angle : 0.539 6.330 15064 Z= 0.278 Chirality : 0.038 0.140 1698 Planarity : 0.005 0.039 1844 Dihedral : 8.299 150.255 1498 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.09 % Allowed : 1.94 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 1.13 (0.23), residues: 1348 helix: 1.89 (0.18), residues: 820 sheet: -1.44 (1.02), residues: 20 loop : -1.10 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 661 TYR 0.013 0.001 TYR A 211 PHE 0.021 0.001 PHE B 393 TRP 0.024 0.001 TRP A 152 HIS 0.003 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00272 (11082) covalent geometry : angle 0.53865 (15052) SS BOND : bond 0.00268 ( 6) SS BOND : angle 0.61235 ( 12) hydrogen bonds : bond 0.04405 ( 636) hydrogen bonds : angle 4.76785 ( 1860) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.3776 (mtt) cc_final: 0.3539 (mtt) REVERT: A 298 TYR cc_start: 0.6746 (t80) cc_final: 0.6465 (t80) REVERT: B 298 TYR cc_start: 0.6758 (t80) cc_final: 0.6389 (t80) outliers start: 1 outliers final: 1 residues processed: 209 average time/residue: 0.1908 time to fit residues: 59.0246 Evaluate side-chains 181 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 97 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 GLN ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.214626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.180391 restraints weight = 48619.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.186496 restraints weight = 25055.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.190316 restraints weight = 16690.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.192710 restraints weight = 12954.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.193655 restraints weight = 11013.161| |-----------------------------------------------------------------------------| r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11088 Z= 0.150 Angle : 0.560 6.556 15064 Z= 0.290 Chirality : 0.038 0.175 1698 Planarity : 0.005 0.044 1844 Dihedral : 7.823 142.030 1498 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.99 (0.23), residues: 1348 helix: 1.75 (0.17), residues: 820 sheet: -0.96 (1.11), residues: 20 loop : -1.15 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 95 TYR 0.016 0.001 TYR A 211 PHE 0.014 0.001 PHE B 399 TRP 0.017 0.001 TRP A 152 HIS 0.006 0.001 HIS A 633 Details of bonding type rmsd covalent geometry : bond 0.00329 (11082) covalent geometry : angle 0.55935 (15052) SS BOND : bond 0.00280 ( 6) SS BOND : angle 0.80479 ( 12) hydrogen bonds : bond 0.04161 ( 636) hydrogen bonds : angle 4.58399 ( 1860) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.3947 (mtt) cc_final: 0.3632 (mtt) REVERT: A 152 TRP cc_start: 0.7046 (t60) cc_final: 0.6642 (t60) REVERT: A 298 TYR cc_start: 0.6763 (t80) cc_final: 0.6544 (t80) REVERT: B 298 TYR cc_start: 0.6654 (t80) cc_final: 0.6336 (t80) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1982 time to fit residues: 61.7687 Evaluate side-chains 184 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 125 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 44 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 HIS ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.213222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.182169 restraints weight = 47047.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.187757 restraints weight = 24575.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.191383 restraints weight = 16264.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.193393 restraints weight = 12467.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.194287 restraints weight = 10646.470| |-----------------------------------------------------------------------------| r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11088 Z= 0.130 Angle : 0.535 7.013 15064 Z= 0.274 Chirality : 0.038 0.164 1698 Planarity : 0.004 0.045 1844 Dihedral : 7.376 129.769 1498 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 1.07 (0.23), residues: 1348 helix: 1.83 (0.17), residues: 822 sheet: -1.20 (1.04), residues: 20 loop : -1.13 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 95 TYR 0.015 0.001 TYR A 211 PHE 0.026 0.001 PHE B 393 TRP 0.011 0.001 TRP A 152 HIS 0.003 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00288 (11082) covalent geometry : angle 0.53483 (15052) SS BOND : bond 0.00296 ( 6) SS BOND : angle 0.69765 ( 12) hydrogen bonds : bond 0.03749 ( 636) hydrogen bonds : angle 4.42734 ( 1860) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.3898 (mtt) cc_final: 0.3595 (mtt) REVERT: A 531 MET cc_start: 0.8112 (mmm) cc_final: 0.7387 (mtt) REVERT: B 254 ARG cc_start: 0.6227 (tpt170) cc_final: 0.6012 (tpt170) REVERT: B 298 TYR cc_start: 0.6651 (t80) cc_final: 0.6415 (t80) REVERT: B 531 MET cc_start: 0.7379 (tpp) cc_final: 0.6916 (mtt) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2049 time to fit residues: 63.4355 Evaluate side-chains 184 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 44 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.211283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.176900 restraints weight = 47969.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.182751 restraints weight = 25032.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.186451 restraints weight = 16897.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.188592 restraints weight = 13244.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.190108 restraints weight = 11400.087| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11088 Z= 0.170 Angle : 0.572 5.692 15064 Z= 0.299 Chirality : 0.038 0.196 1698 Planarity : 0.005 0.047 1844 Dihedral : 7.111 115.475 1498 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.09 % Allowed : 1.94 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.81 (0.22), residues: 1348 helix: 1.61 (0.17), residues: 822 sheet: None (None), residues: 0 loop : -1.23 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 710 TYR 0.019 0.001 TYR A 211 PHE 0.014 0.002 PHE B 393 TRP 0.016 0.001 TRP B 217 HIS 0.005 0.001 HIS A 633 Details of bonding type rmsd covalent geometry : bond 0.00378 (11082) covalent geometry : angle 0.57192 (15052) SS BOND : bond 0.00350 ( 6) SS BOND : angle 0.80027 ( 12) hydrogen bonds : bond 0.03915 ( 636) hydrogen bonds : angle 4.49341 ( 1860) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.4001 (mtt) cc_final: 0.3618 (mtt) REVERT: A 152 TRP cc_start: 0.7193 (t60) cc_final: 0.6858 (t60) REVERT: A 298 TYR cc_start: 0.6706 (t80) cc_final: 0.6409 (t80) REVERT: A 531 MET cc_start: 0.8309 (mmm) cc_final: 0.7591 (mtt) REVERT: B 298 TYR cc_start: 0.6619 (t80) cc_final: 0.6408 (t80) outliers start: 1 outliers final: 1 residues processed: 212 average time/residue: 0.2037 time to fit residues: 62.2728 Evaluate side-chains 190 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 10 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.214168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.180039 restraints weight = 48427.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.186027 restraints weight = 25088.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.189811 restraints weight = 16837.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.192166 restraints weight = 13113.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.193331 restraints weight = 11233.347| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11088 Z= 0.117 Angle : 0.527 5.561 15064 Z= 0.269 Chirality : 0.037 0.150 1698 Planarity : 0.004 0.048 1844 Dihedral : 6.661 102.071 1498 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 1.12 (0.23), residues: 1348 helix: 1.86 (0.17), residues: 820 sheet: None (None), residues: 0 loop : -1.10 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 101 TYR 0.016 0.001 TYR A 211 PHE 0.012 0.001 PHE A 326 TRP 0.008 0.001 TRP A 152 HIS 0.003 0.001 HIS B 553 Details of bonding type rmsd covalent geometry : bond 0.00259 (11082) covalent geometry : angle 0.52741 (15052) SS BOND : bond 0.00194 ( 6) SS BOND : angle 0.51847 ( 12) hydrogen bonds : bond 0.03595 ( 636) hydrogen bonds : angle 4.32822 ( 1860) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.7158 (mmp-170) cc_final: 0.6860 (mmp-170) REVERT: A 118 MET cc_start: 0.3863 (mtt) cc_final: 0.3534 (mtt) REVERT: A 152 TRP cc_start: 0.7174 (t60) cc_final: 0.6967 (t60) REVERT: A 298 TYR cc_start: 0.6645 (t80) cc_final: 0.6416 (t80) REVERT: A 531 MET cc_start: 0.8413 (mmm) cc_final: 0.7611 (mtt) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1906 time to fit residues: 58.0666 Evaluate side-chains 188 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 77 optimal weight: 0.0770 chunk 130 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.213577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.179572 restraints weight = 47988.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.185476 restraints weight = 25029.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.189190 restraints weight = 16866.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.191058 restraints weight = 13174.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.192751 restraints weight = 11492.655| |-----------------------------------------------------------------------------| r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11088 Z= 0.124 Angle : 0.527 5.712 15064 Z= 0.269 Chirality : 0.037 0.160 1698 Planarity : 0.005 0.067 1844 Dihedral : 6.410 94.007 1498 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 1.16 (0.23), residues: 1348 helix: 1.90 (0.17), residues: 820 sheet: None (None), residues: 0 loop : -1.09 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 709 TYR 0.014 0.001 TYR A 211 PHE 0.021 0.001 PHE B 393 TRP 0.011 0.001 TRP A 217 HIS 0.004 0.001 HIS B 553 Details of bonding type rmsd covalent geometry : bond 0.00274 (11082) covalent geometry : angle 0.52750 (15052) SS BOND : bond 0.00219 ( 6) SS BOND : angle 0.52496 ( 12) hydrogen bonds : bond 0.03519 ( 636) hydrogen bonds : angle 4.32038 ( 1860) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.3859 (mtt) cc_final: 0.3531 (mtt) REVERT: A 298 TYR cc_start: 0.6624 (t80) cc_final: 0.6014 (t80) REVERT: A 531 MET cc_start: 0.8328 (mmm) cc_final: 0.7636 (mtt) REVERT: B 298 TYR cc_start: 0.6719 (t80) cc_final: 0.6383 (t80) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.2130 time to fit residues: 65.1647 Evaluate side-chains 191 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 113 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 92 optimal weight: 0.0570 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 135 optimal weight: 0.0770 chunk 11 optimal weight: 4.9990 overall best weight: 1.3860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 HIS ** B 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.213044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.178752 restraints weight = 48157.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.184823 restraints weight = 25130.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.188541 restraints weight = 16888.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.190674 restraints weight = 13200.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.192226 restraints weight = 11376.456| |-----------------------------------------------------------------------------| r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11088 Z= 0.130 Angle : 0.540 6.638 15064 Z= 0.276 Chirality : 0.038 0.201 1698 Planarity : 0.005 0.091 1844 Dihedral : 6.160 86.277 1498 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 1.08 (0.23), residues: 1348 helix: 1.81 (0.17), residues: 830 sheet: None (None), residues: 0 loop : -1.13 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 709 TYR 0.015 0.001 TYR A 211 PHE 0.021 0.001 PHE A 335 TRP 0.027 0.001 TRP A 152 HIS 0.002 0.001 HIS B 553 Details of bonding type rmsd covalent geometry : bond 0.00284 (11082) covalent geometry : angle 0.54001 (15052) SS BOND : bond 0.00229 ( 6) SS BOND : angle 0.49609 ( 12) hydrogen bonds : bond 0.03586 ( 636) hydrogen bonds : angle 4.33076 ( 1860) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.3878 (mtt) cc_final: 0.3556 (mtt) REVERT: A 298 TYR cc_start: 0.6696 (t80) cc_final: 0.6071 (t80) REVERT: A 531 MET cc_start: 0.8328 (mmm) cc_final: 0.7719 (mtt) REVERT: A 620 VAL cc_start: 0.9010 (t) cc_final: 0.8619 (t) REVERT: B 298 TYR cc_start: 0.6724 (t80) cc_final: 0.6392 (t80) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1977 time to fit residues: 62.4600 Evaluate side-chains 193 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.211203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.177059 restraints weight = 48064.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.183160 restraints weight = 24724.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.186957 restraints weight = 16472.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.188854 restraints weight = 12780.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.190605 restraints weight = 11105.428| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11088 Z= 0.145 Angle : 0.554 6.076 15064 Z= 0.287 Chirality : 0.038 0.172 1698 Planarity : 0.005 0.047 1844 Dihedral : 5.880 77.486 1498 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.95 (0.23), residues: 1348 helix: 1.68 (0.17), residues: 830 sheet: None (None), residues: 0 loop : -1.14 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 101 TYR 0.017 0.001 TYR A 211 PHE 0.024 0.002 PHE A 393 TRP 0.034 0.001 TRP A 152 HIS 0.003 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00321 (11082) covalent geometry : angle 0.55426 (15052) SS BOND : bond 0.00316 ( 6) SS BOND : angle 0.64680 ( 12) hydrogen bonds : bond 0.03634 ( 636) hydrogen bonds : angle 4.39543 ( 1860) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.3880 (mtt) cc_final: 0.3522 (mtt) REVERT: A 298 TYR cc_start: 0.6754 (t80) cc_final: 0.6111 (t80) REVERT: A 531 MET cc_start: 0.8337 (mmm) cc_final: 0.7762 (mtt) REVERT: B 298 TYR cc_start: 0.6676 (t80) cc_final: 0.6068 (t80) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.2015 time to fit residues: 63.3295 Evaluate side-chains 193 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 66 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.214106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.180469 restraints weight = 48204.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.186662 restraints weight = 24851.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.190520 restraints weight = 16454.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.192841 restraints weight = 12709.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.194386 restraints weight = 10811.668| |-----------------------------------------------------------------------------| r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11088 Z= 0.112 Angle : 0.531 6.220 15064 Z= 0.268 Chirality : 0.037 0.172 1698 Planarity : 0.005 0.052 1844 Dihedral : 5.528 75.210 1498 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 1.18 (0.23), residues: 1348 helix: 1.88 (0.17), residues: 830 sheet: None (None), residues: 0 loop : -1.07 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 101 TYR 0.014 0.001 TYR A 211 PHE 0.030 0.001 PHE B 393 TRP 0.035 0.001 TRP A 152 HIS 0.002 0.000 HIS B 553 Details of bonding type rmsd covalent geometry : bond 0.00248 (11082) covalent geometry : angle 0.53091 (15052) SS BOND : bond 0.00204 ( 6) SS BOND : angle 0.46223 ( 12) hydrogen bonds : bond 0.03440 ( 636) hydrogen bonds : angle 4.28619 ( 1860) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.3828 (mtt) cc_final: 0.3509 (mtt) REVERT: A 298 TYR cc_start: 0.6642 (t80) cc_final: 0.5919 (t80) REVERT: A 531 MET cc_start: 0.8429 (mmm) cc_final: 0.7768 (mtt) REVERT: B 298 TYR cc_start: 0.6655 (t80) cc_final: 0.5999 (t80) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2100 time to fit residues: 65.1504 Evaluate side-chains 193 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 111 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 chunk 0 optimal weight: 8.9990 chunk 135 optimal weight: 0.9990 chunk 3 optimal weight: 0.0010 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 ASN ** B 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.214030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.180396 restraints weight = 47950.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.186595 restraints weight = 24503.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.190458 restraints weight = 16188.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.192658 restraints weight = 12478.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.193929 restraints weight = 10707.629| |-----------------------------------------------------------------------------| r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11088 Z= 0.102 Angle : 0.514 6.316 15064 Z= 0.258 Chirality : 0.037 0.169 1698 Planarity : 0.004 0.045 1844 Dihedral : 5.109 71.240 1498 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 1.35 (0.23), residues: 1348 helix: 2.03 (0.17), residues: 830 sheet: None (None), residues: 0 loop : -1.03 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 101 TYR 0.011 0.001 TYR A 211 PHE 0.024 0.001 PHE B 393 TRP 0.032 0.001 TRP A 152 HIS 0.003 0.000 HIS A 787 Details of bonding type rmsd covalent geometry : bond 0.00229 (11082) covalent geometry : angle 0.51432 (15052) SS BOND : bond 0.00190 ( 6) SS BOND : angle 0.38047 ( 12) hydrogen bonds : bond 0.03235 ( 636) hydrogen bonds : angle 4.18375 ( 1860) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3164.74 seconds wall clock time: 54 minutes 45.11 seconds (3285.11 seconds total)