Starting phenix.real_space_refine on Thu Jun 4 08:33:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o1q_70017/06_2026/9o1q_70017.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o1q_70017/06_2026/9o1q_70017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o1q_70017/06_2026/9o1q_70017.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o1q_70017/06_2026/9o1q_70017.map" model { file = "/net/cci-nas-00/data/ceres_data/9o1q_70017/06_2026/9o1q_70017.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o1q_70017/06_2026/9o1q_70017.cif" } resolution = 4.2 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= 0.003 sd= 0.014 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: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 74 5.16 5 C 7586 2.51 5 N 1868 2.21 5 O 2022 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11556 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 5775 Classifications: {'peptide': 709} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 32, 'TRANS': 676} Chain breaks: 7 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B Time building chain proxies: 5.33, per 1000 atoms: 0.46 Number of scatterers: 11556 At special positions: 0 Unit cell: (122.925, 111.375, 111.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 74 16.00 O 2022 8.00 N 1868 7.00 C 7586 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " 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: 0.74 Conformation dependent library (CDL) restraints added in 547.8 milliseconds 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2696 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 62.2% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 90 through 109 Processing helix chain 'A' and resid 131 through 142 removed outlier: 3.687A pdb=" N MET A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 220 removed outlier: 4.114A pdb=" N ARG A 219 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 240 Processing helix chain 'A' and resid 264 through 273 removed outlier: 3.507A pdb=" N LEU A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 296 through 326 removed outlier: 4.764A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA A 313 " --> pdb=" O MET A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 removed outlier: 3.580A pdb=" N LYS A 335 " --> pdb=" O CYS A 331 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS A 338 " --> pdb=" O SER A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 363 Processing helix chain 'A' and resid 364 through 374 removed outlier: 4.068A pdb=" N LYS A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 408 removed outlier: 4.036A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 480 removed outlier: 3.862A pdb=" N THR A 454 " --> pdb=" O CYS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 537 Processing helix chain 'A' and resid 543 through 573 removed outlier: 3.854A pdb=" N SER A 565 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 613 removed outlier: 3.754A pdb=" N GLU A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 639 Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 648 through 656 removed outlier: 3.851A pdb=" N GLN A 652 " --> pdb=" O PRO A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 681 removed outlier: 3.674A pdb=" N TYR A 666 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU A 667 " --> pdb=" O GLY A 663 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 674 " --> pdb=" O GLU A 670 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 710 removed outlier: 4.445A pdb=" N LEU A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 700 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 709 " --> pdb=" O TRP A 705 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 710 " --> pdb=" O LYS A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 732 removed outlier: 4.197A pdb=" N MET A 729 " --> pdb=" O TRP A 725 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 746 Processing helix chain 'A' and resid 749 through 759 Processing helix chain 'A' and resid 775 through 780 Processing helix chain 'A' and resid 825 through 857 removed outlier: 3.590A pdb=" N ILE A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 875 removed outlier: 4.521A pdb=" N THR A 864 " --> pdb=" O VAL A 860 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR A 875 " --> pdb=" O GLU A 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 109 Processing helix chain 'B' and resid 131 through 142 removed outlier: 3.688A pdb=" N MET B 142 " --> pdb=" O TYR B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 removed outlier: 4.114A pdb=" N ARG B 219 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 264 through 273 removed outlier: 3.507A pdb=" N LEU B 268 " --> pdb=" O SER B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 292 Processing helix chain 'B' and resid 296 through 326 removed outlier: 4.763A pdb=" N LEU B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA B 313 " --> pdb=" O MET B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 338 removed outlier: 3.580A pdb=" N LYS B 335 " --> pdb=" O CYS B 331 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 363 Processing helix chain 'B' and resid 364 through 374 removed outlier: 4.067A pdb=" N LYS B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 408 removed outlier: 4.036A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 480 removed outlier: 3.861A pdb=" N THR B 454 " --> pdb=" O CYS B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 537 Processing helix chain 'B' and resid 543 through 573 removed outlier: 3.853A pdb=" N SER B 565 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 613 removed outlier: 3.754A pdb=" N GLU B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 639 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 656 removed outlier: 3.851A pdb=" N GLN B 652 " --> pdb=" O PRO B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 681 removed outlier: 3.674A pdb=" N TYR B 666 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 674 " --> pdb=" O GLU B 670 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 710 removed outlier: 4.445A pdb=" N LEU B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B 700 " --> pdb=" O ASN B 696 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 709 " --> pdb=" O TRP B 705 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 710 " --> pdb=" O LYS B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 732 removed outlier: 4.197A pdb=" N MET B 729 " --> pdb=" O TRP B 725 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLN B 730 " --> pdb=" O GLN B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 746 Processing helix chain 'B' and resid 749 through 759 Processing helix chain 'B' and resid 775 through 780 Processing helix chain 'B' and resid 825 through 857 removed outlier: 3.590A pdb=" N ILE B 857 " --> pdb=" O ILE B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 875 removed outlier: 4.521A pdb=" N THR B 864 " --> pdb=" O VAL B 860 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS B 865 " --> pdb=" O SER B 861 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR B 875 " --> pdb=" O GLU B 871 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 116 removed outlier: 3.563A pdb=" N THR A 115 " --> pdb=" O PHE A 125 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE A 74 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE A 246 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 76 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 782 through 784 Processing sheet with id=AA3, first strand: chain 'B' and resid 115 through 116 removed outlier: 3.563A pdb=" N THR B 115 " --> pdb=" O PHE B 125 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE B 74 " --> pdb=" O PHE B 246 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE B 246 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 76 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 782 through 784 628 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3517 1.34 - 1.46: 2471 1.46 - 1.58: 5760 1.58 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 11860 Sorted by residual: bond pdb=" CB TRP A 397 " pdb=" CG TRP A 397 " ideal model delta sigma weight residual 1.498 1.457 0.041 3.10e-02 1.04e+03 1.73e+00 bond pdb=" CB TRP B 397 " pdb=" CG TRP B 397 " ideal model delta sigma weight residual 1.498 1.458 0.040 3.10e-02 1.04e+03 1.70e+00 bond pdb=" N ILE B 786 " pdb=" CA ILE B 786 " ideal model delta sigma weight residual 1.474 1.456 0.018 1.57e-02 4.06e+03 1.38e+00 bond pdb=" N ILE A 786 " pdb=" CA ILE A 786 " ideal model delta sigma weight residual 1.474 1.457 0.018 1.57e-02 4.06e+03 1.29e+00 bond pdb=" CG MET A 309 " pdb=" SD MET A 309 " ideal model delta sigma weight residual 1.803 1.776 0.027 2.50e-02 1.60e+03 1.17e+00 ... (remaining 11855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 15572 1.55 - 3.11: 377 3.11 - 4.66: 79 4.66 - 6.21: 54 6.21 - 7.77: 10 Bond angle restraints: 16092 Sorted by residual: angle pdb=" C GLN A 308 " pdb=" N MET A 309 " pdb=" CA MET A 309 " ideal model delta sigma weight residual 122.54 114.93 7.61 1.65e+00 3.67e-01 2.13e+01 angle pdb=" C GLN B 308 " pdb=" N MET B 309 " pdb=" CA MET B 309 " ideal model delta sigma weight residual 122.54 114.95 7.59 1.65e+00 3.67e-01 2.12e+01 angle pdb=" N GLU A 529 " pdb=" CA GLU A 529 " pdb=" CB GLU A 529 " ideal model delta sigma weight residual 110.28 115.72 -5.44 1.55e+00 4.16e-01 1.23e+01 angle pdb=" N GLU B 529 " pdb=" CA GLU B 529 " pdb=" CB GLU B 529 " ideal model delta sigma weight residual 110.28 115.69 -5.41 1.55e+00 4.16e-01 1.22e+01 angle pdb=" N MET B 842 " pdb=" CA MET B 842 " pdb=" CB MET B 842 " ideal model delta sigma weight residual 110.01 114.95 -4.94 1.45e+00 4.76e-01 1.16e+01 ... (remaining 16087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 6266 16.69 - 33.38: 557 33.38 - 50.07: 141 50.07 - 66.76: 22 66.76 - 83.45: 12 Dihedral angle restraints: 6998 sinusoidal: 2810 harmonic: 4188 Sorted by residual: dihedral pdb=" CB CYS B 338 " pdb=" SG CYS B 338 " pdb=" SG CYS B 365 " pdb=" CB CYS B 365 " ideal model delta sinusoidal sigma weight residual -86.00 -3.67 -82.33 1 1.00e+01 1.00e-02 8.32e+01 dihedral pdb=" CB CYS A 338 " pdb=" SG CYS A 338 " pdb=" SG CYS A 365 " pdb=" CB CYS A 365 " ideal model delta sinusoidal sigma weight residual -86.00 -3.68 -82.32 1 1.00e+01 1.00e-02 8.32e+01 dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 601 " pdb=" CB CYS A 601 " ideal model delta sinusoidal sigma weight residual -86.00 -30.66 -55.34 1 1.00e+01 1.00e-02 4.14e+01 ... (remaining 6995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1184 0.039 - 0.079: 447 0.079 - 0.118: 119 0.118 - 0.158: 20 0.158 - 0.197: 2 Chirality restraints: 1772 Sorted by residual: chirality pdb=" CB ILE A 857 " pdb=" CA ILE A 857 " pdb=" CG1 ILE A 857 " pdb=" CG2 ILE A 857 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" CB ILE B 857 " pdb=" CA ILE B 857 " pdb=" CG1 ILE B 857 " pdb=" CG2 ILE B 857 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" CA MET B 309 " pdb=" N MET B 309 " pdb=" C MET B 309 " pdb=" CB MET B 309 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 1769 not shown) Planarity restraints: 2000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 302 " 0.010 2.00e-02 2.50e+03 1.32e-02 4.32e+00 pdb=" CG TRP A 302 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 302 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 302 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 302 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 302 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 302 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 302 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 302 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 302 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 302 " -0.011 2.00e-02 2.50e+03 1.31e-02 4.30e+00 pdb=" CG TRP B 302 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 302 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 302 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 302 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 302 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 302 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 302 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 302 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 302 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 763 " 0.034 5.00e-02 4.00e+02 5.05e-02 4.09e+00 pdb=" N PRO B 764 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 764 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 764 " 0.029 5.00e-02 4.00e+02 ... (remaining 1997 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1042 2.74 - 3.28: 13100 3.28 - 3.82: 20208 3.82 - 4.36: 23052 4.36 - 4.90: 36471 Nonbonded interactions: 93873 Sorted by model distance: nonbonded pdb=" OE2 GLU B 667 " pdb="CA CA B1002 " model vdw 2.199 2.510 nonbonded pdb=" OE2 GLU A 667 " pdb="CA CA A1002 " model vdw 2.200 2.510 nonbonded pdb=" O ILE B 744 " pdb=" OG SER B 748 " model vdw 2.200 3.040 nonbonded pdb=" O ILE A 744 " pdb=" OG SER A 748 " model vdw 2.200 3.040 nonbonded pdb=" O TYR B 776 " pdb=" OG1 THR B 780 " model vdw 2.202 3.040 ... (remaining 93868 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: 0.02 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: 1.010 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.150 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 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 0.041 11870 Z= 0.137 Angle : 0.688 7.766 16112 Z= 0.373 Chirality : 0.043 0.197 1772 Planarity : 0.004 0.051 2000 Dihedral : 13.763 83.453 4272 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.23), residues: 1386 helix: 0.40 (0.19), residues: 800 sheet: -1.37 (0.75), residues: 52 loop : -1.09 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 701 TYR 0.025 0.001 TYR B 305 PHE 0.030 0.001 PHE A 677 TRP 0.033 0.002 TRP B 302 HIS 0.004 0.001 HIS A 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (11860) covalent geometry : angle 0.68656 / 0.37 (16092) SS BOND : bond 0.00135 / 0.06 ( 10) SS BOND : angle 1.36077 / 0.88 ( 20) hydrogen bonds : bond 0.13755 / 8.76 ( 628) hydrogen bonds : angle 6.33089 / 4.37 ( 1866) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.417 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 273 TRP cc_start: 0.8390 (t-100) cc_final: 0.8021 (t-100) REVERT: A 553 MET cc_start: 0.8606 (pmm) cc_final: 0.8251 (pmm) REVERT: A 559 GLN cc_start: 0.8531 (tp-100) cc_final: 0.6644 (tp-100) REVERT: A 672 ILE cc_start: 0.8862 (mm) cc_final: 0.8387 (mm) REVERT: A 722 ILE cc_start: 0.7176 (mm) cc_final: 0.6963 (mm) REVERT: A 808 ARG cc_start: 0.8754 (tpp80) cc_final: 0.8318 (tpp80) REVERT: B 298 ILE cc_start: 0.8245 (pt) cc_final: 0.8033 (pt) REVERT: B 309 MET cc_start: 0.7644 (pmm) cc_final: 0.7280 (pmm) REVERT: B 546 ASP cc_start: 0.8228 (t0) cc_final: 0.8007 (t70) REVERT: B 553 MET cc_start: 0.8660 (pmm) cc_final: 0.8291 (pmm) REVERT: B 559 GLN cc_start: 0.8586 (tp-100) cc_final: 0.6346 (tp-100) REVERT: B 563 TYR cc_start: 0.7574 (m-10) cc_final: 0.7372 (m-10) REVERT: B 672 ILE cc_start: 0.9001 (mm) cc_final: 0.8502 (mm) REVERT: B 701 ARG cc_start: 0.8984 (mmp-170) cc_final: 0.8559 (mmp80) REVERT: B 850 LYS cc_start: 0.8666 (mmtm) cc_final: 0.8127 (tptp) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.0901 time to fit residues: 37.6989 Evaluate side-chains 219 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS A 549 ASN A 621 ASN A 818 HIS B 129 HIS B 549 ASN B 621 ASN B 818 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.115547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.084055 restraints weight = 43283.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.087020 restraints weight = 28526.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.089029 restraints weight = 21329.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.090486 restraints weight = 17361.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.091498 restraints weight = 14912.985| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11870 Z= 0.134 Angle : 0.611 7.991 16112 Z= 0.323 Chirality : 0.043 0.163 1772 Planarity : 0.004 0.047 2000 Dihedral : 4.129 17.967 1562 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.08 % Allowed : 5.80 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.23), residues: 1386 helix: 0.54 (0.18), residues: 848 sheet: -1.28 (0.78), residues: 52 loop : -1.03 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 701 TYR 0.024 0.001 TYR B 305 PHE 0.026 0.002 PHE B 677 TRP 0.011 0.001 TRP B 302 HIS 0.003 0.001 HIS A 824 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (11860) covalent geometry : angle 0.60951 / 0.32 (16092) SS BOND : bond 0.00429 / 0.18 ( 10) SS BOND : angle 1.36121 / 0.86 ( 20) hydrogen bonds : bond 0.03735 / 2.37 ( 628) hydrogen bonds : angle 4.88507 / 3.34 ( 1866) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 0.399 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: symmetry clash REVERT: A 523 ILE cc_start: 0.9296 (pt) cc_final: 0.9043 (pt) REVERT: A 559 GLN cc_start: 0.8794 (tp-100) cc_final: 0.8499 (tp-100) REVERT: A 672 ILE cc_start: 0.9021 (mm) cc_final: 0.8672 (mm) REVERT: A 722 ILE cc_start: 0.7309 (mm) cc_final: 0.6983 (mm) REVERT: A 729 MET cc_start: 0.8602 (mpp) cc_final: 0.8167 (mpp) REVERT: A 742 MET cc_start: 0.9329 (mmp) cc_final: 0.9097 (mmm) REVERT: B 333 TRP cc_start: 0.8669 (p-90) cc_final: 0.8452 (p-90) REVERT: B 523 ILE cc_start: 0.9307 (pt) cc_final: 0.9048 (pt) REVERT: B 546 ASP cc_start: 0.8299 (t0) cc_final: 0.7944 (t70) REVERT: B 559 GLN cc_start: 0.8790 (tp-100) cc_final: 0.8487 (tp-100) REVERT: B 564 TYR cc_start: 0.8621 (m-80) cc_final: 0.7771 (m-80) REVERT: B 672 ILE cc_start: 0.9089 (mm) cc_final: 0.8685 (mm) REVERT: B 701 ARG cc_start: 0.8919 (mmp-170) cc_final: 0.7990 (mmp80) REVERT: B 729 MET cc_start: 0.8716 (mpp) cc_final: 0.8312 (mpp) REVERT: B 742 MET cc_start: 0.9384 (mmp) cc_final: 0.8997 (mmm) REVERT: B 808 ARG cc_start: 0.8750 (tpp80) cc_final: 0.8268 (tpp80) REVERT: B 850 LYS cc_start: 0.8950 (mmtm) cc_final: 0.8413 (tptp) outliers start: 1 outliers final: 0 residues processed: 274 average time/residue: 0.0991 time to fit residues: 39.8777 Evaluate side-chains 224 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 3 optimal weight: 40.0000 chunk 53 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 117 optimal weight: 20.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS A 657 GLN A 710 GLN ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN A 814 ASN B 655 HIS B 657 GLN B 710 GLN ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 740 ASN B 814 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.107911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.077363 restraints weight = 45281.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.080017 restraints weight = 29532.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.081856 restraints weight = 22090.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.083161 restraints weight = 18040.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.083755 restraints weight = 15615.098| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 11870 Z= 0.227 Angle : 0.702 7.904 16112 Z= 0.380 Chirality : 0.046 0.284 1772 Planarity : 0.005 0.052 2000 Dihedral : 4.675 17.809 1562 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.22), residues: 1386 helix: 0.14 (0.17), residues: 842 sheet: 0.67 (1.06), residues: 32 loop : -1.16 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 808 TYR 0.033 0.002 TYR A 305 PHE 0.051 0.002 PHE A 851 TRP 0.023 0.002 TRP A 408 HIS 0.008 0.001 HIS B 824 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.23 (11860) covalent geometry : angle 0.69992 / 0.38 (16092) SS BOND : bond 0.00522 / 0.23 ( 10) SS BOND : angle 1.68277 / 1.03 ( 20) hydrogen bonds : bond 0.04336 / 2.73 ( 628) hydrogen bonds : angle 5.22967 / 3.56 ( 1866) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.479 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: symmetry clash revert: symmetry clash REVERT: A 298 ILE cc_start: 0.8570 (pt) cc_final: 0.8352 (pt) REVERT: A 309 MET cc_start: 0.8125 (pmm) cc_final: 0.7889 (pmm) REVERT: A 385 PHE cc_start: 0.8787 (t80) cc_final: 0.8505 (t80) REVERT: A 523 ILE cc_start: 0.9335 (pt) cc_final: 0.9090 (pt) REVERT: A 573 PHE cc_start: 0.7841 (m-80) cc_final: 0.7473 (m-80) REVERT: A 608 GLN cc_start: 0.9265 (tm-30) cc_final: 0.9040 (tm-30) REVERT: A 729 MET cc_start: 0.8813 (mpp) cc_final: 0.8469 (mpp) REVERT: A 742 MET cc_start: 0.9387 (mmp) cc_final: 0.9131 (mmm) REVERT: A 808 ARG cc_start: 0.8862 (tpp80) cc_final: 0.8399 (tpp80) REVERT: B 298 ILE cc_start: 0.8651 (pt) cc_final: 0.8394 (pt) REVERT: B 309 MET cc_start: 0.8006 (pmm) cc_final: 0.7602 (pmm) REVERT: B 385 PHE cc_start: 0.8805 (t80) cc_final: 0.8489 (t80) REVERT: B 386 MET cc_start: 0.8398 (mmp) cc_final: 0.8060 (mmp) REVERT: B 398 LYS cc_start: 0.9468 (tppt) cc_final: 0.9216 (tptp) REVERT: B 546 ASP cc_start: 0.8456 (t0) cc_final: 0.8087 (t70) REVERT: B 559 GLN cc_start: 0.8657 (tp-100) cc_final: 0.8327 (tp-100) REVERT: B 564 TYR cc_start: 0.8625 (m-80) cc_final: 0.6452 (m-80) REVERT: B 573 PHE cc_start: 0.7930 (m-80) cc_final: 0.7429 (m-80) REVERT: B 608 GLN cc_start: 0.9349 (tm-30) cc_final: 0.9066 (tm-30) REVERT: B 671 MET cc_start: 0.8230 (ppp) cc_final: 0.7264 (tpp) REVERT: B 729 MET cc_start: 0.8847 (mpp) cc_final: 0.8455 (mpp) REVERT: B 742 MET cc_start: 0.9398 (mmp) cc_final: 0.9066 (mmm) REVERT: B 808 ARG cc_start: 0.8802 (tpp80) cc_final: 0.8212 (tpp80) REVERT: B 839 ILE cc_start: 0.9252 (pt) cc_final: 0.8906 (pt) REVERT: B 842 MET cc_start: 0.9317 (mpp) cc_final: 0.8776 (mpp) REVERT: B 847 TYR cc_start: 0.7384 (t80) cc_final: 0.7165 (t80) REVERT: B 850 LYS cc_start: 0.9060 (mmtm) cc_final: 0.8453 (tptp) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.0991 time to fit residues: 37.7968 Evaluate side-chains 215 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 4 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 129 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 75 optimal weight: 30.0000 chunk 80 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 40.0000 chunk 86 optimal weight: 8.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 GLN B 720 GLN ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.106698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.076379 restraints weight = 45006.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.079005 restraints weight = 29546.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.080819 restraints weight = 22082.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.081915 restraints weight = 18022.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.082957 restraints weight = 15719.350| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 11870 Z= 0.213 Angle : 0.689 7.581 16112 Z= 0.373 Chirality : 0.046 0.219 1772 Planarity : 0.005 0.082 2000 Dihedral : 4.825 22.285 1562 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.16 % Allowed : 4.83 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.22), residues: 1386 helix: 0.08 (0.17), residues: 852 sheet: 0.37 (1.02), residues: 32 loop : -1.23 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 211 TYR 0.026 0.002 TYR A 305 PHE 0.037 0.002 PHE A 838 TRP 0.025 0.002 TRP A 408 HIS 0.011 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.21 (11860) covalent geometry : angle 0.68574 / 0.37 (16092) SS BOND : bond 0.00482 / 0.20 ( 10) SS BOND : angle 1.90833 / 1.19 ( 20) hydrogen bonds : bond 0.04093 / 2.64 ( 628) hydrogen bonds : angle 5.14436 / 3.50 ( 1866) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 261 time to evaluate : 0.498 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 309 MET cc_start: 0.8251 (pmm) cc_final: 0.7831 (pmm) REVERT: A 385 PHE cc_start: 0.8673 (t80) cc_final: 0.8306 (t80) REVERT: A 386 MET cc_start: 0.8928 (tpt) cc_final: 0.8587 (mmm) REVERT: A 523 ILE cc_start: 0.9380 (pt) cc_final: 0.9103 (pt) REVERT: A 546 ASP cc_start: 0.8550 (t0) cc_final: 0.8213 (t70) REVERT: A 558 PHE cc_start: 0.9338 (m-80) cc_final: 0.9121 (m-80) REVERT: A 559 GLN cc_start: 0.8724 (tp-100) cc_final: 0.8317 (tp-100) REVERT: A 608 GLN cc_start: 0.9305 (tm-30) cc_final: 0.9098 (tm-30) REVERT: A 729 MET cc_start: 0.8890 (mpp) cc_final: 0.8467 (mpp) REVERT: A 742 MET cc_start: 0.9360 (mmp) cc_final: 0.9068 (mmm) REVERT: A 808 ARG cc_start: 0.8800 (tpp80) cc_final: 0.8437 (mmt90) REVERT: B 300 PHE cc_start: 0.9192 (m-80) cc_final: 0.8980 (m-10) REVERT: B 309 MET cc_start: 0.8135 (pmm) cc_final: 0.7613 (pmm) REVERT: B 385 PHE cc_start: 0.8798 (t80) cc_final: 0.8400 (t80) REVERT: B 386 MET cc_start: 0.8191 (mmp) cc_final: 0.7905 (mmp) REVERT: B 534 MET cc_start: 0.6743 (mmm) cc_final: 0.6338 (ttt) REVERT: B 546 ASP cc_start: 0.8449 (t0) cc_final: 0.8099 (t70) REVERT: B 558 PHE cc_start: 0.9375 (m-80) cc_final: 0.9150 (m-80) REVERT: B 559 GLN cc_start: 0.8450 (tp-100) cc_final: 0.8080 (tp-100) REVERT: B 608 GLN cc_start: 0.9341 (tm-30) cc_final: 0.9065 (tm-30) REVERT: B 671 MET cc_start: 0.8222 (ppp) cc_final: 0.7768 (tpp) REVERT: B 729 MET cc_start: 0.8924 (mpp) cc_final: 0.8481 (mpp) REVERT: B 742 MET cc_start: 0.9362 (mmp) cc_final: 0.9067 (mmm) REVERT: B 808 ARG cc_start: 0.8847 (tpp80) cc_final: 0.8481 (mmt90) outliers start: 2 outliers final: 2 residues processed: 263 average time/residue: 0.0974 time to fit residues: 37.8270 Evaluate side-chains 209 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 207 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 97 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN A 726 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.110827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.079384 restraints weight = 42969.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.082323 restraints weight = 27247.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.084317 restraints weight = 20085.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.085831 restraints weight = 16194.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.086691 restraints weight = 13811.675| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11870 Z= 0.132 Angle : 0.642 9.122 16112 Z= 0.335 Chirality : 0.044 0.265 1772 Planarity : 0.005 0.075 2000 Dihedral : 4.512 18.766 1562 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.23), residues: 1386 helix: 0.30 (0.17), residues: 854 sheet: 0.16 (0.99), residues: 32 loop : -1.19 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 636 TYR 0.023 0.001 TYR A 305 PHE 0.028 0.002 PHE A 838 TRP 0.013 0.001 TRP A 408 HIS 0.003 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (11860) covalent geometry : angle 0.63941 / 0.33 (16092) SS BOND : bond 0.00379 / 0.16 ( 10) SS BOND : angle 1.68046 / 1.04 ( 20) hydrogen bonds : bond 0.03603 / 2.32 ( 628) hydrogen bonds : angle 4.83811 / 3.30 ( 1866) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.486 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 273 TRP cc_start: 0.8957 (t-100) cc_final: 0.8026 (t-100) REVERT: A 298 ILE cc_start: 0.8651 (pt) cc_final: 0.8405 (pt) REVERT: A 309 MET cc_start: 0.8199 (pmm) cc_final: 0.7881 (pmm) REVERT: A 323 TYR cc_start: 0.9175 (t80) cc_final: 0.8943 (t80) REVERT: A 385 PHE cc_start: 0.8716 (t80) cc_final: 0.8395 (t80) REVERT: A 523 ILE cc_start: 0.9350 (pt) cc_final: 0.9119 (pt) REVERT: A 559 GLN cc_start: 0.8738 (tp-100) cc_final: 0.8233 (tp-100) REVERT: A 729 MET cc_start: 0.8769 (mpp) cc_final: 0.8207 (mpp) REVERT: A 730 GLN cc_start: 0.8742 (pm20) cc_final: 0.8475 (pm20) REVERT: A 742 MET cc_start: 0.9399 (mmp) cc_final: 0.9124 (mmm) REVERT: A 850 LYS cc_start: 0.9226 (mmtp) cc_final: 0.8919 (mmmm) REVERT: B 309 MET cc_start: 0.8170 (pmm) cc_final: 0.7684 (pmm) REVERT: B 385 PHE cc_start: 0.8787 (t80) cc_final: 0.8427 (t80) REVERT: B 386 MET cc_start: 0.8030 (mmp) cc_final: 0.7783 (mmp) REVERT: B 523 ILE cc_start: 0.9316 (pt) cc_final: 0.9067 (pt) REVERT: B 534 MET cc_start: 0.6717 (mmm) cc_final: 0.6351 (ttt) REVERT: B 559 GLN cc_start: 0.8635 (tp-100) cc_final: 0.8228 (tp-100) REVERT: B 564 TYR cc_start: 0.8615 (m-80) cc_final: 0.7976 (m-80) REVERT: B 608 GLN cc_start: 0.9314 (tm-30) cc_final: 0.9112 (tm-30) REVERT: B 671 MET cc_start: 0.8114 (ppp) cc_final: 0.7783 (tpp) REVERT: B 729 MET cc_start: 0.8816 (mpp) cc_final: 0.8263 (mpp) REVERT: B 730 GLN cc_start: 0.8782 (pm20) cc_final: 0.8526 (pm20) REVERT: B 742 MET cc_start: 0.9385 (mmp) cc_final: 0.9078 (mmm) REVERT: B 808 ARG cc_start: 0.8821 (tpp80) cc_final: 0.8469 (tpp80) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.0971 time to fit residues: 38.2243 Evaluate side-chains 218 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 68 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 9 optimal weight: 30.0000 chunk 95 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 5 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS A 674 GLN B 143 HIS ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.106759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.076828 restraints weight = 44466.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.079384 restraints weight = 29146.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.081194 restraints weight = 21876.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.082490 restraints weight = 17840.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.083292 restraints weight = 15369.013| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 11870 Z= 0.205 Angle : 0.706 8.473 16112 Z= 0.379 Chirality : 0.047 0.287 1772 Planarity : 0.005 0.069 2000 Dihedral : 4.806 22.570 1562 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.49 % Favored : 93.36 % Rotamer: Outliers : 0.08 % Allowed : 2.66 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.23), residues: 1386 helix: 0.21 (0.17), residues: 836 sheet: -0.01 (0.99), residues: 32 loop : -1.02 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 712 TYR 0.033 0.002 TYR A 305 PHE 0.062 0.003 PHE B 838 TRP 0.022 0.002 TRP A 302 HIS 0.006 0.001 HIS B 824 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.21 (11860) covalent geometry : angle 0.70277 / 0.38 (16092) SS BOND : bond 0.00480 / 0.27 ( 10) SS BOND : angle 2.00217 / 1.27 ( 20) hydrogen bonds : bond 0.04117 / 2.62 ( 628) hydrogen bonds : angle 5.11534 / 3.47 ( 1866) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 263 time to evaluate : 0.437 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 PHE cc_start: 0.8786 (t80) cc_final: 0.8457 (t80) REVERT: A 386 MET cc_start: 0.8760 (mmm) cc_final: 0.8545 (mmm) REVERT: A 397 TRP cc_start: 0.7834 (t-100) cc_final: 0.7233 (t-100) REVERT: A 523 ILE cc_start: 0.9356 (pt) cc_final: 0.9079 (pt) REVERT: A 559 GLN cc_start: 0.8594 (tp-100) cc_final: 0.8239 (tp-100) REVERT: A 729 MET cc_start: 0.8869 (mpp) cc_final: 0.8455 (mpp) REVERT: A 850 LYS cc_start: 0.9315 (mmtp) cc_final: 0.8691 (tptp) REVERT: B 298 ILE cc_start: 0.8678 (pt) cc_final: 0.8446 (pt) REVERT: B 309 MET cc_start: 0.8178 (pmm) cc_final: 0.7845 (pmm) REVERT: B 385 PHE cc_start: 0.8851 (t80) cc_final: 0.8423 (t80) REVERT: B 386 MET cc_start: 0.8176 (mmp) cc_final: 0.7924 (mmp) REVERT: B 523 ILE cc_start: 0.9327 (pt) cc_final: 0.9067 (pt) REVERT: B 534 MET cc_start: 0.6988 (mmm) cc_final: 0.6624 (ttt) REVERT: B 546 ASP cc_start: 0.8518 (t0) cc_final: 0.8176 (t70) REVERT: B 559 GLN cc_start: 0.8610 (tp-100) cc_final: 0.8258 (tp-100) REVERT: B 564 TYR cc_start: 0.8700 (m-80) cc_final: 0.6854 (m-80) REVERT: B 608 GLN cc_start: 0.9328 (tm-30) cc_final: 0.9077 (tm-30) REVERT: B 656 LEU cc_start: 0.9279 (mt) cc_final: 0.8930 (tt) REVERT: B 671 MET cc_start: 0.8325 (ppp) cc_final: 0.7428 (tpp) REVERT: B 729 MET cc_start: 0.8929 (mpp) cc_final: 0.8489 (mpp) REVERT: B 742 MET cc_start: 0.9407 (mmp) cc_final: 0.9091 (mmm) outliers start: 1 outliers final: 1 residues processed: 263 average time/residue: 0.0973 time to fit residues: 37.7956 Evaluate side-chains 221 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 220 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 101 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS B 674 GLN ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.110508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.079797 restraints weight = 42492.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.082494 restraints weight = 27910.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.084475 restraints weight = 20857.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.085844 restraints weight = 16866.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.086817 restraints weight = 14480.308| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11870 Z= 0.133 Angle : 0.679 9.157 16112 Z= 0.352 Chirality : 0.045 0.223 1772 Planarity : 0.005 0.075 2000 Dihedral : 4.538 20.829 1562 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.23), residues: 1386 helix: 0.30 (0.17), residues: 856 sheet: -1.54 (0.72), residues: 52 loop : -1.14 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 712 TYR 0.029 0.001 TYR B 847 PHE 0.045 0.002 PHE A 838 TRP 0.019 0.002 TRP B 408 HIS 0.007 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (11860) covalent geometry : angle 0.67627 / 0.35 (16092) SS BOND : bond 0.00335 / 0.14 ( 10) SS BOND : angle 1.80515 / 1.13 ( 20) hydrogen bonds : bond 0.03726 / 2.41 ( 628) hydrogen bonds : angle 4.83675 / 3.28 ( 1866) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8161 (pmm) cc_final: 0.7798 (pmm) REVERT: A 323 TYR cc_start: 0.9143 (t80) cc_final: 0.8939 (t80) REVERT: A 385 PHE cc_start: 0.8718 (t80) cc_final: 0.8437 (t80) REVERT: A 386 MET cc_start: 0.8611 (mmm) cc_final: 0.8386 (mmm) REVERT: A 559 GLN cc_start: 0.8583 (tp-100) cc_final: 0.8257 (tp-100) REVERT: A 722 ILE cc_start: 0.7628 (mm) cc_final: 0.7345 (mm) REVERT: A 729 MET cc_start: 0.8797 (mpp) cc_final: 0.8353 (mpp) REVERT: A 742 MET cc_start: 0.9344 (mmp) cc_final: 0.9126 (mmm) REVERT: A 850 LYS cc_start: 0.9274 (mmtp) cc_final: 0.8663 (tptp) REVERT: B 309 MET cc_start: 0.8182 (pmm) cc_final: 0.7604 (pmm) REVERT: B 385 PHE cc_start: 0.8792 (t80) cc_final: 0.8427 (t80) REVERT: B 534 MET cc_start: 0.6908 (mmm) cc_final: 0.6537 (ttt) REVERT: B 559 GLN cc_start: 0.8649 (tp-100) cc_final: 0.8242 (tp-100) REVERT: B 564 TYR cc_start: 0.8538 (m-80) cc_final: 0.6224 (m-80) REVERT: B 608 GLN cc_start: 0.9316 (tm-30) cc_final: 0.9093 (tm-30) REVERT: B 671 MET cc_start: 0.8312 (ppp) cc_final: 0.8015 (ptt) REVERT: B 693 LEU cc_start: 0.9472 (mm) cc_final: 0.9260 (mm) REVERT: B 729 MET cc_start: 0.8842 (mpp) cc_final: 0.8298 (mpp) REVERT: B 742 MET cc_start: 0.9372 (mmp) cc_final: 0.9100 (mmm) REVERT: B 808 ARG cc_start: 0.9052 (tpp80) cc_final: 0.8696 (tpp80) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.0931 time to fit residues: 36.8467 Evaluate side-chains 222 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 70 optimal weight: 50.0000 chunk 83 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 99 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS ** A 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.105986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.075397 restraints weight = 44112.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.078042 restraints weight = 28682.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.079880 restraints weight = 21361.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.081212 restraints weight = 17362.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.082124 restraints weight = 14961.995| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 11870 Z= 0.216 Angle : 0.721 8.229 16112 Z= 0.388 Chirality : 0.047 0.266 1772 Planarity : 0.005 0.072 2000 Dihedral : 4.861 21.006 1562 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.57 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.23), residues: 1386 helix: 0.24 (0.17), residues: 840 sheet: -1.60 (0.72), residues: 52 loop : -1.00 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 636 TYR 0.062 0.002 TYR A 528 PHE 0.048 0.002 PHE A 838 TRP 0.059 0.002 TRP B 463 HIS 0.007 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.22 (11860) covalent geometry : angle 0.71836 / 0.39 (16092) SS BOND : bond 0.00383 / 0.16 ( 10) SS BOND : angle 1.89506 / 1.20 ( 20) hydrogen bonds : bond 0.04126 / 2.64 ( 628) hydrogen bonds : angle 5.09823 / 3.45 ( 1866) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.452 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 273 TRP cc_start: 0.9006 (t-100) cc_final: 0.8548 (t-100) REVERT: A 298 ILE cc_start: 0.8835 (pt) cc_final: 0.8622 (pt) REVERT: A 385 PHE cc_start: 0.8810 (t80) cc_final: 0.8460 (t80) REVERT: A 386 MET cc_start: 0.8791 (mmm) cc_final: 0.8540 (mmm) REVERT: A 397 TRP cc_start: 0.7600 (t-100) cc_final: 0.7004 (t-100) REVERT: A 559 GLN cc_start: 0.8590 (tp-100) cc_final: 0.8220 (tp-100) REVERT: A 608 GLN cc_start: 0.9285 (tm-30) cc_final: 0.9077 (tm-30) REVERT: A 729 MET cc_start: 0.8906 (mpp) cc_final: 0.8535 (mpp) REVERT: A 742 MET cc_start: 0.9383 (mmp) cc_final: 0.9135 (mmm) REVERT: B 298 ILE cc_start: 0.8702 (pt) cc_final: 0.8456 (pt) REVERT: B 300 PHE cc_start: 0.9179 (m-80) cc_final: 0.8951 (m-80) REVERT: B 309 MET cc_start: 0.8327 (pmm) cc_final: 0.8050 (pmm) REVERT: B 385 PHE cc_start: 0.8774 (t80) cc_final: 0.8430 (t80) REVERT: B 386 MET cc_start: 0.8183 (mmp) cc_final: 0.7690 (mmm) REVERT: B 398 LYS cc_start: 0.9572 (tptp) cc_final: 0.9351 (tptp) REVERT: B 463 TRP cc_start: 0.9051 (m-90) cc_final: 0.8773 (m-90) REVERT: B 534 MET cc_start: 0.7031 (mmm) cc_final: 0.6650 (ttt) REVERT: B 559 GLN cc_start: 0.8549 (tp-100) cc_final: 0.8167 (tp-100) REVERT: B 564 TYR cc_start: 0.8782 (m-80) cc_final: 0.6918 (m-80) REVERT: B 608 GLN cc_start: 0.9353 (tm-30) cc_final: 0.9099 (tm-30) REVERT: B 672 ILE cc_start: 0.9277 (mm) cc_final: 0.8879 (mm) REVERT: B 729 MET cc_start: 0.8876 (mpp) cc_final: 0.8473 (mpp) REVERT: B 742 MET cc_start: 0.9427 (mmp) cc_final: 0.9098 (mmm) REVERT: B 808 ARG cc_start: 0.9045 (tpp80) cc_final: 0.8756 (tpp80) REVERT: B 839 ILE cc_start: 0.9250 (pt) cc_final: 0.8900 (pt) REVERT: B 842 MET cc_start: 0.9193 (mpp) cc_final: 0.8782 (mpp) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.0889 time to fit residues: 34.5932 Evaluate side-chains 224 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 65 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 113 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS ** A 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.107288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.076564 restraints weight = 43152.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.079150 restraints weight = 28448.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.081076 restraints weight = 21340.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.082410 restraints weight = 17275.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.083123 restraints weight = 14891.681| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11870 Z= 0.176 Angle : 0.723 8.522 16112 Z= 0.386 Chirality : 0.048 0.323 1772 Planarity : 0.005 0.079 2000 Dihedral : 4.755 21.017 1562 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.13 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.23), residues: 1386 helix: 0.25 (0.17), residues: 852 sheet: -1.53 (0.72), residues: 52 loop : -1.11 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 636 TYR 0.047 0.002 TYR A 528 PHE 0.045 0.002 PHE A 838 TRP 0.057 0.002 TRP B 463 HIS 0.007 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (11860) covalent geometry : angle 0.72067 / 0.39 (16092) SS BOND : bond 0.00377 / 0.15 ( 10) SS BOND : angle 1.84404 / 1.16 ( 20) hydrogen bonds : bond 0.04007 / 2.58 ( 628) hydrogen bonds : angle 5.07910 / 3.46 ( 1866) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.444 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 273 TRP cc_start: 0.8964 (t-100) cc_final: 0.8491 (t-100) REVERT: A 323 TYR cc_start: 0.9175 (t80) cc_final: 0.8962 (t80) REVERT: A 385 PHE cc_start: 0.8745 (t80) cc_final: 0.8418 (t80) REVERT: A 386 MET cc_start: 0.8703 (mmm) cc_final: 0.8472 (mmm) REVERT: A 397 TRP cc_start: 0.7618 (t-100) cc_final: 0.6930 (t-100) REVERT: A 559 GLN cc_start: 0.8584 (tp-100) cc_final: 0.8300 (tp-100) REVERT: A 729 MET cc_start: 0.8883 (mpp) cc_final: 0.8469 (mpp) REVERT: A 742 MET cc_start: 0.9354 (mmp) cc_final: 0.9066 (mmm) REVERT: A 839 ILE cc_start: 0.9148 (pt) cc_final: 0.8700 (pt) REVERT: A 842 MET cc_start: 0.9273 (mpp) cc_final: 0.8821 (mpp) REVERT: B 273 TRP cc_start: 0.8495 (t-100) cc_final: 0.8061 (t-100) REVERT: B 300 PHE cc_start: 0.9135 (m-80) cc_final: 0.8898 (m-80) REVERT: B 309 MET cc_start: 0.8265 (pmm) cc_final: 0.8011 (pmm) REVERT: B 385 PHE cc_start: 0.8734 (t80) cc_final: 0.8436 (t80) REVERT: B 386 MET cc_start: 0.8159 (mmp) cc_final: 0.7893 (mmp) REVERT: B 398 LYS cc_start: 0.9569 (tptp) cc_final: 0.9295 (tptp) REVERT: B 463 TRP cc_start: 0.9012 (m-90) cc_final: 0.8738 (m-90) REVERT: B 523 ILE cc_start: 0.9294 (pt) cc_final: 0.9059 (pt) REVERT: B 534 MET cc_start: 0.7014 (mmm) cc_final: 0.6662 (ttt) REVERT: B 553 MET cc_start: 0.8658 (pmm) cc_final: 0.8437 (pmm) REVERT: B 559 GLN cc_start: 0.8663 (tp-100) cc_final: 0.8264 (tp-100) REVERT: B 564 TYR cc_start: 0.8640 (m-80) cc_final: 0.6568 (m-80) REVERT: B 608 GLN cc_start: 0.9344 (tm-30) cc_final: 0.9096 (tm-30) REVERT: B 729 MET cc_start: 0.8858 (mpp) cc_final: 0.8423 (mpp) REVERT: B 742 MET cc_start: 0.9386 (mmp) cc_final: 0.9100 (mmm) REVERT: B 808 ARG cc_start: 0.9038 (tpp80) cc_final: 0.8746 (tpp80) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.0875 time to fit residues: 34.2043 Evaluate side-chains 224 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 101 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 139 optimal weight: 0.3980 chunk 69 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS A 674 GLN A 844 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.104062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.073687 restraints weight = 44721.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.076278 restraints weight = 28621.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.078092 restraints weight = 21192.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.079428 restraints weight = 17177.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.080298 restraints weight = 14767.312| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 11870 Z= 0.234 Angle : 0.786 8.658 16112 Z= 0.424 Chirality : 0.050 0.390 1772 Planarity : 0.006 0.086 2000 Dihedral : 5.113 23.550 1562 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 23.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.22 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.23), residues: 1386 helix: 0.05 (0.17), residues: 836 sheet: -1.53 (0.71), residues: 52 loop : -1.04 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 636 TYR 0.046 0.002 TYR A 528 PHE 0.044 0.002 PHE B 838 TRP 0.053 0.002 TRP B 463 HIS 0.007 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.23 (11860) covalent geometry : angle 0.78204 / 0.42 (16092) SS BOND : bond 0.00713 / 0.37 ( 10) SS BOND : angle 2.27889 / 1.41 ( 20) hydrogen bonds : bond 0.04437 / 2.86 ( 628) hydrogen bonds : angle 5.33176 / 3.64 ( 1866) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.431 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 323 TYR cc_start: 0.9211 (t80) cc_final: 0.8983 (t80) REVERT: A 385 PHE cc_start: 0.8767 (t80) cc_final: 0.8422 (t80) REVERT: A 386 MET cc_start: 0.8748 (mmm) cc_final: 0.8525 (mmm) REVERT: A 397 TRP cc_start: 0.7600 (t-100) cc_final: 0.6977 (t-100) REVERT: A 559 GLN cc_start: 0.8614 (tp-100) cc_final: 0.8234 (tp-100) REVERT: A 608 GLN cc_start: 0.9338 (tm-30) cc_final: 0.9094 (tm-30) REVERT: A 729 MET cc_start: 0.8950 (mpp) cc_final: 0.8607 (mpp) REVERT: B 300 PHE cc_start: 0.9244 (m-80) cc_final: 0.9003 (m-10) REVERT: B 385 PHE cc_start: 0.8746 (t80) cc_final: 0.8360 (t80) REVERT: B 386 MET cc_start: 0.8266 (mmp) cc_final: 0.7851 (mmp) REVERT: B 397 TRP cc_start: 0.7616 (t-100) cc_final: 0.7240 (t-100) REVERT: B 398 LYS cc_start: 0.9619 (tptp) cc_final: 0.9281 (tptp) REVERT: B 463 TRP cc_start: 0.9007 (m-90) cc_final: 0.8765 (m-90) REVERT: B 523 ILE cc_start: 0.9305 (pt) cc_final: 0.9053 (pt) REVERT: B 559 GLN cc_start: 0.8547 (tp-100) cc_final: 0.8202 (tp-100) REVERT: B 564 TYR cc_start: 0.8652 (m-80) cc_final: 0.6910 (m-80) REVERT: B 608 GLN cc_start: 0.9374 (tm-30) cc_final: 0.9099 (tm-30) REVERT: B 729 MET cc_start: 0.8929 (mpp) cc_final: 0.8646 (mpp) REVERT: B 742 MET cc_start: 0.9400 (mmp) cc_final: 0.9099 (mmm) REVERT: B 808 ARG cc_start: 0.9080 (tpp80) cc_final: 0.8775 (tpp80) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.0968 time to fit residues: 37.7750 Evaluate side-chains 220 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 62 optimal weight: 0.0370 chunk 13 optimal weight: 7.9990 chunk 49 optimal weight: 30.0000 chunk 101 optimal weight: 50.0000 chunk 56 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 74 optimal weight: 30.0000 chunk 129 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS A 674 GLN A 824 HIS A 844 HIS B 674 GLN B 824 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.107275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.076619 restraints weight = 42943.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.079260 restraints weight = 28054.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.081109 restraints weight = 21094.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.082466 restraints weight = 17175.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.083419 restraints weight = 14748.355| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11870 Z= 0.152 Angle : 0.731 9.536 16112 Z= 0.387 Chirality : 0.048 0.266 1772 Planarity : 0.005 0.079 2000 Dihedral : 4.796 22.141 1562 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.23), residues: 1386 helix: 0.27 (0.18), residues: 852 sheet: -1.47 (0.70), residues: 52 loop : -1.19 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 636 TYR 0.043 0.002 TYR A 528 PHE 0.042 0.002 PHE A 838 TRP 0.048 0.002 TRP B 463 HIS 0.007 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (11860) covalent geometry : angle 0.72695 / 0.39 (16092) SS BOND : bond 0.00425 / 0.18 ( 10) SS BOND : angle 2.16948 / 1.34 ( 20) hydrogen bonds : bond 0.03971 / 2.56 ( 628) hydrogen bonds : angle 5.01185 / 3.42 ( 1866) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2462.00 seconds wall clock time: 43 minutes 21.03 seconds (2601.03 seconds total)