Starting phenix.real_space_refine on Thu Aug 6 02:44:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10eu_75119/08_2026/10eu_75119.cif Found real_map, /net/cci-nas-00/data/ceres_data/10eu_75119/08_2026/10eu_75119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10eu_75119/08_2026/10eu_75119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10eu_75119/08_2026/10eu_75119.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10eu_75119/08_2026/10eu_75119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10eu_75119/08_2026/10eu_75119.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 8006 2.51 5 N 2152 2.21 5 O 2386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12586 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6293 Classifications: {'peptide': 797} Link IDs: {'PTRANS': 57, 'TRANS': 739} Chain breaks: 1 Restraints were copied for chains: B Time building chain proxies: 5.27, per 1000 atoms: 0.42 Number of scatterers: 12586 At special positions: 0 Unit cell: (100.01, 163.03, 98.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 2386 8.00 N 2152 7.00 C 8006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 560.1 milliseconds 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2968 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 28 sheets defined 15.9% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 114 through 122 removed outlier: 3.628A pdb=" N ILE A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 removed outlier: 4.025A pdb=" N LEU A 152 " --> pdb=" O PRO A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 326 Processing helix chain 'A' and resid 374 through 378 removed outlier: 3.570A pdb=" N ARG A 377 " --> pdb=" O PRO A 374 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 378 " --> pdb=" O CYS A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 378' Processing helix chain 'A' and resid 718 through 726 removed outlier: 3.647A pdb=" N TRP A 722 " --> pdb=" O ALA A 719 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA A 724 " --> pdb=" O LEU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 747 No H-bonds generated for 'chain 'A' and resid 745 through 747' Processing helix chain 'A' and resid 748 through 768 removed outlier: 4.319A pdb=" N ALA A 755 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER A 756 " --> pdb=" O GLN A 752 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A 765 " --> pdb=" O VAL A 761 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 766 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 794 removed outlier: 3.982A pdb=" N MET A 786 " --> pdb=" O TYR A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 835 removed outlier: 3.700A pdb=" N TYR A 831 " --> pdb=" O ALA A 827 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET A 834 " --> pdb=" O VAL A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 843 removed outlier: 3.699A pdb=" N ALA A 840 " --> pdb=" O PHE A 837 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN A 841 " --> pdb=" O MET A 838 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS A 842 " --> pdb=" O SER A 839 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE A 843 " --> pdb=" O ALA A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 865 Processing helix chain 'A' and resid 866 through 875 removed outlier: 3.796A pdb=" N HIS A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 911 Processing helix chain 'B' and resid 114 through 122 removed outlier: 3.628A pdb=" N ILE B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 153 removed outlier: 4.025A pdb=" N LEU B 152 " --> pdb=" O PRO B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 326 Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.571A pdb=" N ARG B 377 " --> pdb=" O PRO B 374 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 378 " --> pdb=" O CYS B 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 374 through 378' Processing helix chain 'B' and resid 718 through 726 removed outlier: 3.647A pdb=" N TRP B 722 " --> pdb=" O ALA B 719 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA B 724 " --> pdb=" O LEU B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 747 No H-bonds generated for 'chain 'B' and resid 745 through 747' Processing helix chain 'B' and resid 748 through 768 removed outlier: 4.320A pdb=" N ALA B 755 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER B 756 " --> pdb=" O GLN B 752 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL B 765 " --> pdb=" O VAL B 761 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG B 766 " --> pdb=" O GLU B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 794 removed outlier: 3.982A pdb=" N MET B 786 " --> pdb=" O TYR B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 835 removed outlier: 3.699A pdb=" N TYR B 831 " --> pdb=" O ALA B 827 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET B 834 " --> pdb=" O VAL B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 843 removed outlier: 3.698A pdb=" N ALA B 840 " --> pdb=" O PHE B 837 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ASN B 841 " --> pdb=" O MET B 838 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS B 842 " --> pdb=" O SER B 839 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE B 843 " --> pdb=" O ALA B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 865 Processing helix chain 'B' and resid 866 through 875 removed outlier: 3.795A pdb=" N HIS B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 911 Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 131 removed outlier: 3.966A pdb=" N ILE A 182 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 159 removed outlier: 3.652A pdb=" N THR A 170 " --> pdb=" O ASP A 165 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 222 Processing sheet with id=AA4, first strand: chain 'A' and resid 270 through 275 removed outlier: 3.579A pdb=" N ALA A 333 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 294 through 297 removed outlier: 6.424A pdb=" N ILE B 847 " --> pdb=" O ARG B 880 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL B 882 " --> pdb=" O ILE B 847 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU B 849 " --> pdb=" O VAL B 882 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU B 884 " --> pdb=" O LEU B 849 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N HIS B 851 " --> pdb=" O LEU B 884 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 353 removed outlier: 6.544A pdb=" N SER A 363 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU A 351 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU A 361 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR A 359 " --> pdb=" O PRO A 353 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A 384 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN A 394 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 417 through 420 removed outlier: 4.638A pdb=" N SER A 417 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 431 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A 419 " --> pdb=" O TYR A 429 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP A 430 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A 449 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LEU A 465 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N MET A 451 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLU A 463 " --> pdb=" O MET A 451 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 476 through 479 removed outlier: 6.685A pdb=" N LEU A 482 " --> pdb=" O CYS A 478 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 529 through 531 Processing sheet with id=AB1, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AB2, first strand: chain 'A' and resid 551 through 558 removed outlier: 6.543A pdb=" N LEU A 570 " --> pdb=" O ARG A 580 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ARG A 580 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 589 through 590 removed outlier: 3.954A pdb=" N ALA A 595 " --> pdb=" O LEU A 613 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N SER A 615 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL A 593 " --> pdb=" O SER A 615 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 589 through 590 Processing sheet with id=AB5, first strand: chain 'A' and resid 652 through 659 removed outlier: 8.092A pdb=" N LEU A 730 " --> pdb=" O PRO A 685 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A 687 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU A 684 " --> pdb=" O LYS A 774 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ALA A 776 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N CYS A 686 " --> pdb=" O ALA A 776 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 801 through 804 removed outlier: 6.425A pdb=" N ILE A 847 " --> pdb=" O ARG A 880 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL A 882 " --> pdb=" O ILE A 847 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 849 " --> pdb=" O VAL A 882 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU A 884 " --> pdb=" O LEU A 849 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N HIS A 851 " --> pdb=" O LEU A 884 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 128 through 131 removed outlier: 3.965A pdb=" N ILE B 182 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 157 through 159 removed outlier: 3.653A pdb=" N THR B 170 " --> pdb=" O ASP B 165 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 220 through 222 Processing sheet with id=AC1, first strand: chain 'B' and resid 270 through 275 removed outlier: 3.579A pdb=" N ALA B 333 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 348 through 353 removed outlier: 6.543A pdb=" N SER B 363 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU B 351 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B 361 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR B 359 " --> pdb=" O PRO B 353 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL B 384 " --> pdb=" O GLN B 394 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN B 394 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 417 through 420 removed outlier: 4.637A pdb=" N SER B 417 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA B 431 " --> pdb=" O SER B 417 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN B 419 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP B 430 " --> pdb=" O TYR B 450 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL B 449 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LEU B 465 " --> pdb=" O VAL B 449 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N MET B 451 " --> pdb=" O GLU B 463 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLU B 463 " --> pdb=" O MET B 451 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 476 through 479 removed outlier: 6.683A pdb=" N LEU B 482 " --> pdb=" O CYS B 478 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 529 through 531 Processing sheet with id=AC6, first strand: chain 'B' and resid 542 through 543 Processing sheet with id=AC7, first strand: chain 'B' and resid 551 through 558 removed outlier: 6.543A pdb=" N LEU B 570 " --> pdb=" O ARG B 580 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ARG B 580 " --> pdb=" O LEU B 570 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 589 through 590 removed outlier: 3.954A pdb=" N ALA B 595 " --> pdb=" O LEU B 613 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N SER B 615 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B 593 " --> pdb=" O SER B 615 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 589 through 590 Processing sheet with id=AD1, first strand: chain 'B' and resid 652 through 659 removed outlier: 8.093A pdb=" N LEU B 730 " --> pdb=" O PRO B 685 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU B 687 " --> pdb=" O LEU B 730 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU B 684 " --> pdb=" O LYS B 774 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N ALA B 776 " --> pdb=" O LEU B 684 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N CYS B 686 " --> pdb=" O ALA B 776 " (cutoff:3.500A) 332 hydrogen bonds defined for protein. 870 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: 1.86 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4132 1.34 - 1.46: 2793 1.46 - 1.58: 5917 1.58 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 12910 Sorted by residual: bond pdb=" N PRO B 914 " pdb=" CA PRO B 914 " ideal model delta sigma weight residual 1.472 1.489 -0.017 1.32e-02 5.74e+03 1.63e+00 bond pdb=" N PRO A 914 " pdb=" CA PRO A 914 " ideal model delta sigma weight residual 1.472 1.488 -0.016 1.32e-02 5.74e+03 1.49e+00 bond pdb=" CG PRO B 914 " pdb=" CD PRO B 914 " ideal model delta sigma weight residual 1.503 1.465 0.038 3.40e-02 8.65e+02 1.28e+00 bond pdb=" CG PRO A 914 " pdb=" CD PRO A 914 " ideal model delta sigma weight residual 1.503 1.465 0.038 3.40e-02 8.65e+02 1.28e+00 bond pdb=" CB ARG B 390 " pdb=" CG ARG B 390 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.07e+00 ... (remaining 12905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 17080 1.32 - 2.65: 339 2.65 - 3.97: 111 3.97 - 5.30: 27 5.30 - 6.62: 5 Bond angle restraints: 17562 Sorted by residual: angle pdb=" N ILE B 266 " pdb=" CA ILE B 266 " pdb=" C ILE B 266 " ideal model delta sigma weight residual 113.53 109.70 3.83 9.80e-01 1.04e+00 1.53e+01 angle pdb=" N ILE A 266 " pdb=" CA ILE A 266 " pdb=" C ILE A 266 " ideal model delta sigma weight residual 113.53 109.76 3.77 9.80e-01 1.04e+00 1.48e+01 angle pdb=" CA GLN B 184 " pdb=" CB GLN B 184 " pdb=" CG GLN B 184 " ideal model delta sigma weight residual 114.10 119.38 -5.28 2.00e+00 2.50e-01 6.96e+00 angle pdb=" CA GLN A 184 " pdb=" CB GLN A 184 " pdb=" CG GLN A 184 " ideal model delta sigma weight residual 114.10 119.31 -5.21 2.00e+00 2.50e-01 6.78e+00 angle pdb=" CB GLN A 184 " pdb=" CG GLN A 184 " pdb=" CD GLN A 184 " ideal model delta sigma weight residual 112.60 116.86 -4.26 1.70e+00 3.46e-01 6.27e+00 ... (remaining 17557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.38: 6986 16.38 - 32.77: 628 32.77 - 49.15: 104 49.15 - 65.53: 26 65.53 - 81.91: 26 Dihedral angle restraints: 7770 sinusoidal: 3152 harmonic: 4618 Sorted by residual: dihedral pdb=" CA PRO B 509 " pdb=" C PRO B 509 " pdb=" N ARG B 510 " pdb=" CA ARG B 510 " ideal model delta harmonic sigma weight residual -180.00 -162.48 -17.52 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA PRO A 509 " pdb=" C PRO A 509 " pdb=" N ARG A 510 " pdb=" CA ARG A 510 " ideal model delta harmonic sigma weight residual 180.00 -162.48 -17.52 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA TRP A 498 " pdb=" C TRP A 498 " pdb=" N VAL A 499 " pdb=" CA VAL A 499 " ideal model delta harmonic sigma weight residual 180.00 162.49 17.51 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 7767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1202 0.029 - 0.058: 461 0.058 - 0.087: 116 0.087 - 0.115: 119 0.115 - 0.144: 18 Chirality restraints: 1916 Sorted by residual: chirality pdb=" CB VAL A 913 " pdb=" CA VAL A 913 " pdb=" CG1 VAL A 913 " pdb=" CG2 VAL A 913 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CB VAL B 913 " pdb=" CA VAL B 913 " pdb=" CG1 VAL B 913 " pdb=" CG2 VAL B 913 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA ILE A 276 " pdb=" N ILE A 276 " pdb=" C ILE A 276 " pdb=" CB ILE A 276 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 1913 not shown) Planarity restraints: 2288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 913 " -0.038 5.00e-02 4.00e+02 5.70e-02 5.21e+00 pdb=" N PRO B 914 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 914 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 914 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 913 " 0.038 5.00e-02 4.00e+02 5.70e-02 5.20e+00 pdb=" N PRO A 914 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 914 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 914 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 508 " -0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO B 509 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 509 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 509 " -0.027 5.00e-02 4.00e+02 ... (remaining 2285 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2530 2.79 - 3.31: 11041 3.31 - 3.84: 19525 3.84 - 4.37: 21216 4.37 - 4.90: 38244 Nonbonded interactions: 92556 Sorted by model distance: nonbonded pdb=" OH TYR B 676 " pdb=" O GLY B 682 " model vdw 2.257 3.040 nonbonded pdb=" OH TYR A 676 " pdb=" O GLY A 682 " model vdw 2.257 3.040 nonbonded pdb=" OG1 THR B 433 " pdb=" OD1 ASP B 435 " model vdw 2.282 3.040 nonbonded pdb=" OG1 THR A 433 " pdb=" OD1 ASP A 435 " model vdw 2.283 3.040 nonbonded pdb=" O TYR A 490 " pdb=" NH1 ARG A 493 " model vdw 2.309 3.120 ... (remaining 92551 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.370 Find NCS groups from input model: 0.120 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:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 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 : 0.002 0.038 12910 Z= 0.090 Angle : 0.522 6.621 17562 Z= 0.257 Chirality : 0.040 0.144 1916 Planarity : 0.004 0.057 2288 Dihedral : 13.471 81.913 4802 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.60 (0.21), residues: 1586 helix: 0.73 (0.39), residues: 192 sheet: 0.19 (0.25), residues: 418 loop : -0.91 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 280 TYR 0.016 0.001 TYR A 429 PHE 0.024 0.001 PHE A 513 TRP 0.018 0.001 TRP A 498 HIS 0.001 0.000 HIS A 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 (12910) covalent geometry : angle 0.52159 / 0.26 (17562) hydrogen bonds : bond 0.17176 / 10.94 ( 328) hydrogen bonds : angle 7.38959 / 5.27 ( 870) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.7042 (tp) cc_final: 0.6842 (tt) REVERT: A 170 THR cc_start: 0.6065 (m) cc_final: 0.5841 (m) REVERT: A 441 MET cc_start: 0.7973 (mpp) cc_final: 0.7587 (mpt) REVERT: A 451 MET cc_start: 0.7082 (mtt) cc_final: 0.6552 (mmt) REVERT: A 626 SER cc_start: 0.8485 (m) cc_final: 0.8023 (p) REVERT: B 266 ILE cc_start: 0.8510 (tt) cc_final: 0.8168 (pp) REVERT: B 528 MET cc_start: 0.8547 (mmm) cc_final: 0.8251 (mmp) REVERT: B 607 MET cc_start: 0.8979 (tpp) cc_final: 0.8753 (tpt) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.3323 time to fit residues: 63.3126 Evaluate side-chains 130 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 ASN A 636 GLN A 643 HIS A 659 GLN A 899 HIS B 169 ASN B 636 GLN B 643 HIS B 659 GLN B 889 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.152498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.101461 restraints weight = 19020.956| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.51 r_work: 0.3222 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 12910 Z= 0.207 Angle : 0.642 8.130 17562 Z= 0.330 Chirality : 0.046 0.158 1916 Planarity : 0.005 0.045 2288 Dihedral : 3.891 16.153 1742 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.52 % Allowed : 8.76 % Favored : 89.73 % 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: -0.87 (0.20), residues: 1586 helix: 0.69 (0.40), residues: 192 sheet: -0.22 (0.24), residues: 452 loop : -1.03 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 390 TYR 0.015 0.002 TYR B 676 PHE 0.021 0.002 PHE B 513 TRP 0.028 0.002 TRP B 477 HIS 0.003 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 (12910) covalent geometry : angle 0.64182 / 0.33 (17562) hydrogen bonds : bond 0.06222 / 4.24 ( 328) hydrogen bonds : angle 5.41215 / 3.87 ( 870) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 TYR cc_start: 0.7003 (t80) cc_final: 0.6519 (t80) REVERT: A 339 VAL cc_start: 0.8634 (t) cc_final: 0.8363 (p) REVERT: A 390 ARG cc_start: 0.8185 (ttp80) cc_final: 0.7318 (tmm-80) REVERT: A 441 MET cc_start: 0.7778 (mpp) cc_final: 0.7364 (mpt) REVERT: A 479 ASP cc_start: 0.8678 (t0) cc_final: 0.8423 (p0) REVERT: A 536 THR cc_start: 0.8343 (m) cc_final: 0.8014 (p) REVERT: B 360 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6559 (pt) REVERT: B 390 ARG cc_start: 0.7905 (ttp80) cc_final: 0.7118 (tmm-80) REVERT: B 553 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6685 (pt) REVERT: B 607 MET cc_start: 0.8797 (tpp) cc_final: 0.8555 (tpt) outliers start: 21 outliers final: 12 residues processed: 144 average time/residue: 0.4192 time to fit residues: 67.1529 Evaluate side-chains 135 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 684 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 156 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 HIS A 227 ASN A 229 ASN A 257 ASN A 298 ASN B 257 ASN B 889 HIS B 899 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.150365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.099435 restraints weight = 18862.732| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.58 r_work: 0.3241 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12910 Z= 0.157 Angle : 0.575 9.748 17562 Z= 0.291 Chirality : 0.044 0.140 1916 Planarity : 0.005 0.082 2288 Dihedral : 3.894 18.078 1742 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.88 % Allowed : 10.49 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.20), residues: 1586 helix: 0.85 (0.39), residues: 194 sheet: -0.17 (0.24), residues: 442 loop : -1.21 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 154 TYR 0.025 0.002 TYR A 676 PHE 0.029 0.002 PHE A 571 TRP 0.015 0.002 TRP B 477 HIS 0.003 0.001 HIS B 875 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (12910) covalent geometry : angle 0.57549 / 0.29 (17562) hydrogen bonds : bond 0.04980 / 3.30 ( 328) hydrogen bonds : angle 4.98087 / 3.51 ( 870) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 HIS cc_start: 0.6806 (OUTLIER) cc_final: 0.5719 (m-70) REVERT: A 390 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7295 (tmm-80) REVERT: A 441 MET cc_start: 0.7742 (mpp) cc_final: 0.7304 (mpt) REVERT: A 467 LYS cc_start: 0.7129 (mmpt) cc_final: 0.6318 (mmmt) REVERT: A 479 ASP cc_start: 0.8709 (t0) cc_final: 0.8395 (p0) REVERT: A 536 THR cc_start: 0.8273 (m) cc_final: 0.7952 (p) REVERT: B 360 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6487 (pt) REVERT: B 377 ARG cc_start: 0.6908 (mtt-85) cc_final: 0.6694 (mtm-85) REVERT: B 390 ARG cc_start: 0.7797 (ttp80) cc_final: 0.7138 (tmm-80) REVERT: B 607 MET cc_start: 0.8756 (tpp) cc_final: 0.8436 (tpt) outliers start: 26 outliers final: 14 residues processed: 137 average time/residue: 0.4495 time to fit residues: 68.5434 Evaluate side-chains 129 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 684 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 139 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 79 optimal weight: 0.0270 chunk 45 optimal weight: 2.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 ASN A 889 HIS B 217 HIS B 257 ASN B 298 ASN B 889 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.150721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.100024 restraints weight = 18806.138| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.60 r_work: 0.3225 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12910 Z= 0.114 Angle : 0.537 8.626 17562 Z= 0.269 Chirality : 0.042 0.139 1916 Planarity : 0.004 0.041 2288 Dihedral : 3.722 12.786 1742 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.24 % Allowed : 10.78 % Favored : 86.98 % 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: -0.92 (0.20), residues: 1586 helix: 1.11 (0.39), residues: 192 sheet: -0.13 (0.24), residues: 440 loop : -1.24 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 867 TYR 0.023 0.001 TYR A 676 PHE 0.013 0.001 PHE A 785 TRP 0.020 0.001 TRP B 477 HIS 0.005 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 (12910) covalent geometry : angle 0.53724 / 0.27 (17562) hydrogen bonds : bond 0.04198 / 2.85 ( 328) hydrogen bonds : angle 4.76746 / 3.36 ( 870) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ILE cc_start: 0.9096 (tt) cc_final: 0.8886 (mp) REVERT: A 366 HIS cc_start: 0.6757 (OUTLIER) cc_final: 0.5668 (m-70) REVERT: A 390 ARG cc_start: 0.8026 (ttp80) cc_final: 0.7382 (tmm-80) REVERT: A 413 LYS cc_start: 0.7370 (mttp) cc_final: 0.6633 (tptt) REVERT: A 441 MET cc_start: 0.7747 (mpp) cc_final: 0.7302 (mpt) REVERT: A 467 LYS cc_start: 0.7418 (mmpt) cc_final: 0.7021 (mmmt) REVERT: A 479 ASP cc_start: 0.8703 (t0) cc_final: 0.8385 (p0) REVERT: B 316 GLU cc_start: 0.6415 (tm-30) cc_final: 0.6037 (tm-30) REVERT: B 390 ARG cc_start: 0.7684 (ttp80) cc_final: 0.6988 (tmm-80) REVERT: B 477 TRP cc_start: 0.5892 (m-10) cc_final: 0.5645 (m-10) REVERT: B 496 ARG cc_start: 0.7004 (ttt-90) cc_final: 0.6464 (tmt-80) REVERT: B 607 MET cc_start: 0.8817 (tpp) cc_final: 0.8550 (tpt) outliers start: 31 outliers final: 13 residues processed: 134 average time/residue: 0.4389 time to fit residues: 65.5365 Evaluate side-chains 122 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 764 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 56 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 121 optimal weight: 0.0970 chunk 15 optimal weight: 0.0670 chunk 35 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 889 HIS B 889 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.150293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.099260 restraints weight = 19152.025| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.52 r_work: 0.3210 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12910 Z= 0.104 Angle : 0.538 12.564 17562 Z= 0.264 Chirality : 0.042 0.138 1916 Planarity : 0.004 0.040 2288 Dihedral : 3.627 17.322 1742 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.32 % Allowed : 11.65 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.85 (0.20), residues: 1586 helix: 1.29 (0.39), residues: 192 sheet: -0.09 (0.25), residues: 440 loop : -1.23 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 154 TYR 0.020 0.001 TYR A 676 PHE 0.027 0.001 PHE B 571 TRP 0.015 0.001 TRP A 477 HIS 0.004 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.10 (12910) covalent geometry : angle 0.53754 / 0.26 (17562) hydrogen bonds : bond 0.03927 / 2.67 ( 328) hydrogen bonds : angle 4.61842 / 3.30 ( 870) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ILE cc_start: 0.9224 (tt) cc_final: 0.9016 (mp) REVERT: A 300 THR cc_start: 0.8013 (m) cc_final: 0.7745 (t) REVERT: A 366 HIS cc_start: 0.6816 (OUTLIER) cc_final: 0.5725 (m-70) REVERT: A 390 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7391 (tmm-80) REVERT: A 413 LYS cc_start: 0.7507 (mttp) cc_final: 0.6735 (tptt) REVERT: A 441 MET cc_start: 0.7850 (mpp) cc_final: 0.7496 (mpt) REVERT: A 467 LYS cc_start: 0.7485 (mmpt) cc_final: 0.7213 (tppt) REVERT: A 479 ASP cc_start: 0.8826 (t0) cc_final: 0.8454 (p0) REVERT: A 539 ILE cc_start: 0.7913 (pt) cc_final: 0.7507 (pp) REVERT: B 316 GLU cc_start: 0.6490 (tm-30) cc_final: 0.6097 (tm-30) REVERT: B 390 ARG cc_start: 0.7716 (ttp80) cc_final: 0.7226 (tmm-80) REVERT: B 461 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6191 (pm20) REVERT: B 496 ARG cc_start: 0.7025 (ttt-90) cc_final: 0.6791 (tmt170) REVERT: B 607 MET cc_start: 0.8751 (tpp) cc_final: 0.8451 (tpt) outliers start: 32 outliers final: 17 residues processed: 136 average time/residue: 0.4357 time to fit residues: 66.0621 Evaluate side-chains 128 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 764 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 154 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 57 optimal weight: 0.0770 chunk 53 optimal weight: 0.0370 chunk 54 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 889 HIS B 889 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.149489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.098607 restraints weight = 19014.221| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.50 r_work: 0.3204 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12910 Z= 0.115 Angle : 0.548 10.075 17562 Z= 0.268 Chirality : 0.042 0.138 1916 Planarity : 0.004 0.041 2288 Dihedral : 3.633 18.221 1742 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.24 % Allowed : 12.08 % Favored : 85.67 % 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: -0.85 (0.21), residues: 1586 helix: 1.32 (0.39), residues: 192 sheet: -0.12 (0.25), residues: 430 loop : -1.21 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 421 TYR 0.020 0.001 TYR A 676 PHE 0.010 0.001 PHE B 785 TRP 0.013 0.001 TRP B 477 HIS 0.003 0.001 HIS B 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (12910) covalent geometry : angle 0.54777 / 0.27 (17562) hydrogen bonds : bond 0.04052 / 2.76 ( 328) hydrogen bonds : angle 4.61711 / 3.29 ( 870) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ILE cc_start: 0.9236 (tt) cc_final: 0.9017 (mp) REVERT: A 300 THR cc_start: 0.8036 (m) cc_final: 0.7773 (t) REVERT: A 366 HIS cc_start: 0.6814 (OUTLIER) cc_final: 0.5711 (m-70) REVERT: A 390 ARG cc_start: 0.8149 (ttp80) cc_final: 0.7397 (tmm-80) REVERT: A 413 LYS cc_start: 0.7560 (mttp) cc_final: 0.6690 (tptt) REVERT: A 441 MET cc_start: 0.7873 (mpp) cc_final: 0.7518 (mpt) REVERT: A 479 ASP cc_start: 0.8876 (t0) cc_final: 0.8466 (p0) REVERT: A 539 ILE cc_start: 0.7781 (pt) cc_final: 0.7346 (pp) REVERT: B 316 GLU cc_start: 0.6647 (tm-30) cc_final: 0.6329 (tm-30) REVERT: B 360 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6796 (pt) REVERT: B 390 ARG cc_start: 0.7735 (ttp80) cc_final: 0.7242 (tmm-80) REVERT: B 496 ARG cc_start: 0.7132 (ttt-90) cc_final: 0.6847 (tmt170) REVERT: B 529 LEU cc_start: 0.8242 (mm) cc_final: 0.8035 (mm) outliers start: 31 outliers final: 19 residues processed: 135 average time/residue: 0.4127 time to fit residues: 62.3292 Evaluate side-chains 131 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 764 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 89 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 132 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 889 HIS B 889 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.148813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.098519 restraints weight = 18800.406| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.52 r_work: 0.3212 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12910 Z= 0.124 Angle : 0.559 10.365 17562 Z= 0.275 Chirality : 0.042 0.145 1916 Planarity : 0.004 0.041 2288 Dihedral : 3.691 20.231 1742 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.03 % Allowed : 12.81 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.21), residues: 1586 helix: 1.33 (0.39), residues: 190 sheet: -0.15 (0.26), residues: 422 loop : -1.19 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 154 TYR 0.019 0.001 TYR A 676 PHE 0.028 0.001 PHE B 571 TRP 0.019 0.001 TRP B 477 HIS 0.003 0.001 HIS B 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.12 (12910) covalent geometry : angle 0.55859 / 0.27 (17562) hydrogen bonds : bond 0.04185 / 2.86 ( 328) hydrogen bonds : angle 4.65303 / 3.32 ( 870) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ILE cc_start: 0.9175 (tt) cc_final: 0.8968 (mp) REVERT: A 300 THR cc_start: 0.7955 (m) cc_final: 0.7680 (t) REVERT: A 366 HIS cc_start: 0.6743 (OUTLIER) cc_final: 0.5631 (m-70) REVERT: A 390 ARG cc_start: 0.8047 (ttp80) cc_final: 0.7834 (tmm-80) REVERT: A 413 LYS cc_start: 0.7534 (mttp) cc_final: 0.6654 (tptt) REVERT: A 441 MET cc_start: 0.7829 (mpp) cc_final: 0.7457 (mpt) REVERT: A 477 TRP cc_start: 0.5920 (m-10) cc_final: 0.5586 (m-10) REVERT: A 479 ASP cc_start: 0.8796 (t0) cc_final: 0.8358 (p0) REVERT: B 316 GLU cc_start: 0.6709 (tm-30) cc_final: 0.6336 (tm-30) REVERT: B 360 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6644 (pt) REVERT: B 390 ARG cc_start: 0.7635 (ttp80) cc_final: 0.6972 (tmm-80) REVERT: B 461 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6411 (pm20) REVERT: B 477 TRP cc_start: 0.6116 (m-10) cc_final: 0.5829 (m-10) REVERT: B 496 ARG cc_start: 0.7055 (ttt-90) cc_final: 0.6790 (tmt170) outliers start: 28 outliers final: 19 residues processed: 136 average time/residue: 0.3953 time to fit residues: 60.2722 Evaluate side-chains 135 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 764 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 113 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 889 HIS B 227 ASN B 366 HIS B 889 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.142361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.090598 restraints weight = 18944.005| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.45 r_work: 0.3075 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 12910 Z= 0.224 Angle : 0.654 11.396 17562 Z= 0.330 Chirality : 0.046 0.160 1916 Planarity : 0.005 0.048 2288 Dihedral : 4.243 20.759 1742 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.60 % Allowed : 12.37 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.20), residues: 1586 helix: 0.15 (0.35), residues: 218 sheet: -0.35 (0.26), residues: 418 loop : -1.44 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 515 TYR 0.022 0.002 TYR A 676 PHE 0.023 0.002 PHE B 567 TRP 0.017 0.002 TRP A 722 HIS 0.004 0.001 HIS A 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.22 (12910) covalent geometry : angle 0.65376 / 0.33 (17562) hydrogen bonds : bond 0.05983 / 4.15 ( 328) hydrogen bonds : angle 5.17807 / 3.65 ( 870) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 THR cc_start: 0.8033 (m) cc_final: 0.7760 (t) REVERT: A 316 GLU cc_start: 0.6632 (tm-30) cc_final: 0.6218 (tm-30) REVERT: A 366 HIS cc_start: 0.6920 (OUTLIER) cc_final: 0.5748 (m-70) REVERT: A 413 LYS cc_start: 0.7646 (mttp) cc_final: 0.6759 (tptt) REVERT: A 441 MET cc_start: 0.7830 (mpp) cc_final: 0.7426 (mpt) REVERT: A 479 ASP cc_start: 0.8726 (t0) cc_final: 0.8395 (p0) REVERT: B 316 GLU cc_start: 0.6878 (tm-30) cc_final: 0.6520 (tm-30) REVERT: B 360 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6673 (pt) REVERT: B 390 ARG cc_start: 0.7620 (ttp80) cc_final: 0.7306 (tmm-80) REVERT: B 676 TYR cc_start: 0.8612 (t80) cc_final: 0.8295 (t80) outliers start: 36 outliers final: 18 residues processed: 142 average time/residue: 0.3846 time to fit residues: 61.8893 Evaluate side-chains 129 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 764 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 144 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 134 optimal weight: 0.4980 chunk 156 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.145634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.094581 restraints weight = 19053.379| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.50 r_work: 0.3141 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12910 Z= 0.139 Angle : 0.605 11.188 17562 Z= 0.297 Chirality : 0.043 0.144 1916 Planarity : 0.005 0.045 2288 Dihedral : 4.092 21.802 1742 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.03 % Allowed : 13.53 % Favored : 84.44 % 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: -1.27 (0.20), residues: 1586 helix: 0.38 (0.36), residues: 216 sheet: -0.34 (0.25), residues: 434 loop : -1.42 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 390 TYR 0.023 0.001 TYR A 676 PHE 0.032 0.001 PHE B 571 TRP 0.021 0.002 TRP B 477 HIS 0.003 0.001 HIS B 886 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (12910) covalent geometry : angle 0.60516 / 0.30 (17562) hydrogen bonds : bond 0.04594 / 3.15 ( 328) hydrogen bonds : angle 4.94985 / 3.48 ( 870) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 THR cc_start: 0.8036 (m) cc_final: 0.7772 (t) REVERT: A 316 GLU cc_start: 0.6713 (tm-30) cc_final: 0.6269 (tm-30) REVERT: A 366 HIS cc_start: 0.7233 (OUTLIER) cc_final: 0.5875 (m-70) REVERT: A 390 ARG cc_start: 0.7872 (tmm-80) cc_final: 0.7018 (tmm-80) REVERT: A 441 MET cc_start: 0.7658 (mpp) cc_final: 0.7285 (mpt) REVERT: A 479 ASP cc_start: 0.8836 (t0) cc_final: 0.8365 (p0) REVERT: B 316 GLU cc_start: 0.6867 (tm-30) cc_final: 0.6522 (tm-30) REVERT: B 390 ARG cc_start: 0.7668 (ttp80) cc_final: 0.7277 (tmm-80) REVERT: B 415 MET cc_start: 0.5217 (OUTLIER) cc_final: 0.3887 (mmt) REVERT: B 461 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6666 (pm20) REVERT: B 479 ASP cc_start: 0.8989 (t0) cc_final: 0.8395 (p0) REVERT: B 676 TYR cc_start: 0.8567 (t80) cc_final: 0.8258 (t80) outliers start: 28 outliers final: 20 residues processed: 132 average time/residue: 0.4216 time to fit residues: 62.6420 Evaluate side-chains 130 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 764 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 151 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 41 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.146496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.095653 restraints weight = 18925.010| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.49 r_work: 0.3166 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12910 Z= 0.121 Angle : 0.603 11.391 17562 Z= 0.294 Chirality : 0.043 0.140 1916 Planarity : 0.005 0.043 2288 Dihedral : 3.974 21.775 1742 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.03 % Allowed : 13.24 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.20), residues: 1586 helix: 0.49 (0.36), residues: 218 sheet: -0.29 (0.25), residues: 450 loop : -1.45 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 390 TYR 0.022 0.001 TYR A 676 PHE 0.024 0.001 PHE B 567 TRP 0.029 0.002 TRP B 477 HIS 0.003 0.001 HIS B 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (12910) covalent geometry : angle 0.60312 / 0.29 (17562) hydrogen bonds : bond 0.04131 / 2.82 ( 328) hydrogen bonds : angle 4.81270 / 3.40 ( 870) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 THR cc_start: 0.8018 (m) cc_final: 0.7754 (t) REVERT: A 316 GLU cc_start: 0.6660 (tm-30) cc_final: 0.6267 (tm-30) REVERT: A 366 HIS cc_start: 0.7122 (OUTLIER) cc_final: 0.5801 (m-70) REVERT: A 390 ARG cc_start: 0.7860 (tmm-80) cc_final: 0.6985 (tmm-80) REVERT: A 441 MET cc_start: 0.7653 (mpp) cc_final: 0.7281 (mpt) REVERT: A 467 LYS cc_start: 0.7360 (tppt) cc_final: 0.6890 (tppt) REVERT: A 479 ASP cc_start: 0.8845 (t0) cc_final: 0.8426 (p0) REVERT: B 316 GLU cc_start: 0.6819 (tm-30) cc_final: 0.6487 (tm-30) REVERT: B 421 ARG cc_start: 0.5311 (tpt90) cc_final: 0.5108 (tpt170) REVERT: B 461 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6614 (pm20) REVERT: B 467 LYS cc_start: 0.7617 (mmpt) cc_final: 0.7006 (mmpt) REVERT: B 479 ASP cc_start: 0.8977 (t0) cc_final: 0.8393 (p0) REVERT: B 554 LEU cc_start: 0.6228 (OUTLIER) cc_final: 0.6005 (pt) REVERT: B 676 TYR cc_start: 0.8537 (t80) cc_final: 0.8229 (t80) outliers start: 28 outliers final: 19 residues processed: 133 average time/residue: 0.3808 time to fit residues: 57.0845 Evaluate side-chains 129 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 764 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 20 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 134 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 109 optimal weight: 0.2980 chunk 14 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.147474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.096726 restraints weight = 19005.005| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.49 r_work: 0.3146 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12910 Z= 0.110 Angle : 0.594 11.531 17562 Z= 0.288 Chirality : 0.042 0.137 1916 Planarity : 0.004 0.041 2288 Dihedral : 3.882 21.766 1742 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.52 % Allowed : 14.18 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.21), residues: 1586 helix: 1.10 (0.38), residues: 202 sheet: -0.23 (0.25), residues: 448 loop : -1.34 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 390 TYR 0.020 0.001 TYR A 676 PHE 0.032 0.001 PHE A 571 TRP 0.028 0.002 TRP B 477 HIS 0.003 0.001 HIS A 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (12910) covalent geometry : angle 0.59380 / 0.29 (17562) hydrogen bonds : bond 0.03826 / 2.62 ( 328) hydrogen bonds : angle 4.70349 / 3.33 ( 870) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3412.67 seconds wall clock time: 58 minutes 49.10 seconds (3529.10 seconds total)