Starting phenix.real_space_refine on Sun Aug 9 11:30:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u5y_41939/08_2026/8u5y_41939.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u5y_41939/08_2026/8u5y_41939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u5y_41939/08_2026/8u5y_41939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u5y_41939/08_2026/8u5y_41939.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u5y_41939/08_2026/8u5y_41939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u5y_41939/08_2026/8u5y_41939.map" } resolution = 3.01 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 S 78 5.16 5 C 11057 2.51 5 N 2937 2.21 5 O 3251 1.98 5 H 17152 0.53 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: 34491 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 11430 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 700, 11429 Classifications: {'peptide': 700} Link IDs: {'PTRANS': 50, 'TRANS': 649} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 700, 11429 Classifications: {'peptide': 700} Link IDs: {'PTRANS': 50, 'TRANS': 649} Chain breaks: 1 bond proxies already assigned to first conformer: 11575 Chain: "A" Number of atoms: 11320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 11320 Classifications: {'peptide': 697} Link IDs: {'PTRANS': 50, 'TRANS': 646} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 11229 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 692, 11228 Classifications: {'peptide': 692} Link IDs: {'PTRANS': 50, 'TRANS': 641} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'HIS:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 692, 11228 Classifications: {'peptide': 692} Link IDs: {'PTRANS': 50, 'TRANS': 641} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'HIS:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 11368 Chain: "D" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 512 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 7.16, per 1000 atoms: 0.21 Number of scatterers: 34491 At special positions: 0 Unit cell: (104.14, 142.68, 154.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 16 15.00 O 3251 8.00 N 2937 7.00 C 11057 6.00 H 17152 1.00 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: 3.20 Conformation dependent library (CDL) restraints added in 1.3 seconds 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3998 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 13 sheets defined 21.0% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 114 through 120 removed outlier: 4.131A pdb=" N VAL B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 282 through 287 Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 479 through 495 Processing helix chain 'B' and resid 515 through 521 Processing helix chain 'B' and resid 524 through 529 removed outlier: 4.689A pdb=" N LEU B 529 " --> pdb=" O VAL B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 542 removed outlier: 3.699A pdb=" N LEU B 542 " --> pdb=" O GLU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 689 Processing helix chain 'B' and resid 702 through 706 removed outlier: 3.815A pdb=" N ILE B 706 " --> pdb=" O PRO B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 713 No H-bonds generated for 'chain 'B' and resid 711 through 713' Processing helix chain 'B' and resid 714 through 721 Processing helix chain 'B' and resid 773 through 780 Processing helix chain 'B' and resid 807 through 822 removed outlier: 3.820A pdb=" N LEU B 822 " --> pdb=" O ALA B 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 348 through 352 Processing helix chain 'A' and resid 362 through 369 removed outlier: 3.867A pdb=" N ASP A 368 " --> pdb=" O SER A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 479 through 495 removed outlier: 3.930A pdb=" N LYS A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 522 removed outlier: 3.818A pdb=" N SER A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 528 removed outlier: 6.338A pdb=" N GLU A 526 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 528 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 542 removed outlier: 3.589A pdb=" N LEU A 542 " --> pdb=" O GLU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 689 Processing helix chain 'A' and resid 702 through 706 removed outlier: 3.775A pdb=" N ILE A 706 " --> pdb=" O PRO A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 723 Processing helix chain 'A' and resid 738 through 742 removed outlier: 3.816A pdb=" N PHE A 742 " --> pdb=" O LEU A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 780 Processing helix chain 'A' and resid 809 through 822 removed outlier: 3.623A pdb=" N LEU A 822 " --> pdb=" O ALA A 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 54 Processing helix chain 'C' and resid 112 through 114 No H-bonds generated for 'chain 'C' and resid 112 through 114' Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 170 through 175 Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'C' and resid 282 through 287 Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 425 through 430 Processing helix chain 'C' and resid 473 through 477 removed outlier: 3.545A pdb=" N THR C 477 " --> pdb=" O GLN C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 495 Processing helix chain 'C' and resid 515 through 523 Processing helix chain 'C' and resid 534 through 542 Processing helix chain 'C' and resid 702 through 706 Processing helix chain 'C' and resid 711 through 714 Processing helix chain 'C' and resid 715 through 722 removed outlier: 3.736A pdb=" N TYR C 722 " --> pdb=" O LEU C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 742 Processing helix chain 'C' and resid 773 through 780 Processing helix chain 'C' and resid 807 through 822 removed outlier: 4.498A pdb=" N GLY C 813 " --> pdb=" O ARG C 809 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE C 816 " --> pdb=" O ALA C 812 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 822 " --> pdb=" O ALA C 818 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 128 through 129 removed outlier: 5.595A pdb=" N VAL B 71 " --> pdb=" O SER B 100 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N SER B 100 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA B 73 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TYR B 95 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N ILE B 150 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR B 109 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ASN B 152 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ARG B 133 " --> pdb=" O ASP B 151 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 153 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE B 131 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 237 through 244 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 237 through 244 current: chain 'B' and resid 261 through 269 removed outlier: 3.520A pdb=" N GLY B 272 " --> pdb=" O ASP B 269 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 272 through 278 current: chain 'B' and resid 322 through 330 Processing sheet with id=AA3, first strand: chain 'B' and resid 360 through 361 removed outlier: 4.533A pdb=" N ILE B 378 " --> pdb=" O THR B 361 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 375 through 384 current: chain 'B' and resid 399 through 408 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 416 through 421 current: chain 'B' and resid 455 through 460 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 455 through 460 current: chain 'B' and resid 708 through 709 Processing sheet with id=AA4, first strand: chain 'B' and resid 547 through 561 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 679 through 681 current: chain 'B' and resid 762 through 768 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 762 through 768 current: chain 'B' and resid 841 through 849 Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 removed outlier: 6.309A pdb=" N THR A 98 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL A 74 " --> pdb=" O ASP A 96 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASP A 96 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ARG A 76 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N CYS A 94 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N TYR A 95 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 10.792A pdb=" N LEU A 148 " --> pdb=" O GLN A 105 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LYS A 107 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ILE A 150 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TYR A 109 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N ASN A 152 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG A 133 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL A 153 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 131 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 237 through 244 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 237 through 244 current: chain 'A' and resid 261 through 269 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 272 through 278 current: chain 'A' and resid 322 through 327 Processing sheet with id=AA7, first strand: chain 'A' and resid 360 through 361 removed outlier: 4.592A pdb=" N ILE A 378 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N HIS A 406 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL A 384 " --> pdb=" O TRP A 404 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TRP A 404 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG A 386 " --> pdb=" O TYR A 402 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR A 402 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLN A 388 " --> pdb=" O TRP A 400 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP A 400 " --> pdb=" O GLN A 388 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 416 through 421 current: chain 'A' and resid 455 through 460 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 455 through 460 current: chain 'A' and resid 708 through 709 Processing sheet with id=AA8, first strand: chain 'A' and resid 547 through 562 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 679 through 681 current: chain 'A' and resid 762 through 768 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 762 through 768 current: chain 'A' and resid 841 through 849 Processing sheet with id=AA9, first strand: chain 'C' and resid 93 through 100 removed outlier: 4.156A pdb=" N ALA C 73 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N SER C 100 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL C 71 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 109 through 110 removed outlier: 6.378A pdb=" N TYR C 109 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ASN C 152 " --> pdb=" O TYR C 109 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ARG C 133 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 239 through 244 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 239 through 244 current: chain 'C' and resid 261 through 268 Processing sheet with id=AB3, first strand: chain 'C' and resid 375 through 384 removed outlier: 6.178A pdb=" N HIS C 406 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL C 384 " --> pdb=" O TRP C 404 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TRP C 404 " --> pdb=" O VAL C 384 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 418 through 421 current: chain 'C' and resid 457 through 460 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 457 through 460 current: chain 'C' and resid 708 through 709 Processing sheet with id=AB4, first strand: chain 'C' and resid 679 through 681 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 679 through 681 current: chain 'C' and resid 767 through 768 removed outlier: 7.212A pdb=" N ALA C 767 " --> pdb=" O LEU C 845 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N LYS C 847 " --> pdb=" O ALA C 767 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LYS C 840 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE C 830 " --> pdb=" O HIS C 846 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE C 848 " --> pdb=" O VAL C 828 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VAL C 828 " --> pdb=" O ILE C 848 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE C 827 " --> pdb=" O GLY C 554 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 550 " --> pdb=" O LEU C 831 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR C 754 " --> pdb=" O THR C 557 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE C 762 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP C 694 " --> pdb=" O ALA C 763 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ASP C 765 " --> pdb=" O ASP C 694 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU C 696 " --> pdb=" O ASP C 765 " (cutoff:3.500A) 318 hydrogen bonds defined for protein. 849 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: 7.21 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17089 1.03 - 1.23: 91 1.23 - 1.42: 7367 1.42 - 1.61: 10295 1.61 - 1.81: 114 Bond restraints: 34956 Sorted by residual: bond pdb=" N HIS B 564 " pdb=" H HIS B 564 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.68e+01 bond pdb=" N SER B 566 " pdb=" H SER B 566 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.66e+01 bond pdb=" N SER B 565 " pdb=" H SER B 565 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.65e+01 bond pdb=" NE2 HIS B 564 " pdb=" HE2 HIS B 564 " ideal model delta sigma weight residual 0.860 1.015 -0.155 2.00e-02 2.50e+03 6.00e+01 bond pdb=" CD2 HIS B 564 " pdb=" HD2 HIS B 564 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.74e+01 ... (remaining 34951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 62250 1.55 - 3.11: 995 3.11 - 4.66: 122 4.66 - 6.21: 3 6.21 - 7.76: 1 Bond angle restraints: 63371 Sorted by residual: angle pdb=" N3 DT D 12 " pdb=" C4 DT D 12 " pdb=" O4 DT D 12 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT D 6 " pdb=" C4 DT D 6 " pdb=" O4 DT D 6 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT D 2 " pdb=" C4 DT D 2 " pdb=" O4 DT D 2 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT D -1 " pdb=" C4 DT D -1 " pdb=" O4 DT D -1 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT D 0 " pdb=" C4 DT D 0 " pdb=" O4 DT D 0 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (remaining 63366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.23: 15907 32.23 - 64.46: 521 64.46 - 96.69: 19 96.69 - 128.92: 0 128.92 - 161.15: 1 Dihedral angle restraints: 16448 sinusoidal: 9147 harmonic: 7301 Sorted by residual: dihedral pdb=" C4' DT D 5 " pdb=" C3' DT D 5 " pdb=" O3' DT D 5 " pdb=" P DT D 6 " ideal model delta sinusoidal sigma weight residual 220.00 58.85 161.15 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" CA ASP C 409 " pdb=" CB ASP C 409 " pdb=" CG ASP C 409 " pdb=" OD1 ASP C 409 " ideal model delta sinusoidal sigma weight residual -30.00 -88.55 58.55 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CB GLU B 842 " pdb=" CG GLU B 842 " pdb=" CD GLU B 842 " pdb=" OE1 GLU B 842 " ideal model delta sinusoidal sigma weight residual 0.00 89.11 -89.11 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 16445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1759 0.034 - 0.068: 571 0.068 - 0.102: 186 0.102 - 0.137: 137 0.137 - 0.171: 13 Chirality restraints: 2666 Sorted by residual: chirality pdb=" C3' DT D 5 " pdb=" C4' DT D 5 " pdb=" O3' DT D 5 " pdb=" C2' DT D 5 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" C3' DT D 13 " pdb=" C4' DT D 13 " pdb=" O3' DT D 13 " pdb=" C2' DT D 13 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" C3' DT D 7 " pdb=" C4' DT D 7 " pdb=" O3' DT D 7 " pdb=" C2' DT D 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.67e-01 ... (remaining 2663 not shown) Planarity restraints: 4988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 207 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.59e+00 pdb=" N PRO A 208 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 283 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.53e+00 pdb=" N PRO C 284 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 284 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 284 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 474 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO B 475 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 475 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 475 " 0.022 5.00e-02 4.00e+02 ... (remaining 4985 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1806 2.19 - 2.79: 72593 2.79 - 3.39: 98297 3.39 - 4.00: 132454 4.00 - 4.60: 199266 Nonbonded interactions: 504416 Sorted by model distance: nonbonded pdb=" O VAL C 384 " pdb=" H GLY C 504 " model vdw 1.585 2.450 nonbonded pdb=" O PRO B 513 " pdb=" HH TYR B 849 " model vdw 1.626 2.450 nonbonded pdb="HD22 ASN C 500 " pdb=" O PRO C 796 " model vdw 1.627 2.450 nonbonded pdb=" O THR C 441 " pdb=" HG SER C 464 " model vdw 1.644 2.450 nonbonded pdb=" O VAL B 384 " pdb=" H GLY B 504 " model vdw 1.659 2.450 ... (remaining 504411 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 43 through 154 or resid 156 through 564 or (resid 565 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 676 through 682 or (resid 683 and (name N or name CA or name C or name O or n \ ame CB or name CG or name CD or name OE1 or name NE2)) or (resid 691 and (name N \ or name CA or name C or name O )) or (resid 692 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name HB2 \ or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or n \ ame HD22 or name HD23)) or resid 693 through 759 or (resid 760 through 761 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 762 through 825 or (resid 826 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 827 through 851)) selection = (chain 'B' and (resid 43 through 138 or (resid 139 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 143 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or nam \ e CD1)) or (resid 144 and (name N or name CA or name C or name O )) or resid 145 \ through 154 or resid 156 through 451 or (resid 452 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 453 through 473 or (r \ esid 474 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 475 through 524 or (resid 525 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 526 through 564 or (resid 5 \ 65 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 676 through 682 or (resid 683 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name OE1 or name NE2)) or (resid 691 and \ (name N or name CA or name C or name O )) or (resid 692 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD1 or name CD2 or name HA or n \ ame HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD \ 21 or name HD22 or name HD23)) or resid 693 through 759 or (resid 760 through 76 \ 1 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 762 through 825 or (resid 826 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 827 through 851)) selection = (chain 'C' and (resid 43 through 138 or (resid 139 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 143 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or nam \ e CD1)) or (resid 144 and (name N or name CA or name C or name O )) or resid 145 \ through 154 or resid 156 through 451 or (resid 452 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 453 through 473 or (r \ esid 474 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 475 through 524 or (resid 525 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 526 through 851)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 9.960 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: 0.210 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 30.930 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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 0.043 17804 Z= 0.177 Angle : 0.582 7.765 24250 Z= 0.366 Chirality : 0.045 0.171 2666 Planarity : 0.004 0.040 3059 Dihedral : 14.423 161.147 6810 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.57 % Allowed : 13.06 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.19), residues: 2073 helix: 0.37 (0.31), residues: 306 sheet: -1.64 (0.22), residues: 546 loop : -0.91 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 715 TYR 0.014 0.001 TYR B 509 PHE 0.007 0.001 PHE A 416 TRP 0.012 0.001 TRP A 228 HIS 0.002 0.001 HIS B 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.18 (17804) covalent geometry : angle 0.58213 / 0.37 (24250) hydrogen bonds : bond 0.20040 / 13.44 ( 318) hydrogen bonds : angle 8.45942 / 5.81 ( 849) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.949 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: B 224 LEU cc_start: 0.9076 (tp) cc_final: 0.8828 (tp) REVERT: A 49 VAL cc_start: 0.9273 (t) cc_final: 0.8849 (p) REVERT: A 89 LYS cc_start: 0.8736 (mtpp) cc_final: 0.8470 (mmtt) REVERT: A 103 VAL cc_start: 0.8433 (t) cc_final: 0.8174 (t) REVERT: A 334 ASP cc_start: 0.8575 (m-30) cc_final: 0.8372 (m-30) REVERT: C 395 ASN cc_start: 0.8100 (t0) cc_final: 0.7839 (t0) REVERT: C 695 HIS cc_start: 0.6082 (t70) cc_final: 0.5666 (t-170) outliers start: 11 outliers final: 9 residues processed: 162 average time/residue: 0.4123 time to fit residues: 91.0896 Evaluate side-chains 118 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 347 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 721 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.083201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.063737 restraints weight = 150544.832| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.10 r_work: 0.3150 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17804 Z= 0.162 Angle : 0.554 5.872 24250 Z= 0.288 Chirality : 0.045 0.192 2666 Planarity : 0.005 0.062 3059 Dihedral : 9.668 160.603 2481 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.83 % Allowed : 14.05 % Favored : 85.12 % 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: -1.54 (0.19), residues: 2073 helix: 0.45 (0.31), residues: 312 sheet: -1.87 (0.21), residues: 555 loop : -0.94 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 679 TYR 0.015 0.001 TYR C 509 PHE 0.009 0.001 PHE A 416 TRP 0.011 0.001 TRP A 228 HIS 0.005 0.001 HIS C 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (17804) covalent geometry : angle 0.55377 / 0.29 (24250) hydrogen bonds : bond 0.04335 / 2.96 ( 318) hydrogen bonds : angle 6.76039 / 4.66 ( 849) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.658 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: B 224 LEU cc_start: 0.9105 (tp) cc_final: 0.8888 (tp) REVERT: B 833 ILE cc_start: 0.9106 (mm) cc_final: 0.8797 (mt) REVERT: A 49 VAL cc_start: 0.9269 (t) cc_final: 0.8877 (p) REVERT: A 60 CYS cc_start: 0.7242 (p) cc_final: 0.7014 (p) REVERT: A 89 LYS cc_start: 0.8726 (mtpp) cc_final: 0.8431 (mmtt) REVERT: A 103 VAL cc_start: 0.8390 (t) cc_final: 0.8107 (t) REVERT: A 334 ASP cc_start: 0.8608 (m-30) cc_final: 0.8404 (m-30) REVERT: A 467 PHE cc_start: 0.7634 (m-80) cc_final: 0.7367 (m-80) REVERT: C 369 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7573 (ttp) REVERT: C 695 HIS cc_start: 0.5942 (t70) cc_final: 0.5538 (t-170) REVERT: C 771 MET cc_start: 0.7190 (ttp) cc_final: 0.6866 (tmm) outliers start: 16 outliers final: 11 residues processed: 128 average time/residue: 0.4064 time to fit residues: 73.4933 Evaluate side-chains 114 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 773 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 171 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.081644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.061868 restraints weight = 151659.248| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.12 r_work: 0.3102 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 17804 Z= 0.240 Angle : 0.571 5.405 24250 Z= 0.298 Chirality : 0.045 0.177 2666 Planarity : 0.005 0.056 3059 Dihedral : 9.774 160.476 2477 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.93 % Allowed : 14.52 % Favored : 84.55 % 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: -1.73 (0.18), residues: 2073 helix: 0.40 (0.30), residues: 311 sheet: -1.94 (0.21), residues: 543 loop : -1.15 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 545 TYR 0.014 0.002 TYR B 509 PHE 0.014 0.001 PHE C 742 TRP 0.015 0.002 TRP A 279 HIS 0.017 0.001 HIS C 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.24 (17804) covalent geometry : angle 0.57099 / 0.30 (24250) hydrogen bonds : bond 0.04194 / 2.81 ( 318) hydrogen bonds : angle 6.48390 / 4.50 ( 849) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.915 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 89 LYS cc_start: 0.8730 (mtpp) cc_final: 0.8431 (mmtt) REVERT: A 103 VAL cc_start: 0.8419 (t) cc_final: 0.8145 (t) REVERT: A 129 MET cc_start: 0.9007 (ptp) cc_final: 0.8664 (ptm) REVERT: A 334 ASP cc_start: 0.8610 (m-30) cc_final: 0.8391 (m-30) REVERT: A 467 PHE cc_start: 0.7660 (m-80) cc_final: 0.7416 (m-80) REVERT: C 369 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7723 (ttp) REVERT: C 396 ARG cc_start: 0.8466 (mmm160) cc_final: 0.8164 (mmp-170) REVERT: C 695 HIS cc_start: 0.6083 (t70) cc_final: 0.5478 (t70) outliers start: 18 outliers final: 11 residues processed: 119 average time/residue: 0.3738 time to fit residues: 63.2179 Evaluate side-chains 106 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 369 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 91 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 61 optimal weight: 0.0570 chunk 108 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.082277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.062556 restraints weight = 150766.859| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.14 r_work: 0.3120 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17804 Z= 0.139 Angle : 0.524 5.521 24250 Z= 0.270 Chirality : 0.044 0.195 2666 Planarity : 0.004 0.051 3059 Dihedral : 9.656 159.698 2473 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.73 % Allowed : 14.36 % Favored : 84.91 % 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: -1.61 (0.19), residues: 2073 helix: 0.56 (0.31), residues: 312 sheet: -1.95 (0.21), residues: 546 loop : -1.03 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 679 TYR 0.015 0.001 TYR C 849 PHE 0.012 0.001 PHE B 416 TRP 0.011 0.001 TRP A 228 HIS 0.002 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (17804) covalent geometry : angle 0.52366 / 0.27 (24250) hydrogen bonds : bond 0.03469 / 2.38 ( 318) hydrogen bonds : angle 6.15782 / 4.26 ( 849) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 1.018 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: B 444 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.9058 (ttpt) REVERT: A 89 LYS cc_start: 0.8719 (mtpp) cc_final: 0.8411 (mmtt) REVERT: A 103 VAL cc_start: 0.8417 (t) cc_final: 0.8136 (t) REVERT: A 334 ASP cc_start: 0.8603 (m-30) cc_final: 0.8381 (m-30) REVERT: A 467 PHE cc_start: 0.7677 (m-80) cc_final: 0.7409 (m-80) REVERT: C 369 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7674 (ttp) REVERT: C 695 HIS cc_start: 0.6082 (t70) cc_final: 0.5578 (t-170) outliers start: 14 outliers final: 10 residues processed: 110 average time/residue: 0.4157 time to fit residues: 64.3671 Evaluate side-chains 105 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 369 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 3 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 143 optimal weight: 0.0980 chunk 193 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 142 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 451 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.082043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.062324 restraints weight = 151204.030| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.12 r_work: 0.3117 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17804 Z= 0.158 Angle : 0.521 6.117 24250 Z= 0.268 Chirality : 0.044 0.194 2666 Planarity : 0.004 0.050 3059 Dihedral : 9.637 160.146 2472 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.04 % Allowed : 14.15 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.19), residues: 2073 helix: 0.66 (0.31), residues: 312 sheet: -1.93 (0.21), residues: 552 loop : -0.99 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 472 TYR 0.014 0.001 TYR B 478 PHE 0.010 0.001 PHE B 416 TRP 0.011 0.001 TRP A 228 HIS 0.003 0.001 HIS C 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (17804) covalent geometry : angle 0.52107 / 0.27 (24250) hydrogen bonds : bond 0.03210 / 2.19 ( 318) hydrogen bonds : angle 5.97032 / 4.15 ( 849) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.987 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: B 58 ARG cc_start: 0.8629 (mtp-110) cc_final: 0.8276 (mtp-110) REVERT: A 103 VAL cc_start: 0.8432 (t) cc_final: 0.8149 (t) REVERT: A 334 ASP cc_start: 0.8596 (m-30) cc_final: 0.8373 (m-30) REVERT: A 467 PHE cc_start: 0.7684 (m-80) cc_final: 0.7411 (m-80) REVERT: C 369 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7679 (ttp) REVERT: C 467 PHE cc_start: 0.8309 (t80) cc_final: 0.8089 (t80) REVERT: C 695 HIS cc_start: 0.6132 (t70) cc_final: 0.5857 (t70) outliers start: 20 outliers final: 13 residues processed: 119 average time/residue: 0.4056 time to fit residues: 67.9182 Evaluate side-chains 111 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 711 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 172 optimal weight: 4.9990 chunk 16 optimal weight: 0.0980 chunk 174 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.081906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.062179 restraints weight = 150877.123| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.13 r_work: 0.3110 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17804 Z= 0.162 Angle : 0.523 7.133 24250 Z= 0.269 Chirality : 0.044 0.192 2666 Planarity : 0.004 0.049 3059 Dihedral : 9.614 160.122 2471 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.67 % Allowed : 14.57 % Favored : 84.76 % 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: -1.54 (0.19), residues: 2073 helix: 0.68 (0.31), residues: 313 sheet: -1.99 (0.21), residues: 566 loop : -0.93 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 396 TYR 0.013 0.001 TYR C 509 PHE 0.012 0.001 PHE B 416 TRP 0.010 0.001 TRP A 228 HIS 0.002 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (17804) covalent geometry : angle 0.52313 / 0.27 (24250) hydrogen bonds : bond 0.03125 / 2.13 ( 318) hydrogen bonds : angle 5.88197 / 4.08 ( 849) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 1.056 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: B 58 ARG cc_start: 0.8625 (mtp-110) cc_final: 0.8273 (mtp-110) REVERT: A 103 VAL cc_start: 0.8428 (t) cc_final: 0.8147 (t) REVERT: A 334 ASP cc_start: 0.8599 (m-30) cc_final: 0.8378 (m-30) REVERT: A 467 PHE cc_start: 0.7695 (m-80) cc_final: 0.7419 (m-80) REVERT: C 369 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7689 (ttp) REVERT: C 396 ARG cc_start: 0.8462 (mmm160) cc_final: 0.8138 (mmp-170) REVERT: C 467 PHE cc_start: 0.8321 (t80) cc_final: 0.8097 (t80) REVERT: C 695 HIS cc_start: 0.6092 (t70) cc_final: 0.5810 (t70) outliers start: 13 outliers final: 10 residues processed: 111 average time/residue: 0.4028 time to fit residues: 63.0490 Evaluate side-chains 106 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 369 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 124 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 201 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.081790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.062127 restraints weight = 151524.326| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.13 r_work: 0.3111 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17804 Z= 0.158 Angle : 0.522 6.093 24250 Z= 0.269 Chirality : 0.044 0.193 2666 Planarity : 0.004 0.049 3059 Dihedral : 9.614 160.092 2471 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.83 % Allowed : 14.41 % Favored : 84.76 % 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: -1.53 (0.19), residues: 2073 helix: 0.72 (0.31), residues: 313 sheet: -1.98 (0.21), residues: 562 loop : -0.93 (0.19), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 396 TYR 0.014 0.001 TYR B 478 PHE 0.011 0.001 PHE B 416 TRP 0.010 0.001 TRP A 228 HIS 0.003 0.001 HIS C 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (17804) covalent geometry : angle 0.52174 / 0.27 (24250) hydrogen bonds : bond 0.03054 / 2.08 ( 318) hydrogen bonds : angle 5.80068 / 4.03 ( 849) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.876 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: B 58 ARG cc_start: 0.8639 (mtp-110) cc_final: 0.8320 (mtp-110) REVERT: A 103 VAL cc_start: 0.8423 (t) cc_final: 0.8161 (t) REVERT: A 334 ASP cc_start: 0.8598 (m-30) cc_final: 0.8366 (m-30) REVERT: A 467 PHE cc_start: 0.7705 (m-80) cc_final: 0.7424 (m-80) REVERT: C 369 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7687 (ttp) REVERT: C 467 PHE cc_start: 0.8327 (t80) cc_final: 0.8098 (t80) REVERT: C 695 HIS cc_start: 0.6068 (t70) cc_final: 0.5781 (t70) outliers start: 16 outliers final: 13 residues processed: 115 average time/residue: 0.3767 time to fit residues: 61.8073 Evaluate side-chains 112 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 369 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 61 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 116 optimal weight: 0.1980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.081906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.062230 restraints weight = 150868.621| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 3.13 r_work: 0.3115 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17804 Z= 0.140 Angle : 0.514 7.322 24250 Z= 0.263 Chirality : 0.044 0.196 2666 Planarity : 0.004 0.048 3059 Dihedral : 9.595 160.016 2471 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.83 % Allowed : 14.57 % Favored : 84.60 % 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: -1.49 (0.19), residues: 2073 helix: 0.80 (0.31), residues: 313 sheet: -2.01 (0.21), residues: 564 loop : -0.89 (0.19), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 396 TYR 0.013 0.001 TYR B 478 PHE 0.011 0.001 PHE B 416 TRP 0.010 0.001 TRP A 228 HIS 0.003 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (17804) covalent geometry : angle 0.51407 / 0.26 (24250) hydrogen bonds : bond 0.02917 / 2.00 ( 318) hydrogen bonds : angle 5.69868 / 3.96 ( 849) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 1.012 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: B 58 ARG cc_start: 0.8638 (mtp-110) cc_final: 0.8328 (mtp-110) REVERT: A 103 VAL cc_start: 0.8417 (t) cc_final: 0.8183 (t) REVERT: A 334 ASP cc_start: 0.8581 (m-30) cc_final: 0.8355 (m-30) REVERT: A 467 PHE cc_start: 0.7707 (m-80) cc_final: 0.7410 (m-80) REVERT: C 369 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7694 (ttp) REVERT: C 467 PHE cc_start: 0.8332 (t80) cc_final: 0.8103 (t80) REVERT: C 695 HIS cc_start: 0.6070 (t70) cc_final: 0.5780 (t70) outliers start: 16 outliers final: 12 residues processed: 116 average time/residue: 0.3939 time to fit residues: 63.9660 Evaluate side-chains 112 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 369 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 182 optimal weight: 0.1980 chunk 153 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 205 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.081397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.061674 restraints weight = 151099.808| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.12 r_work: 0.3098 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17804 Z= 0.187 Angle : 0.533 6.181 24250 Z= 0.274 Chirality : 0.044 0.189 2666 Planarity : 0.005 0.049 3059 Dihedral : 9.653 160.260 2471 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.88 % Allowed : 14.31 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.56 (0.19), residues: 2073 helix: 0.75 (0.31), residues: 313 sheet: -2.06 (0.21), residues: 562 loop : -0.94 (0.19), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 396 TYR 0.014 0.001 TYR B 478 PHE 0.012 0.001 PHE B 416 TRP 0.012 0.001 TRP A 279 HIS 0.002 0.001 HIS A 846 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (17804) covalent geometry : angle 0.53276 / 0.27 (24250) hydrogen bonds : bond 0.03053 / 2.08 ( 318) hydrogen bonds : angle 5.76100 / 4.01 ( 849) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.910 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: B 58 ARG cc_start: 0.8665 (mtp-110) cc_final: 0.8455 (mtp-110) REVERT: B 490 ARG cc_start: 0.8414 (mmt90) cc_final: 0.8135 (ptp-110) REVERT: A 103 VAL cc_start: 0.8445 (t) cc_final: 0.8218 (t) REVERT: A 334 ASP cc_start: 0.8595 (m-30) cc_final: 0.8357 (m-30) REVERT: A 467 PHE cc_start: 0.7723 (m-80) cc_final: 0.7407 (m-80) REVERT: C 369 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7733 (ttp) REVERT: C 467 PHE cc_start: 0.8350 (t80) cc_final: 0.8119 (t80) REVERT: C 695 HIS cc_start: 0.6125 (t70) cc_final: 0.5825 (t70) outliers start: 17 outliers final: 15 residues processed: 117 average time/residue: 0.4138 time to fit residues: 68.0192 Evaluate side-chains 115 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 369 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 90 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 54 optimal weight: 0.0270 chunk 24 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 9 optimal weight: 0.0670 chunk 98 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 181 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.082514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.062946 restraints weight = 150648.360| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.10 r_work: 0.3133 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17804 Z= 0.097 Angle : 0.503 6.492 24250 Z= 0.257 Chirality : 0.044 0.205 2666 Planarity : 0.004 0.048 3059 Dihedral : 9.568 159.652 2471 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.67 % Allowed : 14.67 % Favored : 84.66 % 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: -1.39 (0.19), residues: 2073 helix: 0.91 (0.31), residues: 313 sheet: -1.96 (0.21), residues: 560 loop : -0.83 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 396 TYR 0.013 0.001 TYR B 509 PHE 0.011 0.001 PHE B 416 TRP 0.012 0.001 TRP A 228 HIS 0.002 0.000 HIS B 750 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (17804) covalent geometry : angle 0.50305 / 0.26 (24250) hydrogen bonds : bond 0.02678 / 1.85 ( 318) hydrogen bonds : angle 5.49880 / 3.81 ( 849) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.766 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: B 58 ARG cc_start: 0.8616 (mtp-110) cc_final: 0.8413 (mtp-110) REVERT: B 490 ARG cc_start: 0.8392 (mmt90) cc_final: 0.8158 (ptp-110) REVERT: A 103 VAL cc_start: 0.8428 (t) cc_final: 0.8192 (t) REVERT: A 334 ASP cc_start: 0.8598 (m-30) cc_final: 0.8360 (m-30) REVERT: A 467 PHE cc_start: 0.7720 (m-80) cc_final: 0.7412 (m-80) REVERT: C 176 LYS cc_start: 0.8428 (mmmt) cc_final: 0.7920 (mmtt) REVERT: C 369 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7661 (ttp) REVERT: C 467 PHE cc_start: 0.8326 (t80) cc_final: 0.8102 (t80) REVERT: C 695 HIS cc_start: 0.6099 (t70) cc_final: 0.5810 (t70) outliers start: 13 outliers final: 10 residues processed: 115 average time/residue: 0.4124 time to fit residues: 66.1791 Evaluate side-chains 111 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 369 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 199 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 chunk 187 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.081900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.062304 restraints weight = 151260.126| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.09 r_work: 0.3116 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17804 Z= 0.142 Angle : 0.511 6.067 24250 Z= 0.261 Chirality : 0.044 0.197 2666 Planarity : 0.004 0.056 3059 Dihedral : 9.587 160.323 2471 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.62 % Allowed : 14.62 % Favored : 84.76 % 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: -1.39 (0.19), residues: 2073 helix: 0.90 (0.31), residues: 313 sheet: -1.96 (0.21), residues: 560 loop : -0.83 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 396 TYR 0.013 0.001 TYR B 478 PHE 0.011 0.001 PHE C 516 TRP 0.010 0.001 TRP A 279 HIS 0.002 0.000 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (17804) covalent geometry : angle 0.51107 / 0.26 (24250) hydrogen bonds : bond 0.02789 / 1.91 ( 318) hydrogen bonds : angle 5.53765 / 3.85 ( 849) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8074.67 seconds wall clock time: 137 minutes 38.67 seconds (8258.67 seconds total)