Starting phenix.real_space_refine on Fri Jul 3 09:01:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ngb_12311/07_2026/7ngb_12311.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ngb_12311/07_2026/7ngb_12311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ngb_12311/07_2026/7ngb_12311.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ngb_12311/07_2026/7ngb_12311.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ngb_12311/07_2026/7ngb_12311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ngb_12311/07_2026/7ngb_12311.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ngb_12311/07_2026/7ngb_12311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ngb_12311/07_2026/7ngb_12311.map" } resolution = 3.64 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= -0.002 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 86 5.16 5 C 8568 2.51 5 N 2178 2.21 5 O 2312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13144 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6519 Classifications: {'peptide': 859} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 33, 'TRANS': 825} Chain breaks: 3 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 2, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, D Time building chain proxies: 5.42, per 1000 atoms: 0.41 Number of scatterers: 13144 At special positions: 0 Unit cell: (112.035, 103.499, 150.447, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 86 16.00 O 2312 8.00 N 2178 7.00 C 8568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 640 " distance=2.05 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.02 Simple disulfide: pdb=" SG CYS A 359 " - pdb=" SG CYS A 369 " distance=2.02 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 640 " distance=2.05 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 339 " distance=2.02 Simple disulfide: pdb=" SG CYS B 359 " - pdb=" SG CYS B 369 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A1101 " - " ASN A 377 " " NAG B1101 " - " ASN B 377 " " NAG C 1 " - " ASN A 328 " " NAG D 1 " - " ASN B 328 " Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 488.4 milliseconds 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3156 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 8 sheets defined 61.6% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 135 through 149 removed outlier: 5.284A pdb=" N LEU A 142 " --> pdb=" O MET A 138 " (cutoff:3.500A) Proline residue: A 143 - end of helix Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 156 through 193 removed outlier: 6.478A pdb=" N VAL A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 9.392A pdb=" N LEU A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLN A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 243 removed outlier: 3.571A pdb=" N MET A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 211 - end of helix Processing helix chain 'A' and resid 260 through 284 Processing helix chain 'A' and resid 285 through 314 removed outlier: 3.803A pdb=" N VAL A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N SER A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 359 Processing helix chain 'A' and resid 370 through 376 Processing helix chain 'A' and resid 386 through 394 removed outlier: 4.204A pdb=" N GLY A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE A 391 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE A 392 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 393 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 removed outlier: 3.691A pdb=" N GLY A 439 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 447 through 453 Processing helix chain 'A' and resid 460 through 491 Proline residue: A 466 - end of helix removed outlier: 3.736A pdb=" N VAL A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 517 through 550 removed outlier: 4.396A pdb=" N ILE A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Proline residue: A 541 - end of helix Processing helix chain 'A' and resid 554 through 561 removed outlier: 3.945A pdb=" N VAL A 558 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS A 561 " --> pdb=" O VAL A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 584 removed outlier: 3.547A pdb=" N LEU A 572 " --> pdb=" O PRO A 568 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 574 " --> pdb=" O TRP A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 616 Proline residue: A 593 - end of helix removed outlier: 3.828A pdb=" N CYS A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 648 removed outlier: 3.572A pdb=" N SER A 633 " --> pdb=" O HIS A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 675 removed outlier: 3.630A pdb=" N ILE A 653 " --> pdb=" O TRP A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 696 removed outlier: 3.585A pdb=" N GLU A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 734 removed outlier: 4.293A pdb=" N LEU A 726 " --> pdb=" O HIS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 770 Processing helix chain 'A' and resid 783 through 795 removed outlier: 4.034A pdb=" N GLN A 793 " --> pdb=" O SER A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 835 removed outlier: 3.597A pdb=" N PHE A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 848 Processing helix chain 'A' and resid 868 through 881 removed outlier: 4.055A pdb=" N LEU A 872 " --> pdb=" O ASP A 868 " (cutoff:3.500A) Proline residue: A 876 - end of helix Processing helix chain 'A' and resid 901 through 917 removed outlier: 3.508A pdb=" N ARG A 917 " --> pdb=" O LEU A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1048 removed outlier: 3.939A pdb=" N LYS A1038 " --> pdb=" O HIS A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1066 through 1078 Processing helix chain 'B' and resid 135 through 149 removed outlier: 5.283A pdb=" N LEU B 142 " --> pdb=" O MET B 138 " (cutoff:3.500A) Proline residue: B 143 - end of helix Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 156 through 193 removed outlier: 6.480A pdb=" N VAL B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 9.393A pdb=" N LEU B 167 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 243 removed outlier: 3.571A pdb=" N MET B 204 " --> pdb=" O GLY B 200 " (cutoff:3.500A) Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 260 through 284 Processing helix chain 'B' and resid 285 through 314 removed outlier: 3.802A pdb=" N VAL B 289 " --> pdb=" O GLY B 285 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N SER B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LEU B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 359 Processing helix chain 'B' and resid 370 through 376 Processing helix chain 'B' and resid 386 through 394 removed outlier: 4.204A pdb=" N GLY B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE B 391 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE B 392 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 393 " --> pdb=" O GLY B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 442 removed outlier: 3.691A pdb=" N GLY B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 445 No H-bonds generated for 'chain 'B' and resid 443 through 445' Processing helix chain 'B' and resid 447 through 453 Processing helix chain 'B' and resid 460 through 491 Proline residue: B 466 - end of helix removed outlier: 3.736A pdb=" N VAL B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 517 through 550 removed outlier: 4.396A pdb=" N ILE B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Proline residue: B 541 - end of helix Processing helix chain 'B' and resid 554 through 561 removed outlier: 3.944A pdb=" N VAL B 558 " --> pdb=" O PHE B 555 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS B 561 " --> pdb=" O VAL B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 584 removed outlier: 3.547A pdb=" N LEU B 572 " --> pdb=" O PRO B 568 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU B 574 " --> pdb=" O TRP B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 616 Proline residue: B 593 - end of helix removed outlier: 3.828A pdb=" N CYS B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 648 removed outlier: 3.572A pdb=" N SER B 633 " --> pdb=" O HIS B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 675 removed outlier: 3.631A pdb=" N ILE B 653 " --> pdb=" O TRP B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 696 removed outlier: 3.585A pdb=" N GLU B 696 " --> pdb=" O LEU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 734 removed outlier: 4.293A pdb=" N LEU B 726 " --> pdb=" O HIS B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 770 Processing helix chain 'B' and resid 783 through 795 removed outlier: 4.034A pdb=" N GLN B 793 " --> pdb=" O SER B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 835 removed outlier: 3.598A pdb=" N PHE B 825 " --> pdb=" O ALA B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 Processing helix chain 'B' and resid 868 through 881 removed outlier: 4.055A pdb=" N LEU B 872 " --> pdb=" O ASP B 868 " (cutoff:3.500A) Proline residue: B 876 - end of helix Processing helix chain 'B' and resid 901 through 917 removed outlier: 3.508A pdb=" N ARG B 917 " --> pdb=" O LEU B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1048 removed outlier: 3.939A pdb=" N LYS B1038 " --> pdb=" O HIS B1034 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1065 No H-bonds generated for 'chain 'B' and resid 1063 through 1065' Processing helix chain 'B' and resid 1066 through 1078 Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA2, first strand: chain 'A' and resid 342 through 345 removed outlier: 3.622A pdb=" N VAL A 350 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 775 through 781 removed outlier: 6.771A pdb=" N LEU A 708 " --> pdb=" O ILE A 740 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLY A 742 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL A 710 " --> pdb=" O GLY A 742 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL A 744 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLY A 808 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A1084 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL A1053 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL A1087 " --> pdb=" O VAL A1053 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU A1055 " --> pdb=" O VAL A1087 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 859 through 860 removed outlier: 6.691A pdb=" N ILE A 890 " --> pdb=" O GLU A 921 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N GLU A 923 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE A 892 " --> pdb=" O GLU A 923 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 329 through 330 Processing sheet with id=AA6, first strand: chain 'B' and resid 342 through 345 removed outlier: 3.622A pdb=" N VAL B 350 " --> pdb=" O LYS B 343 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 775 through 781 removed outlier: 6.772A pdb=" N LEU B 708 " --> pdb=" O ILE B 740 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLY B 742 " --> pdb=" O LEU B 708 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL B 710 " --> pdb=" O GLY B 742 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL B 744 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLY B 808 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B1084 " --> pdb=" O LYS B 843 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL B1053 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL B1087 " --> pdb=" O VAL B1053 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU B1055 " --> pdb=" O VAL B1087 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 859 through 860 removed outlier: 6.691A pdb=" N ILE B 890 " --> pdb=" O GLU B 921 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N GLU B 923 " --> pdb=" O ILE B 890 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ILE B 892 " --> pdb=" O GLU B 923 " (cutoff:3.500A) 786 hydrogen bonds defined for protein. 2262 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.65 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 2945 1.33 - 1.46: 4321 1.46 - 1.60: 6050 1.60 - 1.73: 0 1.73 - 1.87: 134 Bond restraints: 13450 Sorted by residual: bond pdb=" N ILE B 918 " pdb=" CA ILE B 918 " ideal model delta sigma weight residual 1.458 1.499 -0.042 1.14e-02 7.69e+03 1.36e+01 bond pdb=" N ILE A 918 " pdb=" CA ILE A 918 " ideal model delta sigma weight residual 1.458 1.499 -0.042 1.14e-02 7.69e+03 1.33e+01 bond pdb=" C PHE B 274 " pdb=" O PHE B 274 " ideal model delta sigma weight residual 1.237 1.194 0.042 1.17e-02 7.31e+03 1.31e+01 bond pdb=" C PHE A 274 " pdb=" O PHE A 274 " ideal model delta sigma weight residual 1.237 1.195 0.042 1.17e-02 7.31e+03 1.30e+01 bond pdb=" C ASP B 908 " pdb=" O ASP B 908 " ideal model delta sigma weight residual 1.237 1.276 -0.040 1.17e-02 7.31e+03 1.15e+01 ... (remaining 13445 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 16977 1.95 - 3.91: 1136 3.91 - 5.86: 149 5.86 - 7.81: 30 7.81 - 9.77: 12 Bond angle restraints: 18304 Sorted by residual: angle pdb=" N GLN A 904 " pdb=" CA GLN A 904 " pdb=" C GLN A 904 " ideal model delta sigma weight residual 111.28 104.98 6.30 1.09e+00 8.42e-01 3.34e+01 angle pdb=" N GLN B 904 " pdb=" CA GLN B 904 " pdb=" C GLN B 904 " ideal model delta sigma weight residual 111.28 104.99 6.29 1.09e+00 8.42e-01 3.33e+01 angle pdb=" CA TRP A 864 " pdb=" C TRP A 864 " pdb=" O TRP A 864 " ideal model delta sigma weight residual 122.37 116.78 5.59 1.15e+00 7.56e-01 2.37e+01 angle pdb=" CA TRP B 864 " pdb=" C TRP B 864 " pdb=" O TRP B 864 " ideal model delta sigma weight residual 122.37 116.79 5.58 1.15e+00 7.56e-01 2.36e+01 angle pdb=" C ILE A 639 " pdb=" N CYS A 640 " pdb=" CA CYS A 640 " ideal model delta sigma weight residual 122.38 114.41 7.97 1.81e+00 3.05e-01 1.94e+01 ... (remaining 18299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 7224 17.48 - 34.96: 478 34.96 - 52.44: 70 52.44 - 69.92: 14 69.92 - 87.40: 8 Dihedral angle restraints: 7794 sinusoidal: 2884 harmonic: 4910 Sorted by residual: dihedral pdb=" CA CYS B 640 " pdb=" C CYS B 640 " pdb=" N LEU B 641 " pdb=" CA LEU B 641 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA CYS A 640 " pdb=" C CYS A 640 " pdb=" N LEU A 641 " pdb=" CA LEU A 641 " ideal model delta harmonic sigma weight residual 180.00 155.01 24.99 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CB CYS A 179 " pdb=" SG CYS A 179 " pdb=" SG CYS A 640 " pdb=" CB CYS A 640 " ideal model delta sinusoidal sigma weight residual 93.00 58.58 34.42 1 1.00e+01 1.00e-02 1.68e+01 ... (remaining 7791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1825 0.090 - 0.181: 327 0.181 - 0.271: 20 0.271 - 0.361: 4 0.361 - 0.451: 2 Chirality restraints: 2178 Sorted by residual: chirality pdb=" C1 NAG A1101 " pdb=" ND2 ASN A 377 " pdb=" C2 NAG A1101 " pdb=" O5 NAG A1101 " both_signs ideal model delta sigma weight residual False -2.40 -2.85 0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" C1 NAG B1101 " pdb=" ND2 ASN B 377 " pdb=" C2 NAG B1101 " pdb=" O5 NAG B1101 " both_signs ideal model delta sigma weight residual False -2.40 -2.85 0.45 2.00e-01 2.50e+01 5.07e+00 chirality pdb=" CA CYS B 640 " pdb=" N CYS B 640 " pdb=" C CYS B 640 " pdb=" CB CYS B 640 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 2175 not shown) Planarity restraints: 2270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 497 " 0.082 9.50e-02 1.11e+02 4.99e-02 1.50e+01 pdb=" NE ARG A 497 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A 497 " 0.064 2.00e-02 2.50e+03 pdb=" NH1 ARG A 497 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG A 497 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 497 " -0.083 9.50e-02 1.11e+02 5.00e-02 1.49e+01 pdb=" NE ARG B 497 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG B 497 " -0.064 2.00e-02 2.50e+03 pdb=" NH1 ARG B 497 " 0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG B 497 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 240 " -0.018 2.00e-02 2.50e+03 3.64e-02 1.33e+01 pdb=" C PHE B 240 " 0.063 2.00e-02 2.50e+03 pdb=" O PHE B 240 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU B 241 " -0.021 2.00e-02 2.50e+03 ... (remaining 2267 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3512 2.80 - 3.32: 13418 3.32 - 3.85: 21359 3.85 - 4.37: 24132 4.37 - 4.90: 41312 Nonbonded interactions: 103733 Sorted by model distance: nonbonded pdb=" O THR B 431 " pdb=" OG1 THR B 431 " model vdw 2.269 3.040 nonbonded pdb=" O THR A 431 " pdb=" OG1 THR A 431 " model vdw 2.270 3.040 nonbonded pdb=" O PRO A 698 " pdb=" NH1 ARG B 680 " model vdw 2.279 3.120 nonbonded pdb=" OD1 ASP B 715 " pdb=" N HIS B 719 " model vdw 2.280 3.120 nonbonded pdb=" OD1 ASP A 715 " pdb=" N HIS A 719 " model vdw 2.281 3.120 ... (remaining 103728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.190 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 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 : 0.010 0.131 13464 Z= 0.486 Angle : 1.109 11.546 18340 Z= 0.646 Chirality : 0.067 0.451 2178 Planarity : 0.007 0.056 2266 Dihedral : 12.095 87.396 4620 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.47 % Favored : 97.41 % Rotamer: Outliers : 0.59 % Allowed : 6.52 % Favored : 92.90 % 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: -1.80 (0.18), residues: 1702 helix: -0.64 (0.15), residues: 954 sheet: -1.70 (0.46), residues: 92 loop : -1.81 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.065 0.002 ARG A 497 TYR 0.023 0.003 TYR B 222 PHE 0.033 0.004 PHE B 441 TRP 0.053 0.004 TRP B 822 HIS 0.009 0.002 HIS B 790 Details of bonding type rmsd/Z covalent geometry : bond 0.00972 / 0.48 (13450) covalent geometry : angle 1.07876 / 0.64 (18304) SS BOND : bond 0.01232 / 0.73 ( 6) SS BOND : angle 3.16476 / 1.74 ( 12) hydrogen bonds : bond 0.12819 / 8.52 ( 786) hydrogen bonds : angle 5.73095 / 4.21 ( 2262) link_BETA1-4 : bond 0.01423 / 0.83 ( 4) link_BETA1-4 : angle 5.69836 / 3.06 ( 12) link_NAG-ASN : bond 0.10430 / 6.36 ( 4) link_NAG-ASN : angle 7.89333 / 5.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 277 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 MET cc_start: 0.7954 (tpp) cc_final: 0.7707 (tpp) REVERT: A 601 MET cc_start: 0.8000 (tpp) cc_final: 0.7695 (tpp) REVERT: A 917 ARG cc_start: 0.5905 (OUTLIER) cc_final: 0.5372 (mtt180) REVERT: A 923 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6421 (tm-30) REVERT: A 1045 ASN cc_start: 0.8242 (m-40) cc_final: 0.7935 (t0) REVERT: B 263 MET cc_start: 0.7204 (tpp) cc_final: 0.6947 (tpp) REVERT: B 601 MET cc_start: 0.7882 (tpp) cc_final: 0.7608 (tpp) REVERT: B 626 ARG cc_start: 0.7003 (ttt-90) cc_final: 0.6582 (tpt170) REVERT: B 917 ARG cc_start: 0.5838 (OUTLIER) cc_final: 0.5284 (mtt180) REVERT: B 923 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6580 (tm-30) REVERT: B 1081 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6096 (mp) outliers start: 8 outliers final: 0 residues processed: 281 average time/residue: 0.0965 time to fit residues: 39.6563 Evaluate side-chains 167 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 162 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 917 ARG Chi-restraints excluded: chain A residue 923 GLU Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 923 GLU Chi-restraints excluded: chain B residue 1081 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 GLN A 290 ASN A 613 GLN A 731 GLN A1069 ASN B 146 GLN B 290 ASN B 613 GLN B 731 GLN B1069 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.157620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.117377 restraints weight = 18002.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.123833 restraints weight = 8441.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.128371 restraints weight = 5282.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.131597 restraints weight = 3871.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.133764 restraints weight = 3117.556| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13464 Z= 0.154 Angle : 0.652 10.347 18340 Z= 0.333 Chirality : 0.045 0.250 2178 Planarity : 0.004 0.050 2266 Dihedral : 4.937 46.073 1832 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.29 % Favored : 96.59 % Rotamer: Outliers : 1.83 % Allowed : 12.37 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.20), residues: 1702 helix: 1.01 (0.16), residues: 934 sheet: -1.31 (0.49), residues: 92 loop : -1.36 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 497 TYR 0.020 0.001 TYR A 202 PHE 0.021 0.002 PHE B 357 TRP 0.022 0.002 TRP A 822 HIS 0.007 0.001 HIS B 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (13450) covalent geometry : angle 0.63806 / 0.33 (18304) SS BOND : bond 0.00469 / 0.28 ( 6) SS BOND : angle 2.08847 / 1.11 ( 12) hydrogen bonds : bond 0.05317 / 3.52 ( 786) hydrogen bonds : angle 4.64313 / 3.42 ( 2262) link_BETA1-4 : bond 0.00822 / 0.48 ( 4) link_BETA1-4 : angle 3.68992 / 2.08 ( 12) link_NAG-ASN : bond 0.00292 / 0.17 ( 4) link_NAG-ASN : angle 3.35429 / 2.14 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.8262 (tpp) cc_final: 0.7884 (tpp) REVERT: A 743 SER cc_start: 0.8261 (OUTLIER) cc_final: 0.8022 (p) REVERT: A 917 ARG cc_start: 0.5968 (OUTLIER) cc_final: 0.5372 (mmt90) REVERT: A 1071 MET cc_start: 0.6708 (tpp) cc_final: 0.6425 (tpp) REVERT: B 263 MET cc_start: 0.7146 (tpp) cc_final: 0.6918 (tpp) REVERT: B 601 MET cc_start: 0.8168 (tpp) cc_final: 0.7814 (tpp) REVERT: B 626 ARG cc_start: 0.7345 (ttt-90) cc_final: 0.6462 (tpt170) REVERT: B 728 PHE cc_start: 0.7624 (t80) cc_final: 0.7296 (t80) REVERT: B 1057 MET cc_start: 0.6413 (mtp) cc_final: 0.5602 (mtp) REVERT: B 1071 MET cc_start: 0.6827 (tpp) cc_final: 0.6585 (tpp) REVERT: B 1081 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.6785 (mp) outliers start: 25 outliers final: 10 residues processed: 233 average time/residue: 0.0759 time to fit residues: 28.4358 Evaluate side-chains 182 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 917 ARG Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain B residue 1081 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 90 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4235 r_free = 0.4235 target = 0.155439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.116534 restraints weight = 18005.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.122486 restraints weight = 8963.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.126762 restraints weight = 5698.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.129662 restraints weight = 4204.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.131672 restraints weight = 3417.310| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13464 Z= 0.139 Angle : 0.618 10.765 18340 Z= 0.313 Chirality : 0.044 0.301 2178 Planarity : 0.004 0.052 2266 Dihedral : 4.480 43.078 1822 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.29 % Favored : 96.59 % Rotamer: Outliers : 2.71 % Allowed : 14.28 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.20), residues: 1702 helix: 1.53 (0.17), residues: 934 sheet: -0.94 (0.52), residues: 92 loop : -1.23 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 626 TYR 0.018 0.001 TYR A 202 PHE 0.021 0.001 PHE A 728 TRP 0.024 0.002 TRP B 809 HIS 0.008 0.001 HIS B 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (13450) covalent geometry : angle 0.60559 / 0.31 (18304) SS BOND : bond 0.00765 / 0.45 ( 6) SS BOND : angle 2.29273 / 1.25 ( 12) hydrogen bonds : bond 0.04892 / 3.21 ( 786) hydrogen bonds : angle 4.46010 / 3.28 ( 2262) link_BETA1-4 : bond 0.00761 / 0.45 ( 4) link_BETA1-4 : angle 3.40825 / 1.93 ( 12) link_NAG-ASN : bond 0.00303 / 0.18 ( 4) link_NAG-ASN : angle 2.74773 / 1.78 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8221 (m-80) cc_final: 0.7644 (m-80) REVERT: A 597 MET cc_start: 0.7956 (tpp) cc_final: 0.7572 (tpp) REVERT: A 601 MET cc_start: 0.8242 (tpp) cc_final: 0.7803 (tpp) REVERT: A 1071 MET cc_start: 0.7192 (tpp) cc_final: 0.6914 (tpp) REVERT: B 149 PHE cc_start: 0.8163 (m-80) cc_final: 0.7651 (m-80) REVERT: B 263 MET cc_start: 0.7182 (tpp) cc_final: 0.6916 (tpp) REVERT: B 601 MET cc_start: 0.8211 (tpp) cc_final: 0.7807 (tpp) REVERT: B 626 ARG cc_start: 0.7358 (ttt-90) cc_final: 0.6632 (tpt170) REVERT: B 1071 MET cc_start: 0.7068 (tpp) cc_final: 0.6858 (tpp) REVERT: B 1081 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.6986 (mp) outliers start: 37 outliers final: 16 residues processed: 213 average time/residue: 0.0835 time to fit residues: 29.2949 Evaluate side-chains 176 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 800 MET Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain B residue 1081 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 51 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 157 optimal weight: 8.9990 chunk 161 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 382 GLN A 765 HIS B 382 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.151001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.111987 restraints weight = 18577.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.117515 restraints weight = 9376.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.121519 restraints weight = 6086.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.124273 restraints weight = 4565.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.125945 restraints weight = 3751.731| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13464 Z= 0.159 Angle : 0.638 10.466 18340 Z= 0.320 Chirality : 0.045 0.278 2178 Planarity : 0.004 0.047 2266 Dihedral : 4.312 38.971 1818 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.58 % Favored : 96.30 % Rotamer: Outliers : 2.12 % Allowed : 17.20 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.20), residues: 1702 helix: 1.67 (0.17), residues: 926 sheet: -0.96 (0.52), residues: 92 loop : -1.12 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 156 TYR 0.018 0.002 TYR B 202 PHE 0.015 0.002 PHE A 877 TRP 0.016 0.001 TRP B 813 HIS 0.007 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (13450) covalent geometry : angle 0.62826 / 0.32 (18304) SS BOND : bond 0.00706 / 0.42 ( 6) SS BOND : angle 1.87926 / 0.98 ( 12) hydrogen bonds : bond 0.04849 / 3.22 ( 786) hydrogen bonds : angle 4.39239 / 3.22 ( 2262) link_BETA1-4 : bond 0.00644 / 0.39 ( 4) link_BETA1-4 : angle 3.30768 / 1.88 ( 12) link_NAG-ASN : bond 0.00250 / 0.15 ( 4) link_NAG-ASN : angle 2.33248 / 1.53 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8340 (m-80) cc_final: 0.7709 (m-80) REVERT: A 597 MET cc_start: 0.7932 (tpp) cc_final: 0.7542 (tpp) REVERT: A 601 MET cc_start: 0.8273 (tpp) cc_final: 0.7832 (tpp) REVERT: A 726 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8289 (mm) REVERT: A 1071 MET cc_start: 0.7364 (tpp) cc_final: 0.7022 (tpp) REVERT: B 601 MET cc_start: 0.8233 (tpp) cc_final: 0.7779 (tpp) REVERT: B 626 ARG cc_start: 0.7373 (ttt-90) cc_final: 0.6616 (tpt170) REVERT: B 634 PHE cc_start: 0.8826 (t80) cc_final: 0.8305 (t80) REVERT: B 1071 MET cc_start: 0.7185 (tpp) cc_final: 0.6915 (tpp) REVERT: B 1081 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.6937 (mp) outliers start: 29 outliers final: 16 residues processed: 190 average time/residue: 0.0693 time to fit residues: 22.1587 Evaluate side-chains 173 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 800 MET Chi-restraints excluded: chain B residue 1081 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 163 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.151001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.110654 restraints weight = 18446.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.116590 restraints weight = 8911.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.120737 restraints weight = 5662.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.123591 restraints weight = 4196.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.125521 restraints weight = 3439.935| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13464 Z= 0.139 Angle : 0.615 9.837 18340 Z= 0.306 Chirality : 0.044 0.260 2178 Planarity : 0.004 0.045 2266 Dihedral : 4.205 34.373 1818 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.29 % Favored : 96.59 % Rotamer: Outliers : 2.05 % Allowed : 18.16 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.21), residues: 1702 helix: 1.89 (0.17), residues: 926 sheet: -1.14 (0.49), residues: 96 loop : -1.02 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 156 TYR 0.018 0.001 TYR B 202 PHE 0.028 0.001 PHE A 728 TRP 0.014 0.001 TRP B 813 HIS 0.007 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (13450) covalent geometry : angle 0.60610 / 0.30 (18304) SS BOND : bond 0.00531 / 0.32 ( 6) SS BOND : angle 1.71883 / 0.90 ( 12) hydrogen bonds : bond 0.04591 / 3.04 ( 786) hydrogen bonds : angle 4.29746 / 3.14 ( 2262) link_BETA1-4 : bond 0.00643 / 0.38 ( 4) link_BETA1-4 : angle 3.14588 / 1.80 ( 12) link_NAG-ASN : bond 0.00223 / 0.13 ( 4) link_NAG-ASN : angle 2.07134 / 1.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 601 MET cc_start: 0.8226 (tpp) cc_final: 0.7819 (tpp) REVERT: A 726 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8260 (mm) REVERT: A 1071 MET cc_start: 0.7304 (tpp) cc_final: 0.6886 (tpp) REVERT: B 263 MET cc_start: 0.7144 (tpp) cc_final: 0.6717 (tpp) REVERT: B 597 MET cc_start: 0.8146 (tpp) cc_final: 0.7822 (tpp) REVERT: B 601 MET cc_start: 0.8260 (tpp) cc_final: 0.7829 (tpp) REVERT: B 626 ARG cc_start: 0.7400 (ttt-90) cc_final: 0.6647 (tpt170) REVERT: B 638 SER cc_start: 0.8815 (p) cc_final: 0.8384 (p) REVERT: B 728 PHE cc_start: 0.7485 (t80) cc_final: 0.7233 (t80) REVERT: B 1071 MET cc_start: 0.7261 (tpp) cc_final: 0.6917 (tpp) REVERT: B 1081 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.6722 (mp) outliers start: 28 outliers final: 14 residues processed: 201 average time/residue: 0.0724 time to fit residues: 24.0737 Evaluate side-chains 175 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 HIS Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 800 MET Chi-restraints excluded: chain B residue 1081 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 144 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 765 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.150238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.111399 restraints weight = 18404.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.116932 restraints weight = 9321.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.120847 restraints weight = 6041.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.123476 restraints weight = 4530.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.125343 restraints weight = 3733.938| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13464 Z= 0.161 Angle : 0.631 9.271 18340 Z= 0.315 Chirality : 0.045 0.280 2178 Planarity : 0.004 0.057 2266 Dihedral : 4.307 33.055 1818 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.64 % Favored : 96.24 % Rotamer: Outliers : 2.05 % Allowed : 18.52 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.21), residues: 1702 helix: 1.87 (0.17), residues: 924 sheet: -1.35 (0.49), residues: 92 loop : -1.02 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 156 TYR 0.018 0.002 TYR A 202 PHE 0.018 0.002 PHE A 728 TRP 0.013 0.001 TRP B 813 HIS 0.007 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (13450) covalent geometry : angle 0.62233 / 0.31 (18304) SS BOND : bond 0.00887 / 0.53 ( 6) SS BOND : angle 2.09308 / 1.12 ( 12) hydrogen bonds : bond 0.04711 / 3.13 ( 786) hydrogen bonds : angle 4.39136 / 3.21 ( 2262) link_BETA1-4 : bond 0.00753 / 0.45 ( 4) link_BETA1-4 : angle 3.11605 / 1.79 ( 12) link_NAG-ASN : bond 0.00212 / 0.13 ( 4) link_NAG-ASN : angle 1.91459 / 1.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 181 MET cc_start: 0.8784 (tpt) cc_final: 0.8550 (tpp) REVERT: A 280 LEU cc_start: 0.8181 (pp) cc_final: 0.7893 (pp) REVERT: A 597 MET cc_start: 0.7967 (tpp) cc_final: 0.7574 (tpp) REVERT: A 601 MET cc_start: 0.8231 (tpp) cc_final: 0.7789 (tpp) REVERT: A 726 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8387 (mm) REVERT: A 1071 MET cc_start: 0.7435 (tpp) cc_final: 0.6983 (tpp) REVERT: B 263 MET cc_start: 0.7138 (tpp) cc_final: 0.6724 (tpp) REVERT: B 280 LEU cc_start: 0.8085 (pp) cc_final: 0.7802 (pp) REVERT: B 597 MET cc_start: 0.8132 (tpp) cc_final: 0.7792 (tpp) REVERT: B 601 MET cc_start: 0.8166 (tpp) cc_final: 0.7732 (tpp) REVERT: B 626 ARG cc_start: 0.7440 (ttt-90) cc_final: 0.6722 (tpt170) REVERT: B 743 SER cc_start: 0.8263 (OUTLIER) cc_final: 0.7689 (p) REVERT: B 1071 MET cc_start: 0.7329 (tpp) cc_final: 0.6968 (tpp) REVERT: B 1081 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.6558 (mp) outliers start: 28 outliers final: 18 residues processed: 190 average time/residue: 0.0809 time to fit residues: 25.5806 Evaluate side-chains 177 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 800 MET Chi-restraints excluded: chain B residue 1081 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 53 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 126 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4203 r_free = 0.4203 target = 0.152476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.113684 restraints weight = 18449.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.119470 restraints weight = 9178.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.123543 restraints weight = 5877.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.126276 restraints weight = 4375.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.128244 restraints weight = 3576.875| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13464 Z= 0.130 Angle : 0.605 8.900 18340 Z= 0.301 Chirality : 0.044 0.276 2178 Planarity : 0.004 0.058 2266 Dihedral : 4.204 33.441 1818 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.41 % Favored : 96.47 % Rotamer: Outliers : 1.76 % Allowed : 18.81 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.21), residues: 1702 helix: 1.97 (0.17), residues: 924 sheet: -1.44 (0.46), residues: 104 loop : -0.98 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 814 TYR 0.016 0.001 TYR A 202 PHE 0.022 0.001 PHE B 487 TRP 0.022 0.001 TRP B 813 HIS 0.007 0.001 HIS B 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (13450) covalent geometry : angle 0.59624 / 0.30 (18304) SS BOND : bond 0.00741 / 0.44 ( 6) SS BOND : angle 2.14998 / 1.16 ( 12) hydrogen bonds : bond 0.04555 / 3.03 ( 786) hydrogen bonds : angle 4.31452 / 3.16 ( 2262) link_BETA1-4 : bond 0.00682 / 0.41 ( 4) link_BETA1-4 : angle 2.99766 / 1.73 ( 12) link_NAG-ASN : bond 0.00208 / 0.12 ( 4) link_NAG-ASN : angle 1.90262 / 1.22 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: A 181 MET cc_start: 0.8700 (tpt) cc_final: 0.8467 (tpp) REVERT: A 280 LEU cc_start: 0.8167 (pp) cc_final: 0.7885 (pp) REVERT: A 601 MET cc_start: 0.8214 (tpp) cc_final: 0.7795 (tpp) REVERT: A 726 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8298 (mm) REVERT: A 1071 MET cc_start: 0.7505 (tpp) cc_final: 0.7208 (tpp) REVERT: B 263 MET cc_start: 0.7190 (tpp) cc_final: 0.6793 (tpp) REVERT: B 280 LEU cc_start: 0.8072 (pp) cc_final: 0.7790 (pp) REVERT: B 471 LEU cc_start: 0.8731 (mm) cc_final: 0.7492 (tp) REVERT: B 597 MET cc_start: 0.8066 (tpp) cc_final: 0.7769 (tpp) REVERT: B 601 MET cc_start: 0.8157 (tpp) cc_final: 0.7694 (tpp) REVERT: B 626 ARG cc_start: 0.7370 (ttt-90) cc_final: 0.6726 (tpt170) REVERT: B 728 PHE cc_start: 0.7441 (t80) cc_final: 0.7182 (t80) REVERT: B 1071 MET cc_start: 0.7343 (tpp) cc_final: 0.6958 (tpp) REVERT: B 1081 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.6573 (mp) outliers start: 24 outliers final: 17 residues processed: 190 average time/residue: 0.0855 time to fit residues: 26.6925 Evaluate side-chains 179 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 423 HIS Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 627 TYR Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 800 MET Chi-restraints excluded: chain B residue 1081 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 141 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 156 optimal weight: 0.0070 chunk 101 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.3604 ------------------------------------------------------------------------------- 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 = 0.4199 r_free = 0.4199 target = 0.151980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.113105 restraints weight = 18079.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.118707 restraints weight = 8960.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.122668 restraints weight = 5749.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.125435 restraints weight = 4272.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.127202 restraints weight = 3492.799| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13464 Z= 0.160 Angle : 0.635 8.776 18340 Z= 0.319 Chirality : 0.045 0.280 2178 Planarity : 0.004 0.061 2266 Dihedral : 4.290 34.906 1818 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.00 % Favored : 95.89 % Rotamer: Outliers : 2.12 % Allowed : 19.03 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.21), residues: 1702 helix: 1.92 (0.17), residues: 926 sheet: -1.50 (0.47), residues: 100 loop : -1.01 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 814 TYR 0.016 0.002 TYR A 202 PHE 0.017 0.002 PHE B 877 TRP 0.033 0.002 TRP B 813 HIS 0.005 0.001 HIS B 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (13450) covalent geometry : angle 0.62691 / 0.32 (18304) SS BOND : bond 0.00692 / 0.42 ( 6) SS BOND : angle 2.03176 / 1.09 ( 12) hydrogen bonds : bond 0.04634 / 3.09 ( 786) hydrogen bonds : angle 4.36887 / 3.19 ( 2262) link_BETA1-4 : bond 0.00707 / 0.42 ( 4) link_BETA1-4 : angle 3.00850 / 1.73 ( 12) link_NAG-ASN : bond 0.00179 / 0.11 ( 4) link_NAG-ASN : angle 1.74231 / 1.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.418 Fit side-chains REVERT: A 181 MET cc_start: 0.8690 (tpt) cc_final: 0.8465 (tpp) REVERT: A 280 LEU cc_start: 0.8202 (pp) cc_final: 0.7908 (pp) REVERT: A 471 LEU cc_start: 0.8672 (mm) cc_final: 0.7415 (tp) REVERT: A 601 MET cc_start: 0.8205 (tpp) cc_final: 0.7782 (tpp) REVERT: A 809 TRP cc_start: 0.8150 (OUTLIER) cc_final: 0.7506 (t60) REVERT: A 1071 MET cc_start: 0.7502 (tpp) cc_final: 0.6901 (tpp) REVERT: B 181 MET cc_start: 0.8596 (tpt) cc_final: 0.8322 (tpp) REVERT: B 263 MET cc_start: 0.7062 (tpp) cc_final: 0.6645 (tpp) REVERT: B 280 LEU cc_start: 0.8109 (pp) cc_final: 0.7822 (pp) REVERT: B 601 MET cc_start: 0.8169 (tpp) cc_final: 0.7728 (tpp) REVERT: B 626 ARG cc_start: 0.7414 (ttt-90) cc_final: 0.6665 (tpt90) REVERT: B 743 SER cc_start: 0.8242 (OUTLIER) cc_final: 0.7722 (p) REVERT: B 809 TRP cc_start: 0.8281 (OUTLIER) cc_final: 0.8025 (t60) REVERT: B 1071 MET cc_start: 0.7454 (tpp) cc_final: 0.6993 (tpp) outliers start: 29 outliers final: 20 residues processed: 192 average time/residue: 0.0841 time to fit residues: 26.8201 Evaluate side-chains 181 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 423 HIS Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 627 TYR Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 809 TRP Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 800 MET Chi-restraints excluded: chain B residue 809 TRP Chi-restraints excluded: chain B residue 1081 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 160 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4205 r_free = 0.4205 target = 0.152626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.114028 restraints weight = 18325.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.119736 restraints weight = 9059.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.123820 restraints weight = 5810.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.126542 restraints weight = 4325.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.128416 restraints weight = 3541.860| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13464 Z= 0.130 Angle : 0.616 9.405 18340 Z= 0.306 Chirality : 0.045 0.363 2178 Planarity : 0.004 0.061 2266 Dihedral : 4.180 34.921 1818 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.47 % Favored : 96.42 % Rotamer: Outliers : 1.76 % Allowed : 19.69 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.21), residues: 1702 helix: 1.98 (0.17), residues: 926 sheet: -1.32 (0.49), residues: 100 loop : -0.96 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 917 TYR 0.016 0.001 TYR A 202 PHE 0.020 0.001 PHE B 728 TRP 0.037 0.001 TRP B 813 HIS 0.007 0.001 HIS B 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (13450) covalent geometry : angle 0.60842 / 0.30 (18304) SS BOND : bond 0.00638 / 0.38 ( 6) SS BOND : angle 1.89846 / 0.98 ( 12) hydrogen bonds : bond 0.04438 / 2.95 ( 786) hydrogen bonds : angle 4.30304 / 3.15 ( 2262) link_BETA1-4 : bond 0.00688 / 0.41 ( 4) link_BETA1-4 : angle 2.90913 / 1.69 ( 12) link_NAG-ASN : bond 0.00162 / 0.10 ( 4) link_NAG-ASN : angle 1.76041 / 1.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.604 Fit side-chains REVERT: A 181 MET cc_start: 0.8650 (tpt) cc_final: 0.8429 (tpp) REVERT: A 280 LEU cc_start: 0.8198 (pp) cc_final: 0.7914 (pp) REVERT: A 601 MET cc_start: 0.8140 (tpp) cc_final: 0.7738 (tpp) REVERT: A 1071 MET cc_start: 0.7518 (tpp) cc_final: 0.6987 (tpp) REVERT: B 263 MET cc_start: 0.7038 (tpp) cc_final: 0.6618 (tpp) REVERT: B 280 LEU cc_start: 0.8109 (pp) cc_final: 0.7828 (pp) REVERT: B 471 LEU cc_start: 0.8688 (mm) cc_final: 0.7422 (tp) REVERT: B 597 MET cc_start: 0.8028 (tpp) cc_final: 0.7725 (tpp) REVERT: B 601 MET cc_start: 0.8108 (tpp) cc_final: 0.7694 (tpp) REVERT: B 626 ARG cc_start: 0.7426 (ttt-90) cc_final: 0.6656 (tpt90) REVERT: B 1071 MET cc_start: 0.7503 (tpp) cc_final: 0.7164 (tpp) outliers start: 24 outliers final: 19 residues processed: 186 average time/residue: 0.0720 time to fit residues: 22.5626 Evaluate side-chains 181 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 423 HIS Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 627 TYR Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 800 MET Chi-restraints excluded: chain B residue 1081 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 114 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 141 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 58 optimal weight: 0.0270 chunk 127 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.4232 r_free = 0.4232 target = 0.155431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.116700 restraints weight = 18139.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.122612 restraints weight = 8940.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.126692 restraints weight = 5699.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.129496 restraints weight = 4231.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.131435 restraints weight = 3447.528| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13464 Z= 0.119 Angle : 0.607 8.507 18340 Z= 0.300 Chirality : 0.044 0.260 2178 Planarity : 0.004 0.059 2266 Dihedral : 4.039 30.207 1818 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.35 % Favored : 96.53 % Rotamer: Outliers : 1.24 % Allowed : 20.42 % Favored : 78.33 % 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: 1.08 (0.21), residues: 1702 helix: 2.01 (0.17), residues: 934 sheet: -1.09 (0.50), residues: 100 loop : -0.88 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 917 TYR 0.015 0.001 TYR A 202 PHE 0.021 0.001 PHE B 728 TRP 0.046 0.002 TRP A 813 HIS 0.007 0.001 HIS B 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (13450) covalent geometry : angle 0.59965 / 0.30 (18304) SS BOND : bond 0.00599 / 0.36 ( 6) SS BOND : angle 1.75650 / 0.90 ( 12) hydrogen bonds : bond 0.04216 / 2.81 ( 786) hydrogen bonds : angle 4.22406 / 3.10 ( 2262) link_BETA1-4 : bond 0.00676 / 0.41 ( 4) link_BETA1-4 : angle 2.79677 / 1.63 ( 12) link_NAG-ASN : bond 0.00149 / 0.09 ( 4) link_NAG-ASN : angle 1.71422 / 1.09 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.353 Fit side-chains REVERT: A 181 MET cc_start: 0.8623 (tpt) cc_final: 0.8382 (tpp) REVERT: A 238 GLU cc_start: 0.7047 (tp30) cc_final: 0.6763 (tt0) REVERT: A 280 LEU cc_start: 0.8198 (pp) cc_final: 0.7920 (pp) REVERT: A 471 LEU cc_start: 0.8616 (mm) cc_final: 0.7424 (tp) REVERT: A 601 MET cc_start: 0.8114 (tpp) cc_final: 0.7766 (tpp) REVERT: B 238 GLU cc_start: 0.7163 (tp30) cc_final: 0.6926 (tt0) REVERT: B 263 MET cc_start: 0.7061 (tpp) cc_final: 0.6642 (tpp) REVERT: B 280 LEU cc_start: 0.8108 (pp) cc_final: 0.7846 (pp) REVERT: B 471 LEU cc_start: 0.8652 (mm) cc_final: 0.7412 (tp) REVERT: B 601 MET cc_start: 0.8019 (tpp) cc_final: 0.7574 (tpp) REVERT: B 626 ARG cc_start: 0.7463 (ttt-90) cc_final: 0.6813 (tpt90) REVERT: B 1071 MET cc_start: 0.7700 (tpp) cc_final: 0.7355 (tpp) REVERT: B 1081 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6411 (mp) outliers start: 17 outliers final: 16 residues processed: 178 average time/residue: 0.0754 time to fit residues: 22.3148 Evaluate side-chains 172 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 HIS Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 627 TYR Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 800 MET Chi-restraints excluded: chain B residue 1081 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 88 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.4236 r_free = 0.4236 target = 0.155759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.117706 restraints weight = 17875.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.123179 restraints weight = 9186.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.127179 restraints weight = 5978.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.129815 restraints weight = 4457.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.131181 restraints weight = 3648.279| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13464 Z= 0.132 Angle : 0.616 8.729 18340 Z= 0.305 Chirality : 0.044 0.262 2178 Planarity : 0.004 0.055 2266 Dihedral : 4.040 28.924 1818 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.41 % Favored : 96.47 % Rotamer: Outliers : 1.46 % Allowed : 20.13 % Favored : 78.40 % 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: 1.10 (0.21), residues: 1702 helix: 2.02 (0.17), residues: 934 sheet: -1.17 (0.49), residues: 100 loop : -0.85 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 917 TYR 0.015 0.001 TYR A 202 PHE 0.020 0.001 PHE B 728 TRP 0.044 0.002 TRP A 813 HIS 0.006 0.001 HIS B 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (13450) covalent geometry : angle 0.60883 / 0.30 (18304) SS BOND : bond 0.00651 / 0.40 ( 6) SS BOND : angle 1.76680 / 0.93 ( 12) hydrogen bonds : bond 0.04263 / 2.84 ( 786) hydrogen bonds : angle 4.23468 / 3.10 ( 2262) link_BETA1-4 : bond 0.00693 / 0.42 ( 4) link_BETA1-4 : angle 2.82651 / 1.64 ( 12) link_NAG-ASN : bond 0.00116 / 0.06 ( 4) link_NAG-ASN : angle 1.66648 / 1.07 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2349.27 seconds wall clock time: 41 minutes 10.66 seconds (2470.66 seconds total)