Starting phenix.real_space_refine on Sun Oct 25 06:07:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m4c_63622/10_2026/9m4c_63622.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m4c_63622/10_2026/9m4c_63622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m4c_63622/10_2026/9m4c_63622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m4c_63622/10_2026/9m4c_63622.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m4c_63622/10_2026/9m4c_63622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m4c_63622/10_2026/9m4c_63622.map" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 48 5.16 5 C 9870 2.51 5 N 2691 2.21 5 O 2978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15587 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5196 Classifications: {'peptide': 673} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 644} Chain: "C" Number of atoms: 5195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5195 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 28, 'TRANS': 644} Chain: "A" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5196 Classifications: {'peptide': 673} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 644} Time building chain proxies: 3.13, per 1000 atoms: 0.20 Number of scatterers: 15587 At special positions: 0 Unit cell: (107.226, 142.968, 152.329, 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 48 16.00 O 2978 8.00 N 2691 7.00 C 9870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 665.4 milliseconds 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3576 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 15 sheets defined 16.1% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'B' and resid 148 through 153 Processing helix chain 'B' and resid 154 through 169 removed outlier: 4.185A pdb=" N LEU B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 211 through 217 removed outlier: 3.535A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 251 through 265 Processing helix chain 'B' and resid 294 through 300 removed outlier: 3.914A pdb=" N ASN B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 364 Processing helix chain 'B' and resid 441 through 445 removed outlier: 3.557A pdb=" N TYR B 444 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET B 445 " --> pdb=" O ALA B 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 441 through 445' Processing helix chain 'B' and resid 453 through 457 Processing helix chain 'B' and resid 476 through 493 removed outlier: 3.526A pdb=" N LEU B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 500 removed outlier: 3.915A pdb=" N ARG B 500 " --> pdb=" O ALA B 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 168 Proline residue: C 157 - end of helix removed outlier: 3.726A pdb=" N ARG C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 removed outlier: 3.637A pdb=" N VAL C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 187 " --> pdb=" O ALA C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 182 through 187' Processing helix chain 'C' and resid 208 through 217 Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'C' and resid 251 through 266 Processing helix chain 'C' and resid 294 through 300 Processing helix chain 'C' and resid 361 through 364 Processing helix chain 'C' and resid 441 through 445 removed outlier: 3.565A pdb=" N TYR C 444 " --> pdb=" O GLY C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'C' and resid 476 through 493 removed outlier: 3.912A pdb=" N LEU C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 500 removed outlier: 3.573A pdb=" N ARG C 500 " --> pdb=" O ALA C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 584 Processing helix chain 'A' and resid 149 through 162 Proline residue: A 157 - end of helix removed outlier: 3.531A pdb=" N THR A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 251 through 266 Processing helix chain 'A' and resid 294 through 300 Processing helix chain 'A' and resid 361 through 364 Processing helix chain 'A' and resid 453 through 457 Processing helix chain 'A' and resid 476 through 493 removed outlier: 3.894A pdb=" N LEU A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 501 through 505 Processing helix chain 'A' and resid 580 through 584 removed outlier: 3.585A pdb=" N SER A 583 " --> pdb=" O ARG A 580 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 190 through 193 Processing sheet with id=AA2, first strand: chain 'B' and resid 269 through 271 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 269 through 271 current: chain 'B' and resid 313 through 320 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 313 through 320 current: chain 'B' and resid 393 through 429 removed outlier: 6.783A pdb=" N SER B 462 " --> pdb=" O GLN B 413 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE B 415 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N TYR B 464 " --> pdb=" O ILE B 415 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ARG B 417 " --> pdb=" O TYR B 464 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 419 " --> pdb=" O TYR B 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 632 through 636 removed outlier: 6.359A pdb=" N VAL B 632 " --> pdb=" O ILE C 640 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLU C 642 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ALA B 634 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N TRP C 644 " --> pdb=" O ALA B 634 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLY B 636 " --> pdb=" O TRP C 644 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLN C 639 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ARG A 657 " --> pdb=" O GLN C 639 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE C 641 " --> pdb=" O ARG A 657 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N TRP A 659 " --> pdb=" O PHE C 641 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER C 643 " --> pdb=" O TRP A 659 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASP A 658 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N TYR A 668 " --> pdb=" O ASP A 658 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ASN A 660 " --> pdb=" O GLN A 666 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLN A 666 " --> pdb=" O ASN A 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 632 through 634 removed outlier: 6.904A pdb=" N GLN B 639 " --> pdb=" O ALA C 655 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ARG C 657 " --> pdb=" O GLN B 639 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE B 641 " --> pdb=" O ARG C 657 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N TRP C 659 " --> pdb=" O PHE B 641 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SER B 643 " --> pdb=" O TRP C 659 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG C 652 " --> pdb=" O ARG C 673 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG C 673 " --> pdb=" O ARG C 652 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU C 654 " --> pdb=" O ASP C 671 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASP C 671 " --> pdb=" O LEU C 654 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU C 656 " --> pdb=" O ARG C 669 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA C 677 " --> pdb=" O ARG A 683 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 632 through 636 removed outlier: 6.396A pdb=" N VAL C 632 " --> pdb=" O ILE A 640 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N GLU A 642 " --> pdb=" O VAL C 632 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA C 634 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N TRP A 644 " --> pdb=" O ALA C 634 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLY C 636 " --> pdb=" O TRP A 644 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU B 653 " --> pdb=" O GLN A 639 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N PHE A 641 " --> pdb=" O LEU B 653 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA B 655 " --> pdb=" O PHE A 641 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N SER A 643 " --> pdb=" O ALA B 655 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ARG B 657 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP B 658 " --> pdb=" O TYR B 668 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N TYR B 668 " --> pdb=" O ASP B 658 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASN B 660 " --> pdb=" O GLN B 666 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N GLN B 666 " --> pdb=" O ASN B 660 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA B 677 " --> pdb=" O ARG C 683 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 693 through 698 removed outlier: 6.882A pdb=" N ARG B 726 " --> pdb=" O ASP B 815 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP B 815 " --> pdb=" O ARG B 726 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN B 728 " --> pdb=" O GLY B 813 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY B 813 " --> pdb=" O ASN B 728 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR B 730 " --> pdb=" O ILE B 811 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE B 811 " --> pdb=" O TYR B 730 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLU B 732 " --> pdb=" O VAL B 809 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL B 809 " --> pdb=" O GLU B 732 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN B 734 " --> pdb=" O ASN B 807 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 707 through 708 removed outlier: 7.502A pdb=" N LEU B 744 " --> pdb=" O LEU B 789 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU B 789 " --> pdb=" O LEU B 744 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 746 " --> pdb=" O VAL B 787 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 190 through 193 Processing sheet with id=AA9, first strand: chain 'C' and resid 269 through 271 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 269 through 271 current: chain 'C' and resid 313 through 320 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 313 through 320 current: chain 'C' and resid 393 through 416 removed outlier: 7.239A pdb=" N VAL C 420 " --> pdb=" O ASP C 396 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU C 398 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N THR C 422 " --> pdb=" O GLU C 398 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA C 400 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N TYR C 424 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N CYS C 402 " --> pdb=" O TYR C 424 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N GLY C 426 " --> pdb=" O CYS C 402 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ILE C 404 " --> pdb=" O GLY C 426 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL C 428 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLY C 406 " --> pdb=" O VAL C 428 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 693 through 698 removed outlier: 6.298A pdb=" N SER C 735 " --> pdb=" O ASN C 806 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASN C 806 " --> pdb=" O SER C 735 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR C 737 " --> pdb=" O THR C 804 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR C 804 " --> pdb=" O THR C 737 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 707 through 708 removed outlier: 7.591A pdb=" N LEU C 744 " --> pdb=" O LEU C 789 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU C 789 " --> pdb=" O LEU C 744 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 746 " --> pdb=" O VAL C 787 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 189 through 193 Processing sheet with id=AB4, first strand: chain 'A' and resid 269 through 271 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 269 through 271 current: chain 'A' and resid 313 through 320 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 313 through 320 current: chain 'A' and resid 393 through 416 removed outlier: 7.203A pdb=" N VAL A 420 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU A 398 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR A 422 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA A 400 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N TYR A 424 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N CYS A 402 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N GLY A 426 " --> pdb=" O CYS A 402 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ILE A 404 " --> pdb=" O GLY A 426 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL A 428 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLY A 406 " --> pdb=" O VAL A 428 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 693 through 698 removed outlier: 3.540A pdb=" N LYS A 713 " --> pdb=" O GLU A 732 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG A 726 " --> pdb=" O ASP A 815 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASP A 815 " --> pdb=" O ARG A 726 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN A 728 " --> pdb=" O GLY A 813 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY A 813 " --> pdb=" O ASN A 728 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N TYR A 730 " --> pdb=" O ILE A 811 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 811 " --> pdb=" O TYR A 730 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLU A 732 " --> pdb=" O VAL A 809 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL A 809 " --> pdb=" O GLU A 732 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASN A 734 " --> pdb=" O ASN A 807 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 707 through 708 removed outlier: 7.404A pdb=" N LEU A 744 " --> pdb=" O LEU A 789 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU A 789 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 746 " --> pdb=" O VAL A 787 " (cutoff:3.500A) 317 hydrogen bonds defined for protein. 768 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: 2.47 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5075 1.34 - 1.46: 2656 1.46 - 1.57: 8129 1.57 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 15941 Sorted by residual: bond pdb=" CA GLY B 813 " pdb=" C GLY B 813 " ideal model delta sigma weight residual 1.520 1.511 0.010 7.30e-03 1.88e+04 1.72e+00 bond pdb=" CB VAL C 774 " pdb=" CG1 VAL C 774 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.07e+00 bond pdb=" CB LYS A 501 " pdb=" CG LYS A 501 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.31e-01 bond pdb=" CG PRO C 268 " pdb=" CD PRO C 268 " ideal model delta sigma weight residual 1.503 1.472 0.031 3.40e-02 8.65e+02 8.51e-01 bond pdb=" CG LEU C 776 " pdb=" CD2 LEU C 776 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.23e-01 ... (remaining 15936 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 20717 1.26 - 2.52: 833 2.52 - 3.79: 146 3.79 - 5.05: 23 5.05 - 6.31: 14 Bond angle restraints: 21733 Sorted by residual: angle pdb=" N PRO C 446 " pdb=" CA PRO C 446 " pdb=" C PRO C 446 " ideal model delta sigma weight residual 110.70 114.61 -3.91 1.22e+00 6.72e-01 1.03e+01 angle pdb=" C THR C 647 " pdb=" N ASN C 648 " pdb=" CA ASN C 648 " ideal model delta sigma weight residual 121.54 127.59 -6.05 1.91e+00 2.74e-01 1.00e+01 angle pdb=" C ILE B 812 " pdb=" N GLY B 813 " pdb=" CA GLY B 813 " ideal model delta sigma weight residual 122.73 119.87 2.86 9.30e-01 1.16e+00 9.43e+00 angle pdb=" N PRO A 446 " pdb=" CA PRO A 446 " pdb=" C PRO A 446 " ideal model delta sigma weight residual 110.70 114.37 -3.67 1.22e+00 6.72e-01 9.05e+00 angle pdb=" CA GLY B 813 " pdb=" C GLY B 813 " pdb=" N ILE B 814 " ideal model delta sigma weight residual 115.43 118.98 -3.55 1.18e+00 7.18e-01 9.03e+00 ... (remaining 21728 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 8476 17.89 - 35.78: 650 35.78 - 53.68: 103 53.68 - 71.57: 26 71.57 - 89.46: 14 Dihedral angle restraints: 9269 sinusoidal: 3554 harmonic: 5715 Sorted by residual: dihedral pdb=" CA VAL C 605 " pdb=" C VAL C 605 " pdb=" N TRP C 606 " pdb=" CA TRP C 606 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA MET B 445 " pdb=" C MET B 445 " pdb=" N PRO B 446 " pdb=" CA PRO B 446 " ideal model delta harmonic sigma weight residual 180.00 -161.01 -18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA TYR B 685 " pdb=" C TYR B 685 " pdb=" N THR B 686 " pdb=" CA THR B 686 " ideal model delta harmonic sigma weight residual 180.00 -161.06 -18.94 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 9266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1549 0.039 - 0.077: 554 0.077 - 0.116: 262 0.116 - 0.154: 60 0.154 - 0.193: 5 Chirality restraints: 2430 Sorted by residual: chirality pdb=" CA ASN B 266 " pdb=" N ASN B 266 " pdb=" C ASN B 266 " pdb=" CB ASN B 266 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" CB ILE B 736 " pdb=" CA ILE B 736 " pdb=" CG1 ILE B 736 " pdb=" CG2 ILE B 736 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA ASN C 648 " pdb=" N ASN C 648 " pdb=" C ASN C 648 " pdb=" CB ASN C 648 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.76e-01 ... (remaining 2427 not shown) Planarity restraints: 2789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 446 " 0.055 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO B 447 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 447 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 447 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 446 " -0.042 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO A 447 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 447 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 447 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 446 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO C 447 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 447 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 447 " -0.029 5.00e-02 4.00e+02 ... (remaining 2786 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1374 2.75 - 3.29: 14349 3.29 - 3.82: 25692 3.82 - 4.36: 32077 4.36 - 4.90: 54669 Nonbonded interactions: 128161 Sorted by model distance: nonbonded pdb=" O LYS B 791 " pdb=" OG SER B 794 " model vdw 2.211 3.040 nonbonded pdb=" NH1 ARG A 319 " pdb=" O LEU A 320 " model vdw 2.219 3.120 nonbonded pdb=" OG SER B 503 " pdb=" OH TYR B 510 " model vdw 2.220 3.040 nonbonded pdb=" O THR B 220 " pdb=" OG SER B 223 " model vdw 2.247 3.040 nonbonded pdb=" OD1 ASN A 194 " pdb=" N ASP A 198 " model vdw 2.263 3.120 ... (remaining 128156 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 148 through 819 or (resid 820 and (name N or name CA or na \ me C or name O or name CB or name OG )))) selection = (chain 'B' and (resid 148 through 819 or (resid 820 and (name N or name CA or na \ me C or name O or name CB or name OG )))) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.120 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:9.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 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 : 0.004 0.038 15941 Z= 0.158 Angle : 0.601 6.311 21733 Z= 0.331 Chirality : 0.049 0.193 2430 Planarity : 0.005 0.083 2789 Dihedral : 13.590 89.462 5693 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: -1.11 (0.19), residues: 2013 helix: -0.24 (0.35), residues: 244 sheet: -0.33 (0.23), residues: 567 loop : -1.04 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 175 TYR 0.021 0.002 TYR A 356 PHE 0.010 0.001 PHE C 254 TRP 0.011 0.001 TRP B 599 HIS 0.006 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (15941) covalent geometry : angle 0.60069 / 0.33 (21733) hydrogen bonds : bond 0.18011 / 12.69 ( 317) hydrogen bonds : angle 7.09658 / 4.90 ( 768) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.586 Fit side-chains REVERT: B 501 LYS cc_start: 0.7764 (mmtp) cc_final: 0.7540 (mmmm) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.5658 time to fit residues: 109.6161 Evaluate side-chains 135 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 77, 122] chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.3980 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 782 GLN C 511 GLN C 705 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.120188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.089812 restraints weight = 21566.803| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.58 r_work: 0.2993 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15941 Z= 0.112 Angle : 0.529 7.086 21733 Z= 0.287 Chirality : 0.047 0.157 2430 Planarity : 0.005 0.073 2789 Dihedral : 4.814 35.351 2264 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.21 % Allowed : 5.65 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.19), residues: 2013 helix: 0.19 (0.35), residues: 256 sheet: -0.27 (0.22), residues: 585 loop : -1.01 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.012 0.001 TYR C 356 PHE 0.008 0.001 PHE C 254 TRP 0.012 0.001 TRP C 454 HIS 0.005 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (15941) covalent geometry : angle 0.52868 / 0.29 (21733) hydrogen bonds : bond 0.04427 / 2.98 ( 317) hydrogen bonds : angle 5.60360 / 3.87 ( 768) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.521 Fit side-chains REVERT: B 465 GLU cc_start: 0.7600 (pp20) cc_final: 0.7359 (pp20) REVERT: B 501 LYS cc_start: 0.7907 (mmtp) cc_final: 0.7647 (mmmm) REVERT: B 786 VAL cc_start: 0.8255 (t) cc_final: 0.7943 (m) REVERT: C 185 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: C 241 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7615 (mtpp) REVERT: C 257 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8757 (mttm) REVERT: C 296 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: C 764 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7914 (pptt) outliers start: 20 outliers final: 7 residues processed: 154 average time/residue: 0.5821 time to fit residues: 99.4830 Evaluate side-chains 143 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 808 VAL Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 815 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: [110, 67, 151, 92, 138, 16, 194, 83, 23, 137, 133] chunk 110 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 151 optimal weight: 10.0000 chunk 92 optimal weight: 0.0030 chunk 138 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 194 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 137 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 overall best weight: 2.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 ASN B 782 GLN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.119554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.089148 restraints weight = 21671.601| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.59 r_work: 0.2983 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15941 Z= 0.124 Angle : 0.527 7.225 21733 Z= 0.288 Chirality : 0.048 0.158 2430 Planarity : 0.005 0.070 2789 Dihedral : 4.785 35.488 2264 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.76 % Allowed : 7.41 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.19), residues: 2013 helix: 0.31 (0.35), residues: 255 sheet: -0.31 (0.22), residues: 588 loop : -1.02 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 580 TYR 0.017 0.001 TYR C 730 PHE 0.008 0.001 PHE C 254 TRP 0.010 0.001 TRP C 454 HIS 0.006 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (15941) covalent geometry : angle 0.52740 / 0.29 (21733) hydrogen bonds : bond 0.04299 / 2.87 ( 317) hydrogen bonds : angle 5.37100 / 3.71 ( 768) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.578 Fit side-chains REVERT: B 465 GLU cc_start: 0.7634 (pp20) cc_final: 0.7384 (pp20) REVERT: B 501 LYS cc_start: 0.7911 (mmtp) cc_final: 0.7623 (mmmm) REVERT: B 504 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7594 (pm20) REVERT: B 786 VAL cc_start: 0.8263 (t) cc_final: 0.7951 (m) REVERT: C 185 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7147 (mt-10) REVERT: C 241 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7617 (mtpp) REVERT: C 257 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8752 (mttm) REVERT: C 296 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7838 (mp0) REVERT: C 307 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8195 (ttm110) REVERT: C 764 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7857 (pptt) outliers start: 29 outliers final: 10 residues processed: 155 average time/residue: 0.6123 time to fit residues: 104.8227 Evaluate side-chains 152 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 808 VAL Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 815 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: [185, 177, 132, 61, 150, 134, 98, 31, 176, 45, 36] chunk 185 optimal weight: 0.9990 chunk 177 optimal weight: 0.0170 chunk 132 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 overall best weight: 2.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 ASN B 782 GLN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.088601 restraints weight = 21560.430| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.58 r_work: 0.2973 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15941 Z= 0.145 Angle : 0.550 7.558 21733 Z= 0.300 Chirality : 0.048 0.166 2430 Planarity : 0.005 0.068 2789 Dihedral : 4.872 34.659 2264 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.13 % Allowed : 9.59 % Favored : 88.28 % 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: -0.98 (0.19), residues: 2013 helix: 0.36 (0.35), residues: 255 sheet: -0.30 (0.22), residues: 586 loop : -1.06 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 652 TYR 0.016 0.001 TYR C 730 PHE 0.009 0.001 PHE C 254 TRP 0.010 0.001 TRP C 454 HIS 0.006 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (15941) covalent geometry : angle 0.54952 / 0.30 (21733) hydrogen bonds : bond 0.04495 / 2.98 ( 317) hydrogen bonds : angle 5.34571 / 3.70 ( 768) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.596 Fit side-chains REVERT: B 189 MET cc_start: 0.7852 (tpp) cc_final: 0.7526 (mmp) REVERT: B 465 GLU cc_start: 0.7647 (pp20) cc_final: 0.7424 (pp20) REVERT: B 501 LYS cc_start: 0.7900 (mmtp) cc_final: 0.7607 (mmmm) REVERT: B 504 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7557 (pm20) REVERT: B 786 VAL cc_start: 0.8290 (t) cc_final: 0.7969 (m) REVERT: C 185 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7170 (mt-10) REVERT: C 241 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7614 (mtpp) REVERT: C 257 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8756 (mttm) REVERT: C 296 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: C 307 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8222 (ttm110) REVERT: C 764 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7866 (pptt) outliers start: 35 outliers final: 15 residues processed: 154 average time/residue: 0.6122 time to fit residues: 104.2453 Evaluate side-chains 152 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 725 MET Chi-restraints excluded: chain C residue 727 CYS Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 808 VAL Chi-restraints excluded: chain A residue 679 MET Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 815 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: [102, 191, 112, 170, 21, 148, 186, 128, 61, 117, 171] chunk 102 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 chunk 186 optimal weight: 0.0060 chunk 128 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 171 optimal weight: 0.7980 overall best weight: 3.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 ASN B 782 GLN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.117950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.087654 restraints weight = 21592.589| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.59 r_work: 0.2955 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15941 Z= 0.179 Angle : 0.593 8.081 21733 Z= 0.324 Chirality : 0.050 0.173 2430 Planarity : 0.005 0.068 2789 Dihedral : 5.084 32.350 2264 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.43 % Allowed : 11.05 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.19), residues: 2013 helix: 0.21 (0.34), residues: 259 sheet: -0.33 (0.22), residues: 584 loop : -1.16 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 652 TYR 0.018 0.002 TYR C 730 PHE 0.011 0.001 PHE C 254 TRP 0.011 0.002 TRP A 599 HIS 0.007 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (15941) covalent geometry : angle 0.59262 / 0.32 (21733) hydrogen bonds : bond 0.04939 / 3.25 ( 317) hydrogen bonds : angle 5.42898 / 3.76 ( 768) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.626 Fit side-chains REVERT: B 501 LYS cc_start: 0.7901 (mmtp) cc_final: 0.7620 (mmmm) REVERT: C 185 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7210 (mt-10) REVERT: C 241 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7657 (mtpp) REVERT: C 257 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8757 (mttm) REVERT: C 296 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: C 307 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8241 (ttm110) REVERT: A 189 MET cc_start: 0.7889 (mmm) cc_final: 0.7064 (mtm) outliers start: 40 outliers final: 20 residues processed: 157 average time/residue: 0.5834 time to fit residues: 101.7245 Evaluate side-chains 157 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 725 MET Chi-restraints excluded: chain C residue 727 CYS Chi-restraints excluded: chain C residue 808 VAL Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 679 MET Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 713 LYS Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 815 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: [179, 86, 128, 36, 109, 54, 100, 174, 196, 76, 194] chunk 179 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 196 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 194 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 ASN B 782 GLN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.117990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.087706 restraints weight = 21619.283| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.60 r_work: 0.2956 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15941 Z= 0.173 Angle : 0.587 8.089 21733 Z= 0.321 Chirality : 0.050 0.175 2430 Planarity : 0.005 0.067 2789 Dihedral : 5.083 32.183 2264 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.31 % Allowed : 11.66 % Favored : 86.04 % 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: -1.13 (0.19), residues: 2013 helix: 0.21 (0.34), residues: 259 sheet: -0.35 (0.22), residues: 584 loop : -1.18 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 652 TYR 0.017 0.002 TYR C 730 PHE 0.010 0.001 PHE C 254 TRP 0.011 0.002 TRP A 718 HIS 0.006 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (15941) covalent geometry : angle 0.58748 / 0.32 (21733) hydrogen bonds : bond 0.04824 / 3.18 ( 317) hydrogen bonds : angle 5.39830 / 3.73 ( 768) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.604 Fit side-chains REVERT: B 337 ARG cc_start: 0.8741 (ttm-80) cc_final: 0.8458 (ttt180) REVERT: B 501 LYS cc_start: 0.7908 (mmtp) cc_final: 0.7621 (mmmm) REVERT: C 185 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7214 (mt-10) REVERT: C 198 ASP cc_start: 0.7181 (m-30) cc_final: 0.6530 (m-30) REVERT: C 241 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7656 (mtpp) REVERT: C 257 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8765 (mttm) REVERT: C 296 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: C 307 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8233 (ttm110) outliers start: 38 outliers final: 27 residues processed: 158 average time/residue: 0.6136 time to fit residues: 107.3792 Evaluate side-chains 167 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 725 MET Chi-restraints excluded: chain C residue 727 CYS Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 808 VAL Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 679 MET Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 713 LYS Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 815 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: [133, 49, 52, 69, 56, 35, 95, 25, 113, 89, 165] chunk 133 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 ASN B 782 GLN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.116914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.086810 restraints weight = 21603.812| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.58 r_work: 0.2939 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 15941 Z= 0.238 Angle : 0.655 8.423 21733 Z= 0.359 Chirality : 0.052 0.188 2430 Planarity : 0.006 0.069 2789 Dihedral : 5.328 29.779 2264 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.61 % Allowed : 12.26 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.18), residues: 2013 helix: -0.03 (0.34), residues: 264 sheet: -0.45 (0.22), residues: 554 loop : -1.25 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 652 TYR 0.019 0.002 TYR C 730 PHE 0.012 0.002 PHE C 254 TRP 0.013 0.002 TRP A 718 HIS 0.007 0.002 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.24 (15941) covalent geometry : angle 0.65498 / 0.36 (21733) hydrogen bonds : bond 0.05532 / 3.63 ( 317) hydrogen bonds : angle 5.53502 / 3.82 ( 768) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 0.502 Fit side-chains REVERT: B 296 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7592 (tt0) REVERT: B 337 ARG cc_start: 0.8755 (ttm-80) cc_final: 0.8477 (ttt180) REVERT: B 501 LYS cc_start: 0.7907 (mmtp) cc_final: 0.7630 (mmmm) REVERT: C 198 ASP cc_start: 0.7221 (m-30) cc_final: 0.6777 (m-30) REVERT: C 241 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7658 (mtpp) REVERT: C 257 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8756 (mttm) REVERT: C 296 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: C 307 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8240 (ttm110) REVERT: A 189 MET cc_start: 0.7858 (mmm) cc_final: 0.6961 (mtm) outliers start: 43 outliers final: 28 residues processed: 165 average time/residue: 0.5913 time to fit residues: 108.2057 Evaluate side-chains 172 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 603 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 725 MET Chi-restraints excluded: chain C residue 727 CYS Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 808 VAL Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 679 MET Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 713 LYS Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 815 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: [113, 52, 88, 46, 181, 190, 99, 104, 177, 44, 67] chunk 113 optimal weight: 0.0470 chunk 52 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 181 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 0.0050 chunk 177 optimal weight: 0.0670 chunk 44 optimal weight: 0.6980 chunk 67 optimal weight: 9.9990 overall best weight: 0.2630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 782 GLN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.122472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.092337 restraints weight = 21597.844| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.60 r_work: 0.3034 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15941 Z= 0.085 Angle : 0.471 6.376 21733 Z= 0.255 Chirality : 0.045 0.159 2430 Planarity : 0.004 0.066 2789 Dihedral : 4.425 37.256 2264 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.15 % Allowed : 13.78 % Favored : 85.06 % 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: -0.82 (0.19), residues: 2013 helix: 0.55 (0.35), residues: 254 sheet: -0.12 (0.23), residues: 566 loop : -1.01 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 580 TYR 0.016 0.001 TYR B 685 PHE 0.005 0.000 PHE C 254 TRP 0.012 0.001 TRP A 599 HIS 0.004 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00169 / 0.09 (15941) covalent geometry : angle 0.47111 / 0.26 (21733) hydrogen bonds : bond 0.02911 / 1.98 ( 317) hydrogen bonds : angle 5.04211 / 3.48 ( 768) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.643 Fit side-chains REVERT: B 189 MET cc_start: 0.7732 (tpp) cc_final: 0.7425 (mmp) REVERT: B 266 ASN cc_start: 0.7500 (p0) cc_final: 0.6868 (m-40) REVERT: B 450 ASP cc_start: 0.7381 (m-30) cc_final: 0.7156 (m-30) REVERT: B 501 LYS cc_start: 0.7918 (mmtp) cc_final: 0.7707 (mmmm) REVERT: B 786 VAL cc_start: 0.8287 (t) cc_final: 0.7975 (m) REVERT: C 198 ASP cc_start: 0.7144 (m-30) cc_final: 0.6503 (m-30) REVERT: C 241 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7586 (mtpp) REVERT: C 296 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: A 175 ARG cc_start: 0.6745 (mtm180) cc_final: 0.6539 (mtm180) REVERT: A 210 SER cc_start: 0.8469 (m) cc_final: 0.8042 (p) REVERT: A 738 LEU cc_start: 0.6404 (OUTLIER) cc_final: 0.6141 (mt) outliers start: 19 outliers final: 5 residues processed: 165 average time/residue: 0.5405 time to fit residues: 99.6059 Evaluate side-chains 148 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 808 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: [64, 141, 87, 109, 22, 91, 114, 153, 17, 62, 77] chunk 64 optimal weight: 9.9990 chunk 141 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 ASN B 782 GLN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 GLN A 752 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.120441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.091137 restraints weight = 21604.966| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.65 r_work: 0.3006 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15941 Z= 0.103 Angle : 0.500 6.498 21733 Z= 0.270 Chirality : 0.047 0.167 2430 Planarity : 0.004 0.065 2789 Dihedral : 4.486 35.791 2264 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.97 % Allowed : 14.57 % Favored : 84.46 % 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: -0.73 (0.19), residues: 2013 helix: 0.83 (0.36), residues: 244 sheet: -0.17 (0.22), residues: 600 loop : -0.93 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 580 TYR 0.016 0.001 TYR C 730 PHE 0.008 0.001 PHE C 254 TRP 0.011 0.001 TRP C 454 HIS 0.005 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (15941) covalent geometry : angle 0.49978 / 0.27 (21733) hydrogen bonds : bond 0.03618 / 2.40 ( 317) hydrogen bonds : angle 4.97979 / 3.44 ( 768) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.514 Fit side-chains REVERT: B 189 MET cc_start: 0.7767 (tpp) cc_final: 0.7461 (mmp) REVERT: B 266 ASN cc_start: 0.7734 (OUTLIER) cc_final: 0.7066 (m-40) REVERT: B 501 LYS cc_start: 0.7877 (mmtp) cc_final: 0.7650 (mmmm) REVERT: C 198 ASP cc_start: 0.7180 (m-30) cc_final: 0.6527 (m-30) REVERT: C 241 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7632 (mtpp) REVERT: C 296 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7776 (mp0) REVERT: A 210 SER cc_start: 0.8474 (m) cc_final: 0.8038 (p) REVERT: A 738 LEU cc_start: 0.6290 (OUTLIER) cc_final: 0.6000 (mt) outliers start: 16 outliers final: 8 residues processed: 154 average time/residue: 0.5671 time to fit residues: 97.3225 Evaluate side-chains 153 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 808 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: [16, 110, 14, 74, 60, 49, 162, 149, 120, 72, 5] chunk 16 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 120 optimal weight: 0.3980 chunk 72 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 ASN B 782 GLN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 GLN A 752 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.119938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.089722 restraints weight = 21325.357| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.59 r_work: 0.3000 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 15941 Z= 0.152 Angle : 0.722 59.196 21733 Z= 0.421 Chirality : 0.049 0.600 2430 Planarity : 0.004 0.065 2789 Dihedral : 4.501 35.767 2264 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.97 % Allowed : 14.69 % Favored : 84.34 % 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: -0.73 (0.19), residues: 2013 helix: 0.82 (0.36), residues: 244 sheet: -0.17 (0.22), residues: 600 loop : -0.93 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 307 TYR 0.016 0.001 TYR C 730 PHE 0.008 0.001 PHE C 254 TRP 0.011 0.001 TRP C 454 HIS 0.006 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (15941) covalent geometry : angle 0.72179 / 0.42 (21733) hydrogen bonds : bond 0.03643 / 2.42 ( 317) hydrogen bonds : angle 4.98774 / 3.44 ( 768) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.587 Fit side-chains REVERT: B 189 MET cc_start: 0.7766 (tpp) cc_final: 0.7467 (mmp) REVERT: B 501 LYS cc_start: 0.7883 (mmtp) cc_final: 0.7656 (mmmm) REVERT: C 198 ASP cc_start: 0.7184 (m-30) cc_final: 0.6530 (m-30) REVERT: C 241 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7631 (mtpp) REVERT: C 296 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: A 210 SER cc_start: 0.8483 (m) cc_final: 0.8048 (p) REVERT: A 738 LEU cc_start: 0.6288 (OUTLIER) cc_final: 0.5996 (mt) outliers start: 16 outliers final: 10 residues processed: 151 average time/residue: 0.5681 time to fit residues: 95.6110 Evaluate side-chains 152 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 808 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: [48, 40, 15, 12, 3, 137, 65, 42, 196, 5, 93] chunk 48 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 196 optimal weight: 8.9990 chunk 5 optimal weight: 0.5980 chunk 93 optimal weight: 10.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 782 GLN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 GLN A 752 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.120331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.091286 restraints weight = 21443.058| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.71 r_work: 0.2999 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 15941 Z= 0.152 Angle : 0.722 59.196 21733 Z= 0.421 Chirality : 0.049 0.600 2430 Planarity : 0.004 0.065 2789 Dihedral : 4.501 35.767 2264 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.85 % Allowed : 14.75 % Favored : 84.40 % 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: -0.73 (0.19), residues: 2013 helix: 0.82 (0.36), residues: 244 sheet: -0.17 (0.22), residues: 600 loop : -0.93 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 307 TYR 0.016 0.001 TYR C 730 PHE 0.008 0.001 PHE C 254 TRP 0.011 0.001 TRP C 454 HIS 0.006 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (15941) covalent geometry : angle 0.72179 / 0.42 (21733) hydrogen bonds : bond 0.03643 / 2.42 ( 317) hydrogen bonds : angle 4.98774 / 3.44 ( 768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5435.78 seconds wall clock time: 93 minutes 11.93 seconds (5591.93 seconds total)