Starting phenix.real_space_refine on Mon Aug 25 23:33:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9exr_50047/08_2025/9exr_50047.cif Found real_map, /net/cci-nas-00/data/ceres_data/9exr_50047/08_2025/9exr_50047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9exr_50047/08_2025/9exr_50047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9exr_50047/08_2025/9exr_50047.map" model { file = "/net/cci-nas-00/data/ceres_data/9exr_50047/08_2025/9exr_50047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9exr_50047/08_2025/9exr_50047.cif" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 104 5.16 5 C 20424 2.51 5 N 5376 2.21 5 O 6024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 149 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31952 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3966 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 492} Chain breaks: 3 Chain: "B" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3966 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 492} Chain breaks: 3 Chain: "C" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3966 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 492} Chain breaks: 3 Chain: "D" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3966 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 492} Chain breaks: 3 Chain: "E" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3966 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 492} Chain breaks: 3 Chain: "F" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3966 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 492} Chain breaks: 3 Chain: "G" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3966 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 492} Chain breaks: 3 Chain: "H" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3966 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 492} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.41, per 1000 atoms: 0.26 Number of scatterers: 31952 At special positions: 0 Unit cell: (161.403, 161.403, 140.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 104 16.00 P 16 15.00 Mg 8 11.99 O 6024 8.00 N 5376 7.00 C 20424 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: 3.00 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.2 microseconds 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7600 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 32 sheets defined 44.7% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 18 through 29 Processing helix chain 'A' and resid 29 through 51 Processing helix chain 'A' and resid 87 through 94 removed outlier: 3.821A pdb=" N ALA A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 107 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 208 through 219 removed outlier: 3.575A pdb=" N SER A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 260 removed outlier: 3.841A pdb=" N SER A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 451 Processing helix chain 'A' and resid 457 through 465 removed outlier: 4.132A pdb=" N LEU A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 Processing helix chain 'A' and resid 504 through 521 removed outlier: 3.687A pdb=" N PHE A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 553 Processing helix chain 'A' and resid 569 through 575 Processing helix chain 'A' and resid 581 through 587 Processing helix chain 'A' and resid 615 through 620 Processing helix chain 'A' and resid 622 through 633 removed outlier: 4.258A pdb=" N GLU A 626 " --> pdb=" O HIS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 656 Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 672 through 686 removed outlier: 3.573A pdb=" N SER A 686 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 29 through 51 Processing helix chain 'B' and resid 87 through 94 removed outlier: 3.821A pdb=" N ALA B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 94 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 107 Processing helix chain 'B' and resid 120 through 128 Processing helix chain 'B' and resid 208 through 219 removed outlier: 3.577A pdb=" N SER B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 260 removed outlier: 3.840A pdb=" N SER B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 451 Processing helix chain 'B' and resid 457 through 465 removed outlier: 4.132A pdb=" N LEU B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'B' and resid 504 through 521 removed outlier: 3.688A pdb=" N PHE B 519 " --> pdb=" O THR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 553 Processing helix chain 'B' and resid 569 through 575 Processing helix chain 'B' and resid 581 through 587 Processing helix chain 'B' and resid 615 through 620 Processing helix chain 'B' and resid 622 through 633 removed outlier: 4.259A pdb=" N GLU B 626 " --> pdb=" O HIS B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 656 Processing helix chain 'B' and resid 657 through 659 No H-bonds generated for 'chain 'B' and resid 657 through 659' Processing helix chain 'B' and resid 672 through 686 removed outlier: 3.573A pdb=" N SER B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 29 Processing helix chain 'C' and resid 29 through 51 Processing helix chain 'C' and resid 87 through 94 removed outlier: 3.822A pdb=" N ALA C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN C 94 " --> pdb=" O THR C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 107 Processing helix chain 'C' and resid 120 through 128 Processing helix chain 'C' and resid 208 through 219 removed outlier: 3.576A pdb=" N SER C 219 " --> pdb=" O ASP C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 260 removed outlier: 3.841A pdb=" N SER C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 451 Processing helix chain 'C' and resid 457 through 465 removed outlier: 4.132A pdb=" N LEU C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE C 464 " --> pdb=" O GLN C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 501 Processing helix chain 'C' and resid 504 through 521 removed outlier: 3.687A pdb=" N PHE C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 553 Processing helix chain 'C' and resid 569 through 575 Processing helix chain 'C' and resid 581 through 587 Processing helix chain 'C' and resid 615 through 620 Processing helix chain 'C' and resid 622 through 633 removed outlier: 4.258A pdb=" N GLU C 626 " --> pdb=" O HIS C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 656 Processing helix chain 'C' and resid 657 through 659 No H-bonds generated for 'chain 'C' and resid 657 through 659' Processing helix chain 'C' and resid 672 through 686 removed outlier: 3.573A pdb=" N SER C 686 " --> pdb=" O ARG C 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 29 Processing helix chain 'D' and resid 29 through 51 Processing helix chain 'D' and resid 87 through 94 removed outlier: 3.821A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 107 Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 208 through 219 removed outlier: 3.576A pdb=" N SER D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 260 removed outlier: 3.841A pdb=" N SER D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 451 Processing helix chain 'D' and resid 457 through 465 removed outlier: 4.132A pdb=" N LEU D 461 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE D 464 " --> pdb=" O GLN D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 501 Processing helix chain 'D' and resid 504 through 521 removed outlier: 3.688A pdb=" N PHE D 519 " --> pdb=" O THR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 553 Processing helix chain 'D' and resid 569 through 575 Processing helix chain 'D' and resid 581 through 587 Processing helix chain 'D' and resid 615 through 620 Processing helix chain 'D' and resid 622 through 633 removed outlier: 4.259A pdb=" N GLU D 626 " --> pdb=" O HIS D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 656 Processing helix chain 'D' and resid 657 through 659 No H-bonds generated for 'chain 'D' and resid 657 through 659' Processing helix chain 'D' and resid 672 through 686 removed outlier: 3.573A pdb=" N SER D 686 " --> pdb=" O ARG D 682 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 29 Processing helix chain 'E' and resid 29 through 51 Processing helix chain 'E' and resid 87 through 94 removed outlier: 3.821A pdb=" N ALA E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN E 94 " --> pdb=" O THR E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 107 Processing helix chain 'E' and resid 120 through 128 Processing helix chain 'E' and resid 208 through 219 removed outlier: 3.577A pdb=" N SER E 219 " --> pdb=" O ASP E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 260 removed outlier: 3.841A pdb=" N SER E 245 " --> pdb=" O PRO E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 451 Processing helix chain 'E' and resid 457 through 465 removed outlier: 4.132A pdb=" N LEU E 461 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE E 464 " --> pdb=" O GLN E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 501 Processing helix chain 'E' and resid 504 through 521 removed outlier: 3.687A pdb=" N PHE E 519 " --> pdb=" O THR E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 553 Processing helix chain 'E' and resid 569 through 575 Processing helix chain 'E' and resid 581 through 587 Processing helix chain 'E' and resid 615 through 620 Processing helix chain 'E' and resid 622 through 633 removed outlier: 4.258A pdb=" N GLU E 626 " --> pdb=" O HIS E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 656 Processing helix chain 'E' and resid 657 through 659 No H-bonds generated for 'chain 'E' and resid 657 through 659' Processing helix chain 'E' and resid 672 through 686 removed outlier: 3.573A pdb=" N SER E 686 " --> pdb=" O ARG E 682 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 29 Processing helix chain 'F' and resid 29 through 51 Processing helix chain 'F' and resid 87 through 94 removed outlier: 3.821A pdb=" N ALA F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN F 94 " --> pdb=" O THR F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 107 Processing helix chain 'F' and resid 120 through 128 Processing helix chain 'F' and resid 208 through 219 removed outlier: 3.576A pdb=" N SER F 219 " --> pdb=" O ASP F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 260 removed outlier: 3.840A pdb=" N SER F 245 " --> pdb=" O PRO F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 451 Processing helix chain 'F' and resid 457 through 465 removed outlier: 4.131A pdb=" N LEU F 461 " --> pdb=" O SER F 457 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE F 464 " --> pdb=" O GLN F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 501 Processing helix chain 'F' and resid 504 through 521 removed outlier: 3.688A pdb=" N PHE F 519 " --> pdb=" O THR F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 553 Processing helix chain 'F' and resid 569 through 575 Processing helix chain 'F' and resid 581 through 587 Processing helix chain 'F' and resid 615 through 620 Processing helix chain 'F' and resid 622 through 633 removed outlier: 4.259A pdb=" N GLU F 626 " --> pdb=" O HIS F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 656 Processing helix chain 'F' and resid 657 through 659 No H-bonds generated for 'chain 'F' and resid 657 through 659' Processing helix chain 'F' and resid 672 through 686 removed outlier: 3.574A pdb=" N SER F 686 " --> pdb=" O ARG F 682 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 29 Processing helix chain 'G' and resid 29 through 51 Processing helix chain 'G' and resid 87 through 94 removed outlier: 3.821A pdb=" N ALA G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN G 94 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 208 through 219 removed outlier: 3.576A pdb=" N SER G 219 " --> pdb=" O ASP G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 260 removed outlier: 3.841A pdb=" N SER G 245 " --> pdb=" O PRO G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 451 Processing helix chain 'G' and resid 457 through 465 removed outlier: 4.132A pdb=" N LEU G 461 " --> pdb=" O SER G 457 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE G 464 " --> pdb=" O GLN G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 501 Processing helix chain 'G' and resid 504 through 521 removed outlier: 3.687A pdb=" N PHE G 519 " --> pdb=" O THR G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 539 through 553 Processing helix chain 'G' and resid 569 through 575 Processing helix chain 'G' and resid 581 through 587 Processing helix chain 'G' and resid 615 through 620 Processing helix chain 'G' and resid 622 through 633 removed outlier: 4.259A pdb=" N GLU G 626 " --> pdb=" O HIS G 622 " (cutoff:3.500A) Processing helix chain 'G' and resid 650 through 656 Processing helix chain 'G' and resid 657 through 659 No H-bonds generated for 'chain 'G' and resid 657 through 659' Processing helix chain 'G' and resid 672 through 686 removed outlier: 3.572A pdb=" N SER G 686 " --> pdb=" O ARG G 682 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 29 Processing helix chain 'H' and resid 29 through 51 Processing helix chain 'H' and resid 87 through 94 removed outlier: 3.821A pdb=" N ALA H 91 " --> pdb=" O ALA H 87 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 Processing helix chain 'H' and resid 120 through 128 Processing helix chain 'H' and resid 208 through 219 removed outlier: 3.576A pdb=" N SER H 219 " --> pdb=" O ASP H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 260 removed outlier: 3.841A pdb=" N SER H 245 " --> pdb=" O PRO H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 425 through 451 Processing helix chain 'H' and resid 457 through 465 removed outlier: 4.132A pdb=" N LEU H 461 " --> pdb=" O SER H 457 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE H 464 " --> pdb=" O GLN H 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 501 Processing helix chain 'H' and resid 504 through 521 removed outlier: 3.687A pdb=" N PHE H 519 " --> pdb=" O THR H 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 539 through 553 Processing helix chain 'H' and resid 569 through 575 Processing helix chain 'H' and resid 581 through 587 Processing helix chain 'H' and resid 615 through 620 Processing helix chain 'H' and resid 622 through 633 removed outlier: 4.259A pdb=" N GLU H 626 " --> pdb=" O HIS H 622 " (cutoff:3.500A) Processing helix chain 'H' and resid 650 through 656 Processing helix chain 'H' and resid 657 through 659 No H-bonds generated for 'chain 'H' and resid 657 through 659' Processing helix chain 'H' and resid 672 through 686 removed outlier: 3.573A pdb=" N SER H 686 " --> pdb=" O ARG H 682 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 223 removed outlier: 8.719A pdb=" N ILE A 54 " --> pdb=" O ASP A 418 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ASP A 418 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU A 56 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A 416 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP A 58 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ASN A 414 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU A 60 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 141 removed outlier: 7.397A pdb=" N ASN A 134 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ILE A 194 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU A 190 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU A 140 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER A 188 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 468 through 473 removed outlier: 6.293A pdb=" N CYS A 693 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA A 470 " --> pdb=" O CYS A 693 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY A 692 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 528 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N LEU A 663 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET A 530 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL A 665 " --> pdb=" O MET A 530 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N SER A 532 " --> pdb=" O VAL A 665 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ARG A 667 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL A 558 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE A 607 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE A 560 " --> pdb=" O ILE A 607 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 220 through 223 removed outlier: 8.718A pdb=" N ILE B 54 " --> pdb=" O ASP B 418 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N ASP B 418 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU B 56 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 416 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP B 58 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ASN B 414 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU B 60 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AA7, first strand: chain 'B' and resid 134 through 141 removed outlier: 7.398A pdb=" N ASN B 134 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ILE B 194 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B 190 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU B 140 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER B 188 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 468 through 473 removed outlier: 6.293A pdb=" N CYS B 693 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA B 470 " --> pdb=" O CYS B 693 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY B 692 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL B 528 " --> pdb=" O THR B 661 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU B 663 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N MET B 530 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL B 665 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N SER B 532 " --> pdb=" O VAL B 665 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ARG B 667 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL B 558 " --> pdb=" O ASP B 605 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE B 607 " --> pdb=" O VAL B 558 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE B 560 " --> pdb=" O ILE B 607 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 220 through 223 removed outlier: 8.719A pdb=" N ILE C 54 " --> pdb=" O ASP C 418 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N ASP C 418 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU C 56 " --> pdb=" O VAL C 416 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL C 416 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP C 58 " --> pdb=" O ASN C 414 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ASN C 414 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU C 60 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 114 Processing sheet with id=AB2, first strand: chain 'C' and resid 134 through 141 removed outlier: 7.398A pdb=" N ASN C 134 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE C 194 " --> pdb=" O ASN C 134 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU C 190 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU C 140 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER C 188 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 468 through 473 removed outlier: 6.293A pdb=" N CYS C 693 " --> pdb=" O VAL C 468 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA C 470 " --> pdb=" O CYS C 693 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY C 692 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL C 528 " --> pdb=" O THR C 661 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N LEU C 663 " --> pdb=" O VAL C 528 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N MET C 530 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL C 665 " --> pdb=" O MET C 530 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER C 532 " --> pdb=" O VAL C 665 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ARG C 667 " --> pdb=" O SER C 532 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL C 558 " --> pdb=" O ASP C 605 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE C 607 " --> pdb=" O VAL C 558 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE C 560 " --> pdb=" O ILE C 607 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 220 through 223 removed outlier: 8.718A pdb=" N ILE D 54 " --> pdb=" O ASP D 418 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N ASP D 418 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU D 56 " --> pdb=" O VAL D 416 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL D 416 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASP D 58 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ASN D 414 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU D 60 " --> pdb=" O ILE D 412 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 110 through 114 Processing sheet with id=AB6, first strand: chain 'D' and resid 134 through 141 removed outlier: 7.398A pdb=" N ASN D 134 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE D 194 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU D 190 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU D 140 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER D 188 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 468 through 473 removed outlier: 6.292A pdb=" N CYS D 693 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA D 470 " --> pdb=" O CYS D 693 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY D 692 " --> pdb=" O CYS D 662 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL D 528 " --> pdb=" O THR D 661 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N LEU D 663 " --> pdb=" O VAL D 528 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET D 530 " --> pdb=" O LEU D 663 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL D 665 " --> pdb=" O MET D 530 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER D 532 " --> pdb=" O VAL D 665 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ARG D 667 " --> pdb=" O SER D 532 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL D 558 " --> pdb=" O ASP D 605 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE D 607 " --> pdb=" O VAL D 558 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE D 560 " --> pdb=" O ILE D 607 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 220 through 223 removed outlier: 8.719A pdb=" N ILE E 54 " --> pdb=" O ASP E 418 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N ASP E 418 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU E 56 " --> pdb=" O VAL E 416 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL E 416 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP E 58 " --> pdb=" O ASN E 414 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ASN E 414 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU E 60 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 110 through 114 Processing sheet with id=AC1, first strand: chain 'E' and resid 134 through 141 removed outlier: 7.397A pdb=" N ASN E 134 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ILE E 194 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU E 190 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU E 140 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER E 188 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 468 through 473 removed outlier: 6.293A pdb=" N CYS E 693 " --> pdb=" O VAL E 468 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA E 470 " --> pdb=" O CYS E 693 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY E 692 " --> pdb=" O CYS E 662 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL E 528 " --> pdb=" O THR E 661 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N LEU E 663 " --> pdb=" O VAL E 528 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET E 530 " --> pdb=" O LEU E 663 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL E 665 " --> pdb=" O MET E 530 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N SER E 532 " --> pdb=" O VAL E 665 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ARG E 667 " --> pdb=" O SER E 532 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL E 558 " --> pdb=" O ASP E 605 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE E 607 " --> pdb=" O VAL E 558 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE E 560 " --> pdb=" O ILE E 607 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 220 through 223 removed outlier: 8.719A pdb=" N ILE F 54 " --> pdb=" O ASP F 418 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N ASP F 418 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU F 56 " --> pdb=" O VAL F 416 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL F 416 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASP F 58 " --> pdb=" O ASN F 414 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ASN F 414 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU F 60 " --> pdb=" O ILE F 412 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 110 through 114 Processing sheet with id=AC5, first strand: chain 'F' and resid 134 through 141 removed outlier: 7.399A pdb=" N ASN F 134 " --> pdb=" O ILE F 194 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE F 194 " --> pdb=" O ASN F 134 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU F 190 " --> pdb=" O THR F 138 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU F 140 " --> pdb=" O SER F 188 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER F 188 " --> pdb=" O LEU F 140 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 468 through 473 removed outlier: 6.293A pdb=" N CYS F 693 " --> pdb=" O VAL F 468 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA F 470 " --> pdb=" O CYS F 693 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY F 692 " --> pdb=" O CYS F 662 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL F 528 " --> pdb=" O THR F 661 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N LEU F 663 " --> pdb=" O VAL F 528 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET F 530 " --> pdb=" O LEU F 663 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL F 665 " --> pdb=" O MET F 530 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER F 532 " --> pdb=" O VAL F 665 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ARG F 667 " --> pdb=" O SER F 532 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL F 558 " --> pdb=" O ASP F 605 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE F 607 " --> pdb=" O VAL F 558 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE F 560 " --> pdb=" O ILE F 607 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 220 through 223 removed outlier: 8.719A pdb=" N ILE G 54 " --> pdb=" O ASP G 418 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N ASP G 418 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU G 56 " --> pdb=" O VAL G 416 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL G 416 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP G 58 " --> pdb=" O ASN G 414 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ASN G 414 " --> pdb=" O ASP G 58 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU G 60 " --> pdb=" O ILE G 412 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 110 through 114 Processing sheet with id=AC9, first strand: chain 'G' and resid 134 through 141 removed outlier: 7.398A pdb=" N ASN G 134 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ILE G 194 " --> pdb=" O ASN G 134 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU G 190 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU G 140 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER G 188 " --> pdb=" O LEU G 140 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 468 through 473 removed outlier: 6.292A pdb=" N CYS G 693 " --> pdb=" O VAL G 468 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA G 470 " --> pdb=" O CYS G 693 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY G 692 " --> pdb=" O CYS G 662 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL G 528 " --> pdb=" O THR G 661 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N LEU G 663 " --> pdb=" O VAL G 528 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET G 530 " --> pdb=" O LEU G 663 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL G 665 " --> pdb=" O MET G 530 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER G 532 " --> pdb=" O VAL G 665 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N ARG G 667 " --> pdb=" O SER G 532 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL G 558 " --> pdb=" O ASP G 605 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE G 607 " --> pdb=" O VAL G 558 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE G 560 " --> pdb=" O ILE G 607 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 220 through 223 removed outlier: 8.719A pdb=" N ILE H 54 " --> pdb=" O ASP H 418 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N ASP H 418 " --> pdb=" O ILE H 54 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU H 56 " --> pdb=" O VAL H 416 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL H 416 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP H 58 " --> pdb=" O ASN H 414 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ASN H 414 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU H 60 " --> pdb=" O ILE H 412 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 110 through 114 Processing sheet with id=AD4, first strand: chain 'H' and resid 134 through 141 removed outlier: 7.398A pdb=" N ASN H 134 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ILE H 194 " --> pdb=" O ASN H 134 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU H 190 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU H 140 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER H 188 " --> pdb=" O LEU H 140 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 468 through 473 removed outlier: 6.293A pdb=" N CYS H 693 " --> pdb=" O VAL H 468 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA H 470 " --> pdb=" O CYS H 693 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY H 692 " --> pdb=" O CYS H 662 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL H 528 " --> pdb=" O THR H 661 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU H 663 " --> pdb=" O VAL H 528 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET H 530 " --> pdb=" O LEU H 663 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL H 665 " --> pdb=" O MET H 530 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N SER H 532 " --> pdb=" O VAL H 665 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ARG H 667 " --> pdb=" O SER H 532 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL H 558 " --> pdb=" O ASP H 605 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE H 607 " --> pdb=" O VAL H 558 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE H 560 " --> pdb=" O ILE H 607 " (cutoff:3.500A) 1600 hydrogen bonds defined for protein. 4728 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: 8.23 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8334 1.33 - 1.45: 5181 1.45 - 1.57: 18709 1.57 - 1.69: 40 1.69 - 1.81: 192 Bond restraints: 32456 Sorted by residual: bond pdb=" C3' ADP A1000 " pdb=" C4' ADP A1000 " ideal model delta sigma weight residual 1.524 1.269 0.255 2.00e-02 2.50e+03 1.63e+02 bond pdb=" C3' ADP E1000 " pdb=" C4' ADP E1000 " ideal model delta sigma weight residual 1.524 1.269 0.255 2.00e-02 2.50e+03 1.62e+02 bond pdb=" C3' ADP C1000 " pdb=" C4' ADP C1000 " ideal model delta sigma weight residual 1.524 1.270 0.254 2.00e-02 2.50e+03 1.62e+02 bond pdb=" C3' ADP D1000 " pdb=" C4' ADP D1000 " ideal model delta sigma weight residual 1.524 1.270 0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C3' ADP B1000 " pdb=" C4' ADP B1000 " ideal model delta sigma weight residual 1.524 1.270 0.254 2.00e-02 2.50e+03 1.61e+02 ... (remaining 32451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 43360 2.69 - 5.39: 541 5.39 - 8.08: 67 8.08 - 10.78: 24 10.78 - 13.47: 40 Bond angle restraints: 44032 Sorted by residual: angle pdb=" O1A ADP B1000 " pdb=" PA ADP B1000 " pdb=" O2A ADP B1000 " ideal model delta sigma weight residual 119.90 106.43 13.47 3.00e+00 1.11e-01 2.02e+01 angle pdb=" O1A ADP H1000 " pdb=" PA ADP H1000 " pdb=" O2A ADP H1000 " ideal model delta sigma weight residual 119.90 106.46 13.44 3.00e+00 1.11e-01 2.01e+01 angle pdb=" O1A ADP D1000 " pdb=" PA ADP D1000 " pdb=" O2A ADP D1000 " ideal model delta sigma weight residual 119.90 106.48 13.42 3.00e+00 1.11e-01 2.00e+01 angle pdb=" O1A ADP E1000 " pdb=" PA ADP E1000 " pdb=" O2A ADP E1000 " ideal model delta sigma weight residual 119.90 106.48 13.42 3.00e+00 1.11e-01 2.00e+01 angle pdb=" O1A ADP C1000 " pdb=" PA ADP C1000 " pdb=" O2A ADP C1000 " ideal model delta sigma weight residual 119.90 106.49 13.41 3.00e+00 1.11e-01 2.00e+01 ... (remaining 44027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.78: 18234 19.78 - 39.55: 1106 39.55 - 59.33: 279 59.33 - 79.11: 38 79.11 - 98.88: 23 Dihedral angle restraints: 19680 sinusoidal: 7864 harmonic: 11816 Sorted by residual: dihedral pdb=" CA HIS E 576 " pdb=" C HIS E 576 " pdb=" N LYS E 577 " pdb=" CA LYS E 577 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA HIS B 576 " pdb=" C HIS B 576 " pdb=" N LYS B 577 " pdb=" CA LYS B 577 " ideal model delta harmonic sigma weight residual 180.00 151.70 28.30 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA HIS D 576 " pdb=" C HIS D 576 " pdb=" N LYS D 577 " pdb=" CA LYS D 577 " ideal model delta harmonic sigma weight residual 180.00 151.71 28.29 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 19677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3463 0.050 - 0.101: 1348 0.101 - 0.151: 433 0.151 - 0.202: 20 0.202 - 0.252: 8 Chirality restraints: 5272 Sorted by residual: chirality pdb=" CB ILE A 553 " pdb=" CA ILE A 553 " pdb=" CG1 ILE A 553 " pdb=" CG2 ILE A 553 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB ILE E 553 " pdb=" CA ILE E 553 " pdb=" CG1 ILE E 553 " pdb=" CG2 ILE E 553 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB ILE C 553 " pdb=" CA ILE C 553 " pdb=" CG1 ILE C 553 " pdb=" CG2 ILE C 553 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 5269 not shown) Planarity restraints: 5560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 622 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO B 623 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 623 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 623 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 622 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO A 623 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 623 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 623 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS G 622 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO G 623 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO G 623 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO G 623 " -0.020 5.00e-02 4.00e+02 ... (remaining 5557 not shown) Histogram of nonbonded interaction distances: 0.56 - 1.43: 3 1.43 - 2.30: 53 2.30 - 3.16: 26913 3.16 - 4.03: 81172 4.03 - 4.90: 149091 Warning: very small nonbonded interaction distances. Nonbonded interactions: 257232 Sorted by model distance: nonbonded pdb=" NH1 ARG D 707 " pdb=" OE1 GLU E 675 " model vdw 0.561 3.120 nonbonded pdb=" NH1 ARG D 707 " pdb=" CD GLU E 675 " model vdw 0.841 3.350 nonbonded pdb=" CZ ARG D 707 " pdb=" OE1 GLU E 675 " model vdw 1.428 3.270 nonbonded pdb=" O LEU C 19 " pdb=" CD1 ILE C 23 " model vdw 1.440 3.460 nonbonded pdb=" O LEU G 19 " pdb=" CD1 ILE G 23 " model vdw 1.503 3.460 ... (remaining 257227 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 5.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 32.970 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.120 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:7.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 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 : 0.011 0.255 32456 Z= 0.504 Angle : 0.883 13.472 44032 Z= 0.435 Chirality : 0.055 0.252 5272 Planarity : 0.004 0.036 5560 Dihedral : 14.321 98.884 12080 Min Nonbonded Distance : 0.561 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 13.01 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: -0.02 (0.12), residues: 4056 helix: 0.80 (0.12), residues: 1760 sheet: 1.18 (0.18), residues: 672 loop : -1.46 (0.13), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 566 TYR 0.012 0.002 TYR G 658 PHE 0.017 0.003 PHE B 604 TRP 0.007 0.002 TRP H 477 HIS 0.003 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.01083 (32456) covalent geometry : angle 0.88349 (44032) hydrogen bonds : bond 0.13253 ( 1600) hydrogen bonds : angle 5.66604 ( 4728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 GLN cc_start: 0.7508 (pt0) cc_final: 0.6926 (pm20) REVERT: B 218 LYS cc_start: 0.7789 (ttpp) cc_final: 0.7497 (ttpp) REVERT: B 450 PHE cc_start: 0.7090 (t80) cc_final: 0.6853 (m-80) REVERT: E 101 LYS cc_start: 0.7706 (ttmt) cc_final: 0.6892 (tmtt) REVERT: E 109 GLN cc_start: 0.7747 (pt0) cc_final: 0.7262 (pm20) outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.7678 time to fit residues: 376.7663 Evaluate side-chains 402 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 ASN D 518 HIS ** D 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.223998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.173458 restraints weight = 28173.650| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.12 r_work: 0.3479 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 32456 Z= 0.120 Angle : 0.588 7.313 44032 Z= 0.295 Chirality : 0.045 0.161 5272 Planarity : 0.004 0.062 5560 Dihedral : 6.080 71.723 4472 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.83 % Allowed : 11.16 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.50 (0.13), residues: 4056 helix: 1.33 (0.12), residues: 1808 sheet: 1.42 (0.17), residues: 664 loop : -1.37 (0.13), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 624 TYR 0.010 0.001 TYR G 255 PHE 0.012 0.001 PHE D 542 TRP 0.004 0.001 TRP A 631 HIS 0.012 0.001 HIS D 518 Details of bonding type rmsd covalent geometry : bond 0.00249 (32456) covalent geometry : angle 0.58779 (44032) hydrogen bonds : bond 0.04268 ( 1600) hydrogen bonds : angle 4.33820 ( 4728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 442 time to evaluate : 1.263 Fit side-chains REVERT: A 109 GLN cc_start: 0.7601 (pt0) cc_final: 0.7085 (pm20) REVERT: A 439 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7387 (mp) REVERT: A 580 LYS cc_start: 0.7763 (mmtt) cc_final: 0.7480 (mmpt) REVERT: B 634 GLN cc_start: 0.8402 (mt0) cc_final: 0.8034 (mp10) REVERT: C 104 ASP cc_start: 0.7845 (m-30) cc_final: 0.7632 (m-30) REVERT: D 450 PHE cc_start: 0.7224 (OUTLIER) cc_final: 0.6515 (t80) REVERT: D 580 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7259 (mmpt) REVERT: D 657 ARG cc_start: 0.7744 (mtm-85) cc_final: 0.7419 (tpp-160) REVERT: E 101 LYS cc_start: 0.8104 (ttmt) cc_final: 0.7394 (tmtt) REVERT: E 109 GLN cc_start: 0.7801 (pt0) cc_final: 0.7154 (pm20) REVERT: G 242 LYS cc_start: 0.7900 (mtpt) cc_final: 0.7522 (mttp) REVERT: G 669 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.7033 (tp30) REVERT: H 23 ILE cc_start: 0.6024 (mt) cc_final: 0.5816 (mp) REVERT: H 214 SER cc_start: 0.8047 (t) cc_final: 0.7764 (p) REVERT: H 450 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6572 (t80) outliers start: 64 outliers final: 11 residues processed: 460 average time/residue: 0.7367 time to fit residues: 397.5641 Evaluate side-chains 410 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 394 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 243 ARG Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 580 LYS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 243 ARG Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 669 GLU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 450 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 382 optimal weight: 10.0000 chunk 273 optimal weight: 9.9990 chunk 350 optimal weight: 2.9990 chunk 113 optimal weight: 30.0000 chunk 175 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 378 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 299 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 ASN ** D 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 414 ASN ** H 571 HIS ** 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 = 0.4363 r_free = 0.4363 target = 0.220978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.169217 restraints weight = 27704.022| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.10 r_work: 0.3428 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 32456 Z= 0.193 Angle : 0.671 8.869 44032 Z= 0.334 Chirality : 0.049 0.168 5272 Planarity : 0.004 0.060 5560 Dihedral : 6.994 84.605 4472 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.95 % Allowed : 13.01 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.44 (0.13), residues: 4056 helix: 1.20 (0.12), residues: 1808 sheet: 1.50 (0.18), residues: 664 loop : -1.35 (0.13), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 243 TYR 0.011 0.002 TYR B 658 PHE 0.012 0.002 PHE C 604 TRP 0.007 0.001 TRP B 631 HIS 0.003 0.001 HIS F 622 Details of bonding type rmsd covalent geometry : bond 0.00441 (32456) covalent geometry : angle 0.67090 (44032) hydrogen bonds : bond 0.05114 ( 1600) hydrogen bonds : angle 4.42204 ( 4728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 420 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7357 (mp) REVERT: A 580 LYS cc_start: 0.7744 (mmtt) cc_final: 0.7449 (mmpt) REVERT: B 450 PHE cc_start: 0.7480 (t80) cc_final: 0.7210 (t80) REVERT: B 456 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7754 (mm-30) REVERT: B 598 LYS cc_start: 0.7997 (mttt) cc_final: 0.7492 (mtpm) REVERT: B 611 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.7102 (mp10) REVERT: B 634 GLN cc_start: 0.8412 (mt0) cc_final: 0.8029 (mp10) REVERT: C 243 ARG cc_start: 0.8065 (ttt90) cc_final: 0.7818 (ttt180) REVERT: C 439 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7296 (mp) REVERT: C 580 LYS cc_start: 0.7714 (mmtt) cc_final: 0.7374 (mmpt) REVERT: C 598 LYS cc_start: 0.8027 (mttt) cc_final: 0.7768 (mttm) REVERT: D 450 PHE cc_start: 0.7342 (OUTLIER) cc_final: 0.6572 (t80) REVERT: D 456 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7758 (mm-30) REVERT: D 580 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7266 (mmpt) REVERT: D 611 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.7037 (mp10) REVERT: D 657 ARG cc_start: 0.7808 (mtm-85) cc_final: 0.7483 (tpp-160) REVERT: E 101 LYS cc_start: 0.8158 (ttmt) cc_final: 0.7379 (tmtt) REVERT: E 450 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.6583 (t80) REVERT: E 598 LYS cc_start: 0.8072 (mttp) cc_final: 0.7842 (mttt) REVERT: E 700 LYS cc_start: 0.7134 (mtpp) cc_final: 0.6932 (mttm) REVERT: F 97 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.7207 (ptm) REVERT: G 598 LYS cc_start: 0.8037 (mttp) cc_final: 0.7824 (mttt) REVERT: G 700 LYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6953 (mttm) REVERT: H 450 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.6630 (t80) REVERT: H 611 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.7119 (mp10) outliers start: 68 outliers final: 17 residues processed: 453 average time/residue: 0.7751 time to fit residues: 409.8723 Evaluate side-chains 419 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 391 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 611 GLN Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 580 LYS Chi-restraints excluded: chain D residue 611 GLN Chi-restraints excluded: chain E residue 450 PHE Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 557 LYS Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 633 SER Chi-restraints excluded: chain G residue 700 LYS Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 450 PHE Chi-restraints excluded: chain H residue 557 LYS Chi-restraints excluded: chain H residue 611 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 119 optimal weight: 2.9990 chunk 195 optimal weight: 0.0970 chunk 118 optimal weight: 10.0000 chunk 283 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 292 optimal weight: 0.9980 chunk 330 optimal weight: 1.9990 chunk 398 optimal weight: 4.9990 chunk 267 optimal weight: 10.0000 chunk 275 optimal weight: 6.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 GLN ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 414 ASN ** H 571 HIS ** 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 = 0.4381 r_free = 0.4381 target = 0.222853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.171939 restraints weight = 27883.560| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.11 r_work: 0.3457 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32456 Z= 0.125 Angle : 0.575 7.191 44032 Z= 0.285 Chirality : 0.045 0.154 5272 Planarity : 0.004 0.035 5560 Dihedral : 6.110 70.774 4472 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.80 % Allowed : 14.10 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.72 (0.13), residues: 4056 helix: 1.56 (0.13), residues: 1800 sheet: 1.62 (0.18), residues: 664 loop : -1.35 (0.13), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 21 TYR 0.006 0.001 TYR A 658 PHE 0.011 0.001 PHE F 542 TRP 0.008 0.001 TRP B 631 HIS 0.002 0.000 HIS H 518 Details of bonding type rmsd covalent geometry : bond 0.00270 (32456) covalent geometry : angle 0.57476 (44032) hydrogen bonds : bond 0.04066 ( 1600) hydrogen bonds : angle 4.13507 ( 4728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 409 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.7332 (mp) REVERT: A 522 MET cc_start: 0.6880 (OUTLIER) cc_final: 0.6561 (tpp) REVERT: A 557 LYS cc_start: 0.8144 (mtmm) cc_final: 0.7881 (mtpt) REVERT: A 580 LYS cc_start: 0.7757 (mmtt) cc_final: 0.7459 (mmpt) REVERT: B 450 PHE cc_start: 0.7488 (t80) cc_final: 0.7189 (t80) REVERT: B 456 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7675 (mm-30) REVERT: B 598 LYS cc_start: 0.7987 (mttt) cc_final: 0.7501 (mtpm) REVERT: B 634 GLN cc_start: 0.8423 (mt0) cc_final: 0.8047 (mp10) REVERT: C 439 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.7294 (mp) REVERT: C 580 LYS cc_start: 0.7688 (mmtt) cc_final: 0.7342 (mmpt) REVERT: C 598 LYS cc_start: 0.7980 (mttt) cc_final: 0.7720 (mttm) REVERT: C 700 LYS cc_start: 0.7126 (mtpp) cc_final: 0.6908 (mttm) REVERT: D 231 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.4461 (mpt) REVERT: D 450 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.6537 (t80) REVERT: D 456 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7721 (mm-30) REVERT: D 580 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7275 (mmpt) REVERT: D 598 LYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6711 (mtpp) REVERT: D 657 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.7491 (tpp-160) REVERT: E 101 LYS cc_start: 0.8142 (ttmt) cc_final: 0.7367 (tmtt) REVERT: E 598 LYS cc_start: 0.8024 (mttp) cc_final: 0.7817 (mttt) REVERT: F 97 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7125 (ptp) REVERT: F 243 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7598 (mmm-85) REVERT: F 452 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7032 (mtm-85) REVERT: G 242 LYS cc_start: 0.7884 (mtpt) cc_final: 0.7522 (mttp) REVERT: G 598 LYS cc_start: 0.8002 (mttp) cc_final: 0.7798 (mttt) REVERT: H 450 PHE cc_start: 0.7366 (OUTLIER) cc_final: 0.6585 (t80) REVERT: H 522 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6461 (tpp) REVERT: H 598 LYS cc_start: 0.8105 (mttp) cc_final: 0.7616 (mtpm) REVERT: H 611 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6935 (mp10) outliers start: 63 outliers final: 15 residues processed: 442 average time/residue: 0.7373 time to fit residues: 381.1654 Evaluate side-chains 413 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 385 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 580 LYS Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 669 GLU Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 243 ARG Chi-restraints excluded: chain F residue 452 ARG Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain H residue 243 ARG Chi-restraints excluded: chain H residue 450 PHE Chi-restraints excluded: chain H residue 522 MET Chi-restraints excluded: chain H residue 611 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 24 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 406 optimal weight: 4.9990 chunk 181 optimal weight: 0.3980 chunk 223 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 235 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 345 optimal weight: 7.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.223360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.169807 restraints weight = 27924.467| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.27 r_work: 0.3432 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32456 Z= 0.119 Angle : 0.567 8.332 44032 Z= 0.282 Chirality : 0.045 0.154 5272 Planarity : 0.007 0.458 5560 Dihedral : 6.084 87.432 4472 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.72 % Allowed : 14.93 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.87 (0.13), residues: 4056 helix: 1.71 (0.13), residues: 1800 sheet: 1.70 (0.18), residues: 664 loop : -1.32 (0.13), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 21 TYR 0.006 0.001 TYR G 658 PHE 0.012 0.001 PHE F 542 TRP 0.011 0.001 TRP B 631 HIS 0.001 0.000 HIS H 246 Details of bonding type rmsd covalent geometry : bond 0.00255 (32456) covalent geometry : angle 0.56654 (44032) hydrogen bonds : bond 0.03964 ( 1600) hydrogen bonds : angle 4.08307 ( 4728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 406 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7353 (mp) REVERT: A 522 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.6543 (tpp) REVERT: A 557 LYS cc_start: 0.8165 (mtmm) cc_final: 0.7890 (mtpt) REVERT: A 580 LYS cc_start: 0.7732 (mmtt) cc_final: 0.7420 (mmpt) REVERT: B 450 PHE cc_start: 0.7546 (t80) cc_final: 0.7251 (t80) REVERT: B 456 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7644 (mm-30) REVERT: B 522 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6489 (tpp) REVERT: B 598 LYS cc_start: 0.7967 (mttt) cc_final: 0.7331 (mtpp) REVERT: B 611 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6967 (mp10) REVERT: C 439 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7352 (mp) REVERT: C 580 LYS cc_start: 0.7682 (mmtt) cc_final: 0.7335 (mmpt) REVERT: C 598 LYS cc_start: 0.7955 (mttt) cc_final: 0.7673 (mttm) REVERT: C 700 LYS cc_start: 0.7130 (mtpp) cc_final: 0.6913 (mttm) REVERT: D 231 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.4507 (mpt) REVERT: D 450 PHE cc_start: 0.7379 (OUTLIER) cc_final: 0.6609 (t80) REVERT: D 456 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7700 (mm-30) REVERT: D 522 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.6417 (tpp) REVERT: D 580 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7272 (mmpt) REVERT: D 598 LYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6728 (mtpp) REVERT: D 611 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6973 (mp10) REVERT: E 101 LYS cc_start: 0.8169 (ttmt) cc_final: 0.7425 (tmtt) REVERT: E 598 LYS cc_start: 0.8029 (mttp) cc_final: 0.7779 (mttm) REVERT: F 97 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.7144 (ptp) REVERT: F 450 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.6597 (t80) REVERT: F 452 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.6272 (mtm-85) REVERT: F 598 LYS cc_start: 0.8105 (mttp) cc_final: 0.7470 (mtpp) REVERT: G 242 LYS cc_start: 0.7906 (mtpt) cc_final: 0.7544 (mttp) REVERT: G 598 LYS cc_start: 0.7995 (mttp) cc_final: 0.7794 (mttt) REVERT: H 450 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.6627 (t80) REVERT: H 522 MET cc_start: 0.6895 (OUTLIER) cc_final: 0.6440 (tpp) REVERT: H 598 LYS cc_start: 0.8075 (mttp) cc_final: 0.7592 (mtpm) REVERT: H 611 GLN cc_start: 0.7279 (OUTLIER) cc_final: 0.6965 (mp10) outliers start: 60 outliers final: 21 residues processed: 438 average time/residue: 0.6218 time to fit residues: 320.0759 Evaluate side-chains 425 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 387 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain B residue 611 GLN Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 522 MET Chi-restraints excluded: chain D residue 580 LYS Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 611 GLN Chi-restraints excluded: chain E residue 414 ASN Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 243 ARG Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 450 PHE Chi-restraints excluded: chain F residue 452 ARG Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 476 GLU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 450 PHE Chi-restraints excluded: chain H residue 522 MET Chi-restraints excluded: chain H residue 611 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 395 optimal weight: 0.9990 chunk 206 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 368 optimal weight: 0.9980 chunk 345 optimal weight: 6.9990 chunk 169 optimal weight: 0.7980 chunk 209 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 114 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.223454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.171601 restraints weight = 27953.704| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.27 r_work: 0.3449 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 32456 Z= 0.113 Angle : 0.553 8.186 44032 Z= 0.273 Chirality : 0.045 0.155 5272 Planarity : 0.003 0.054 5560 Dihedral : 5.785 63.971 4472 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.12 % Allowed : 14.79 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.00 (0.13), residues: 4056 helix: 1.84 (0.13), residues: 1800 sheet: 1.76 (0.18), residues: 664 loop : -1.28 (0.13), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 21 TYR 0.006 0.001 TYR C 658 PHE 0.011 0.001 PHE F 542 TRP 0.010 0.001 TRP B 631 HIS 0.001 0.000 HIS G 710 Details of bonding type rmsd covalent geometry : bond 0.00242 (32456) covalent geometry : angle 0.55325 (44032) hydrogen bonds : bond 0.03768 ( 1600) hydrogen bonds : angle 4.00727 ( 4728) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 410 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7356 (mp) REVERT: A 522 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6540 (tpp) REVERT: A 580 LYS cc_start: 0.7707 (mmtt) cc_final: 0.7361 (mmpt) REVERT: B 456 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7635 (mm-30) REVERT: B 598 LYS cc_start: 0.7942 (mttt) cc_final: 0.7316 (mtpp) REVERT: B 611 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.7000 (mp10) REVERT: C 439 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7343 (mp) REVERT: C 456 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7773 (mm-30) REVERT: C 580 LYS cc_start: 0.7634 (mmtt) cc_final: 0.7268 (mmpt) REVERT: C 598 LYS cc_start: 0.7888 (mttt) cc_final: 0.7591 (mttm) REVERT: C 700 LYS cc_start: 0.7121 (mtpp) cc_final: 0.6897 (mttm) REVERT: D 231 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.4510 (mpt) REVERT: D 450 PHE cc_start: 0.7371 (OUTLIER) cc_final: 0.6601 (t80) REVERT: D 452 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.6087 (mtm-85) REVERT: D 456 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7712 (mm-30) REVERT: D 522 MET cc_start: 0.6869 (OUTLIER) cc_final: 0.6423 (tpp) REVERT: D 580 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7181 (mmpt) REVERT: D 598 LYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6673 (mtpp) REVERT: D 611 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.7009 (mp10) REVERT: E 101 LYS cc_start: 0.8145 (ttmt) cc_final: 0.7388 (tmtt) REVERT: E 456 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7766 (mm-30) REVERT: E 522 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.6521 (tpp) REVERT: E 598 LYS cc_start: 0.7997 (mttp) cc_final: 0.7738 (mttm) REVERT: F 97 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.7090 (ptp) REVERT: F 450 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.6593 (t80) REVERT: F 452 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.6260 (mtm-85) REVERT: F 522 MET cc_start: 0.6896 (mtt) cc_final: 0.6460 (tpp) REVERT: F 580 LYS cc_start: 0.7515 (mmpt) cc_final: 0.7308 (mmpt) REVERT: F 598 LYS cc_start: 0.8094 (mttp) cc_final: 0.7455 (mtpp) REVERT: F 611 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.7002 (mp10) REVERT: G 242 LYS cc_start: 0.7871 (mtpt) cc_final: 0.7510 (mttp) REVERT: G 700 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6941 (mttm) REVERT: H 450 PHE cc_start: 0.7383 (OUTLIER) cc_final: 0.6593 (t80) REVERT: H 452 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.6130 (mtm-85) REVERT: H 522 MET cc_start: 0.6821 (OUTLIER) cc_final: 0.6362 (tpp) REVERT: H 594 MET cc_start: 0.7722 (mtp) cc_final: 0.7447 (mmt) REVERT: H 598 LYS cc_start: 0.8048 (mttp) cc_final: 0.7451 (mtpp) REVERT: H 611 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.6986 (mp10) outliers start: 74 outliers final: 26 residues processed: 449 average time/residue: 0.6536 time to fit residues: 344.6952 Evaluate side-chains 431 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 384 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 611 GLN Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 669 GLU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 522 MET Chi-restraints excluded: chain D residue 580 LYS Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 611 GLN Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 414 ASN Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 522 MET Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 450 PHE Chi-restraints excluded: chain F residue 452 ARG Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 611 GLN Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 476 GLU Chi-restraints excluded: chain G residue 522 MET Chi-restraints excluded: chain G residue 700 LYS Chi-restraints excluded: chain H residue 450 PHE Chi-restraints excluded: chain H residue 452 ARG Chi-restraints excluded: chain H residue 522 MET Chi-restraints excluded: chain H residue 611 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 372 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 359 optimal weight: 10.0000 chunk 289 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 298 optimal weight: 5.9990 chunk 390 optimal weight: 2.9990 chunk 243 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 chunk 275 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 GLN ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.222997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.170541 restraints weight = 27876.961| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.15 r_work: 0.3452 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32456 Z= 0.129 Angle : 0.575 8.098 44032 Z= 0.284 Chirality : 0.045 0.161 5272 Planarity : 0.003 0.040 5560 Dihedral : 6.050 69.590 4472 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.29 % Allowed : 14.82 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.94 (0.13), residues: 4056 helix: 1.71 (0.13), residues: 1816 sheet: 1.80 (0.18), residues: 664 loop : -1.27 (0.14), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 21 TYR 0.006 0.001 TYR G 658 PHE 0.012 0.001 PHE F 542 TRP 0.011 0.001 TRP B 631 HIS 0.001 0.000 HIS D 518 Details of bonding type rmsd covalent geometry : bond 0.00285 (32456) covalent geometry : angle 0.57544 (44032) hydrogen bonds : bond 0.04033 ( 1600) hydrogen bonds : angle 4.06060 ( 4728) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 403 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7374 (mp) REVERT: A 580 LYS cc_start: 0.7719 (mmtt) cc_final: 0.7388 (mmpt) REVERT: B 450 PHE cc_start: 0.7547 (t80) cc_final: 0.7232 (t80) REVERT: B 456 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7693 (mm-30) REVERT: B 522 MET cc_start: 0.6902 (OUTLIER) cc_final: 0.6470 (tpp) REVERT: B 598 LYS cc_start: 0.7954 (mttt) cc_final: 0.7347 (mtpp) REVERT: B 611 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.7093 (mp10) REVERT: C 439 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7359 (mp) REVERT: C 456 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7786 (mm-30) REVERT: C 580 LYS cc_start: 0.7629 (mmtt) cc_final: 0.7295 (mmpt) REVERT: C 611 GLN cc_start: 0.7076 (OUTLIER) cc_final: 0.6854 (tp40) REVERT: D 231 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.4570 (mpt) REVERT: D 450 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.6610 (t80) REVERT: D 452 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.6232 (mtm-85) REVERT: D 456 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7715 (mm-30) REVERT: D 522 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6454 (tpp) REVERT: D 580 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7218 (mmpt) REVERT: D 598 LYS cc_start: 0.7107 (OUTLIER) cc_final: 0.6735 (mtpp) REVERT: D 611 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.7009 (mp10) REVERT: E 101 LYS cc_start: 0.8181 (ttmt) cc_final: 0.7418 (tmtt) REVERT: E 450 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.6600 (t80) REVERT: E 456 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7760 (mm-30) REVERT: E 598 LYS cc_start: 0.8003 (mttp) cc_final: 0.7734 (mttm) REVERT: F 97 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.7111 (ptp) REVERT: F 243 ARG cc_start: 0.7915 (mmm160) cc_final: 0.7544 (ttp80) REVERT: F 450 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.6588 (t80) REVERT: F 452 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.6911 (mtm-85) REVERT: F 522 MET cc_start: 0.6943 (mtt) cc_final: 0.6513 (tpp) REVERT: F 598 LYS cc_start: 0.8092 (mttp) cc_final: 0.7489 (mtpp) REVERT: F 611 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.7001 (mp10) REVERT: G 700 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6982 (mttm) REVERT: H 231 MET cc_start: 0.6792 (OUTLIER) cc_final: 0.5071 (mpt) REVERT: H 450 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.6590 (t80) REVERT: H 452 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.6259 (mtm-85) REVERT: H 598 LYS cc_start: 0.8073 (mttp) cc_final: 0.7624 (mtpm) REVERT: H 611 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.7073 (mp10) outliers start: 80 outliers final: 30 residues processed: 452 average time/residue: 0.7380 time to fit residues: 392.1813 Evaluate side-chains 436 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 384 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain B residue 611 GLN Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 611 GLN Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 522 MET Chi-restraints excluded: chain D residue 580 LYS Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 611 GLN Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 669 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 450 PHE Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 669 GLU Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 450 PHE Chi-restraints excluded: chain F residue 452 ARG Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 611 GLN Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 476 GLU Chi-restraints excluded: chain G residue 700 LYS Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 231 MET Chi-restraints excluded: chain H residue 450 PHE Chi-restraints excluded: chain H residue 452 ARG Chi-restraints excluded: chain H residue 476 GLU Chi-restraints excluded: chain H residue 611 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 69 optimal weight: 9.9990 chunk 292 optimal weight: 0.9980 chunk 380 optimal weight: 6.9990 chunk 162 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 144 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 299 optimal weight: 0.5980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.223904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.173666 restraints weight = 27960.527| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.10 r_work: 0.3478 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 32456 Z= 0.114 Angle : 0.557 14.811 44032 Z= 0.274 Chirality : 0.045 0.154 5272 Planarity : 0.003 0.030 5560 Dihedral : 5.753 63.717 4472 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.00 % Allowed : 15.47 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.07 (0.13), residues: 4056 helix: 1.89 (0.13), residues: 1800 sheet: 1.82 (0.18), residues: 664 loop : -1.25 (0.14), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 21 TYR 0.006 0.001 TYR C 658 PHE 0.011 0.001 PHE F 542 TRP 0.012 0.001 TRP B 631 HIS 0.001 0.000 HIS G 712 Details of bonding type rmsd covalent geometry : bond 0.00245 (32456) covalent geometry : angle 0.55675 (44032) hydrogen bonds : bond 0.03714 ( 1600) hydrogen bonds : angle 3.98781 ( 4728) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 396 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7336 (mp) REVERT: A 700 LYS cc_start: 0.7051 (mtpp) cc_final: 0.6834 (mttm) REVERT: B 450 PHE cc_start: 0.7551 (t80) cc_final: 0.7234 (t80) REVERT: B 456 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7624 (mm-30) REVERT: B 522 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.6402 (tpp) REVERT: B 598 LYS cc_start: 0.7941 (mttt) cc_final: 0.7343 (mtpp) REVERT: B 611 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6972 (mp10) REVERT: C 456 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7763 (mm-30) REVERT: C 580 LYS cc_start: 0.7631 (mmtt) cc_final: 0.7268 (mmpt) REVERT: D 231 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.4558 (mpt) REVERT: D 450 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.6571 (t80) REVERT: D 452 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.6104 (mtm-85) REVERT: D 456 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7689 (mm-30) REVERT: D 522 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.6390 (tpp) REVERT: D 580 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7199 (mmpt) REVERT: D 598 LYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6745 (mtpp) REVERT: D 611 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6980 (mp10) REVERT: E 101 LYS cc_start: 0.8118 (ttmt) cc_final: 0.7349 (tmtt) REVERT: E 450 PHE cc_start: 0.7262 (OUTLIER) cc_final: 0.6535 (t80) REVERT: E 456 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7743 (mm-30) REVERT: E 594 MET cc_start: 0.7747 (mtp) cc_final: 0.7451 (mmt) REVERT: E 598 LYS cc_start: 0.7978 (mttp) cc_final: 0.7737 (mttm) REVERT: F 97 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.7049 (ptp) REVERT: F 450 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.6526 (t80) REVERT: F 452 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.6866 (mtm-85) REVERT: F 522 MET cc_start: 0.6820 (mtt) cc_final: 0.6391 (tpp) REVERT: F 598 LYS cc_start: 0.8064 (mttp) cc_final: 0.7489 (mtpp) REVERT: F 611 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.7004 (mp10) REVERT: G 242 LYS cc_start: 0.7817 (mtpt) cc_final: 0.7453 (mttp) REVERT: G 594 MET cc_start: 0.7687 (mtp) cc_final: 0.7438 (mmt) REVERT: G 598 LYS cc_start: 0.7884 (mttt) cc_final: 0.7625 (mttm) REVERT: G 700 LYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6963 (mttm) REVERT: H 450 PHE cc_start: 0.7321 (OUTLIER) cc_final: 0.6532 (t80) REVERT: H 452 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.6248 (mtm-85) REVERT: H 522 MET cc_start: 0.6810 (OUTLIER) cc_final: 0.6413 (tpp) REVERT: H 594 MET cc_start: 0.7692 (mtp) cc_final: 0.7471 (mmt) REVERT: H 598 LYS cc_start: 0.8040 (mttp) cc_final: 0.7490 (mtpp) REVERT: H 611 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.7015 (mp10) outliers start: 70 outliers final: 32 residues processed: 445 average time/residue: 0.6416 time to fit residues: 335.9665 Evaluate side-chains 432 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 380 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain B residue 611 GLN Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 522 MET Chi-restraints excluded: chain D residue 580 LYS Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 611 GLN Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 669 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 450 PHE Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 450 PHE Chi-restraints excluded: chain F residue 452 ARG Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 611 GLN Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 476 GLU Chi-restraints excluded: chain G residue 669 GLU Chi-restraints excluded: chain G residue 700 LYS Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 450 PHE Chi-restraints excluded: chain H residue 452 ARG Chi-restraints excluded: chain H residue 476 GLU Chi-restraints excluded: chain H residue 522 MET Chi-restraints excluded: chain H residue 611 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 68 optimal weight: 5.9990 chunk 345 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 230 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 287 optimal weight: 0.0170 chunk 69 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 377 optimal weight: 2.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.220950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.166228 restraints weight = 27523.173| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.27 r_work: 0.3389 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 32456 Z= 0.204 Angle : 0.676 13.849 44032 Z= 0.335 Chirality : 0.049 0.184 5272 Planarity : 0.004 0.047 5560 Dihedral : 6.964 83.625 4472 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.83 % Allowed : 16.10 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.66 (0.13), residues: 4056 helix: 1.35 (0.12), residues: 1816 sheet: 1.68 (0.18), residues: 672 loop : -1.26 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 682 TYR 0.012 0.002 TYR A 658 PHE 0.013 0.002 PHE A 604 TRP 0.011 0.001 TRP G 631 HIS 0.002 0.001 HIS C 622 Details of bonding type rmsd covalent geometry : bond 0.00475 (32456) covalent geometry : angle 0.67637 (44032) hydrogen bonds : bond 0.04908 ( 1600) hydrogen bonds : angle 4.29355 ( 4728) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 394 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.7370 (mp) REVERT: A 456 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7813 (mm-30) REVERT: B 450 PHE cc_start: 0.7603 (t80) cc_final: 0.7248 (t80) REVERT: B 456 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7687 (mm-30) REVERT: B 598 LYS cc_start: 0.7965 (mttt) cc_final: 0.7440 (mtpm) REVERT: B 611 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.7186 (mp10) REVERT: B 634 GLN cc_start: 0.8474 (mt0) cc_final: 0.8066 (mp10) REVERT: C 439 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7452 (mp) REVERT: C 456 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7800 (mm-30) REVERT: C 611 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6956 (tp40) REVERT: D 92 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7772 (mm) REVERT: D 231 MET cc_start: 0.6873 (OUTLIER) cc_final: 0.4553 (mpt) REVERT: D 450 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.6597 (t80) REVERT: D 452 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.6866 (mtm-85) REVERT: D 456 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7767 (mm-30) REVERT: D 580 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7304 (mmpt) REVERT: D 598 LYS cc_start: 0.7125 (OUTLIER) cc_final: 0.6726 (mtpp) REVERT: D 611 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.7118 (mp10) REVERT: E 101 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7439 (tmtt) REVERT: E 450 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.6594 (t80) REVERT: E 456 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7817 (mm-30) REVERT: E 634 GLN cc_start: 0.8389 (mt0) cc_final: 0.8024 (mm110) REVERT: F 97 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7199 (ptp) REVERT: F 450 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.6619 (t80) REVERT: F 452 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.6911 (mtm-85) REVERT: F 611 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.7189 (mp10) REVERT: H 231 MET cc_start: 0.6858 (OUTLIER) cc_final: 0.4998 (mpt) REVERT: H 450 PHE cc_start: 0.7427 (OUTLIER) cc_final: 0.6621 (t80) REVERT: H 452 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.6439 (mtm-85) REVERT: H 611 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.7162 (tp40) outliers start: 64 outliers final: 25 residues processed: 437 average time/residue: 0.6729 time to fit residues: 346.0008 Evaluate side-chains 419 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 374 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 611 GLN Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 611 GLN Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 580 LYS Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 611 GLN Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 450 PHE Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 450 PHE Chi-restraints excluded: chain F residue 452 ARG Chi-restraints excluded: chain F residue 611 GLN Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 476 GLU Chi-restraints excluded: chain G residue 669 GLU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 231 MET Chi-restraints excluded: chain H residue 450 PHE Chi-restraints excluded: chain H residue 452 ARG Chi-restraints excluded: chain H residue 476 GLU Chi-restraints excluded: chain H residue 611 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 354 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 95 optimal weight: 0.1980 chunk 173 optimal weight: 0.6980 chunk 353 optimal weight: 3.9990 chunk 296 optimal weight: 5.9990 chunk 400 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 398 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.224395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.173555 restraints weight = 28153.417| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.13 r_work: 0.3483 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 32456 Z= 0.105 Angle : 0.553 16.051 44032 Z= 0.273 Chirality : 0.045 0.163 5272 Planarity : 0.003 0.031 5560 Dihedral : 5.639 62.422 4472 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.23 % Allowed : 16.76 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.04 (0.13), residues: 4056 helix: 1.85 (0.13), residues: 1800 sheet: 1.83 (0.18), residues: 664 loop : -1.25 (0.14), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 21 TYR 0.005 0.001 TYR F 255 PHE 0.009 0.001 PHE F 542 TRP 0.008 0.001 TRP B 631 HIS 0.001 0.000 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00219 (32456) covalent geometry : angle 0.55279 (44032) hydrogen bonds : bond 0.03501 ( 1600) hydrogen bonds : angle 3.97930 ( 4728) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 388 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 ILE cc_start: 0.7561 (OUTLIER) cc_final: 0.7335 (mp) REVERT: A 456 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7748 (mm-30) REVERT: B 92 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7501 (mm) REVERT: B 450 PHE cc_start: 0.7542 (t80) cc_final: 0.7191 (t80) REVERT: B 456 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7656 (mm-30) REVERT: B 598 LYS cc_start: 0.7947 (mttt) cc_final: 0.7359 (mtpp) REVERT: C 439 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7347 (mp) REVERT: C 456 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7754 (mm-30) REVERT: D 92 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7565 (mm) REVERT: D 450 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6556 (t80) REVERT: D 456 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7701 (mm-30) REVERT: D 580 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7218 (mmpt) REVERT: D 598 LYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6752 (mtpp) REVERT: E 101 LYS cc_start: 0.8121 (ttmt) cc_final: 0.7350 (tmtt) REVERT: E 450 PHE cc_start: 0.7296 (OUTLIER) cc_final: 0.6565 (t80) REVERT: E 456 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7748 (mm-30) REVERT: E 598 LYS cc_start: 0.7944 (mttp) cc_final: 0.7735 (mttm) REVERT: F 97 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.7031 (ptp) REVERT: F 450 PHE cc_start: 0.7379 (OUTLIER) cc_final: 0.6544 (t80) REVERT: F 522 MET cc_start: 0.6774 (mtt) cc_final: 0.6374 (tpp) REVERT: F 598 LYS cc_start: 0.8064 (mttp) cc_final: 0.7451 (mtpp) REVERT: G 242 LYS cc_start: 0.7781 (mtpt) cc_final: 0.7430 (mttp) REVERT: H 450 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.6552 (t80) REVERT: H 452 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.6319 (mtm-85) REVERT: H 522 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6429 (tpp) REVERT: H 598 LYS cc_start: 0.8033 (mttp) cc_final: 0.7506 (mtpp) outliers start: 43 outliers final: 19 residues processed: 419 average time/residue: 0.6039 time to fit residues: 298.7628 Evaluate side-chains 410 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 378 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 580 LYS Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 450 PHE Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 450 PHE Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 476 GLU Chi-restraints excluded: chain G residue 669 GLU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 450 PHE Chi-restraints excluded: chain H residue 452 ARG Chi-restraints excluded: chain H residue 476 GLU Chi-restraints excluded: chain H residue 522 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 303 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 350 optimal weight: 0.7980 chunk 174 optimal weight: 8.9990 chunk 311 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 384 optimal weight: 0.9980 chunk 226 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.222758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.171704 restraints weight = 27748.096| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.14 r_work: 0.3453 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32456 Z= 0.138 Angle : 0.597 17.261 44032 Z= 0.294 Chirality : 0.046 0.159 5272 Planarity : 0.004 0.034 5560 Dihedral : 6.117 72.282 4472 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.17 % Allowed : 16.96 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.95 (0.13), residues: 4056 helix: 1.73 (0.13), residues: 1800 sheet: 1.74 (0.18), residues: 672 loop : -1.22 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 21 TYR 0.007 0.001 TYR A 658 PHE 0.012 0.001 PHE D 542 TRP 0.010 0.001 TRP B 631 HIS 0.002 0.000 HIS G 622 Details of bonding type rmsd covalent geometry : bond 0.00307 (32456) covalent geometry : angle 0.59744 (44032) hydrogen bonds : bond 0.04107 ( 1600) hydrogen bonds : angle 4.10059 ( 4728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14491.18 seconds wall clock time: 246 minutes 33.64 seconds (14793.64 seconds total)