Starting phenix.real_space_refine on Thu May 29 04:43:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9exr_50047/05_2025/9exr_50047.cif Found real_map, /net/cci-nas-00/data/ceres_data/9exr_50047/05_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_50047/05_2025/9exr_50047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9exr_50047/05_2025/9exr_50047.map" model { file = "/net/cci-nas-00/data/ceres_data/9exr_50047/05_2025/9exr_50047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9exr_50047/05_2025/9exr_50047.cif" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 18.68, per 1000 atoms: 0.58 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: 8.36 Conformation dependent library (CDL) restraints added in 4.1 seconds 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: 4.13 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: 12.72 Time building geometry restraints manager: 9.68 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: 0.04 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: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.160 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 69.510 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.160 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:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.480 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.002 TRP H 477 HIS 0.003 0.001 HIS A 576 PHE 0.017 0.003 PHE B 604 TYR 0.012 0.002 TYR G 658 ARG 0.005 0.001 ARG G 566 Details of bonding type rmsd hydrogen bonds : bond 0.13253 ( 1600) hydrogen bonds : angle 5.66604 ( 4728) covalent geometry : bond 0.01083 (32456) covalent geometry : angle 0.88349 (44032) *********************** 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 : 3.527 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: 1.4551 time to fit residues: 719.6501 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 : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 0.9990 chunk 309 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 208 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 chunk 319 optimal weight: 30.0000 chunk 123 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 238 optimal weight: 0.7980 chunk 370 optimal weight: 40.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.221043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.169466 restraints weight = 27751.430| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.19 r_work: 0.3425 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32456 Z= 0.182 Angle : 0.674 8.791 44032 Z= 0.339 Chirality : 0.049 0.170 5272 Planarity : 0.004 0.045 5560 Dihedral : 6.696 78.848 4472 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.09 % Allowed : 12.07 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.12), residues: 4056 helix: 1.03 (0.12), residues: 1800 sheet: 1.35 (0.18), residues: 664 loop : -1.39 (0.13), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 631 HIS 0.013 0.001 HIS D 518 PHE 0.012 0.002 PHE A 447 TYR 0.011 0.002 TYR A 658 ARG 0.007 0.001 ARG F 624 Details of bonding type rmsd hydrogen bonds : bond 0.05054 ( 1600) hydrogen bonds : angle 4.58261 ( 4728) covalent geometry : bond 0.00407 (32456) covalent geometry : angle 0.67351 (44032) *********************** 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 515 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 442 time to evaluate : 3.671 Fit side-chains REVERT: A 439 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7457 (mp) REVERT: A 444 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7453 (mp) REVERT: A 580 LYS cc_start: 0.7764 (mmtt) cc_final: 0.7483 (mmpt) REVERT: B 444 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7444 (mp) REVERT: B 598 LYS cc_start: 0.8053 (mttt) cc_final: 0.7585 (mtpm) REVERT: B 611 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.7119 (mp10) REVERT: B 634 GLN cc_start: 0.8433 (mt0) cc_final: 0.8035 (mp10) REVERT: C 456 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7798 (mm-30) REVERT: D 450 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.6638 (t80) REVERT: D 611 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.7076 (mp10) REVERT: D 657 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7462 (tpp-160) REVERT: E 101 LYS cc_start: 0.8173 (ttmt) cc_final: 0.7493 (tmtt) REVERT: E 450 PHE cc_start: 0.7383 (OUTLIER) cc_final: 0.6648 (t80) REVERT: F 444 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7350 (mp) REVERT: F 580 LYS cc_start: 0.7654 (mppt) cc_final: 0.7384 (mmpt) REVERT: G 242 LYS cc_start: 0.8048 (mtpt) cc_final: 0.7691 (mttp) REVERT: G 700 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.7020 (mttm) REVERT: H 450 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.6662 (t80) REVERT: H 611 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.7139 (mp10) outliers start: 73 outliers final: 18 residues processed: 469 average time/residue: 1.4508 time to fit residues: 802.2637 Evaluate side-chains 413 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 384 time to evaluate : 3.287 ------------------------------------------------------------------------------- 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 444 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 611 GLN Chi-restraints excluded: chain C residue 416 VAL 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 D residue 611 GLN Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 450 PHE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 700 LYS Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 450 PHE Chi-restraints excluded: chain H residue 611 GLN Chi-restraints excluded: chain H residue 633 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 180 optimal weight: 0.7980 chunk 242 optimal weight: 0.6980 chunk 278 optimal weight: 0.2980 chunk 92 optimal weight: 5.9990 chunk 299 optimal weight: 1.9990 chunk 307 optimal weight: 5.9990 chunk 315 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 285 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4390 r_free = 0.4390 target = 0.223705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.171801 restraints weight = 28032.076| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.14 r_work: 0.3465 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 32456 Z= 0.112 Angle : 0.563 7.054 44032 Z= 0.282 Chirality : 0.045 0.153 5272 Planarity : 0.003 0.036 5560 Dihedral : 5.851 64.228 4472 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.03 % Allowed : 13.39 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.13), residues: 4056 helix: 1.55 (0.12), residues: 1800 sheet: 1.53 (0.18), residues: 664 loop : -1.38 (0.13), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 631 HIS 0.001 0.000 HIS A 712 PHE 0.010 0.001 PHE F 542 TYR 0.007 0.001 TYR G 706 ARG 0.008 0.000 ARG E 21 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 1600) hydrogen bonds : angle 4.18173 ( 4728) covalent geometry : bond 0.00235 (32456) covalent geometry : angle 0.56325 (44032) *********************** 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 500 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 429 time to evaluate : 3.196 Fit side-chains revert: symmetry clash REVERT: A 439 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7295 (mp) REVERT: A 522 MET cc_start: 0.6876 (OUTLIER) cc_final: 0.6543 (tpp) REVERT: A 557 LYS cc_start: 0.8151 (mtmm) cc_final: 0.7877 (mtpt) REVERT: A 580 LYS cc_start: 0.7762 (mmtt) cc_final: 0.7470 (mmpt) REVERT: B 450 PHE cc_start: 0.7416 (t80) cc_final: 0.7052 (t80) REVERT: B 598 LYS cc_start: 0.7963 (mttt) cc_final: 0.7405 (mtpp) REVERT: B 634 GLN cc_start: 0.8442 (mt0) cc_final: 0.8052 (mp10) REVERT: C 439 ILE cc_start: 0.7435 (OUTLIER) cc_final: 0.7205 (mp) REVERT: C 456 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7770 (mm-30) REVERT: C 522 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6643 (tpp) REVERT: C 580 LYS cc_start: 0.7685 (mmtt) cc_final: 0.7335 (mmpt) REVERT: D 450 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6517 (t80) REVERT: D 456 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7703 (mm-30) REVERT: D 580 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7277 (mmpt) REVERT: D 598 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6712 (mtpp) REVERT: E 101 LYS cc_start: 0.8116 (ttmt) cc_final: 0.7338 (tmtt) REVERT: E 450 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6572 (t80) REVERT: E 700 LYS cc_start: 0.7028 (mtpp) cc_final: 0.6792 (mttm) REVERT: F 97 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.7141 (ptp) REVERT: F 522 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.6452 (tpp) REVERT: F 580 LYS cc_start: 0.7593 (mppt) cc_final: 0.7069 (mptm) REVERT: G 242 LYS cc_start: 0.7882 (mtpt) cc_final: 0.7510 (mttp) REVERT: H 450 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6565 (t80) outliers start: 71 outliers final: 13 residues processed: 462 average time/residue: 1.3993 time to fit residues: 763.4899 Evaluate side-chains 424 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 400 time to evaluate : 3.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 522 MET Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 451 LEU 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 92 LEU Chi-restraints excluded: chain E residue 450 PHE Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 522 MET Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 450 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 229 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 71 optimal weight: 0.2980 chunk 119 optimal weight: 5.9990 chunk 380 optimal weight: 20.0000 chunk 239 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- 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 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.221015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.169279 restraints weight = 27757.278| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.10 r_work: 0.3425 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32456 Z= 0.190 Angle : 0.664 8.852 44032 Z= 0.330 Chirality : 0.049 0.172 5272 Planarity : 0.004 0.046 5560 Dihedral : 6.906 83.406 4472 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.80 % Allowed : 13.90 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.13), residues: 4056 helix: 1.32 (0.12), residues: 1800 sheet: 1.61 (0.18), residues: 664 loop : -1.32 (0.13), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 631 HIS 0.003 0.001 HIS F 622 PHE 0.013 0.002 PHE A 604 TYR 0.010 0.002 TYR G 658 ARG 0.008 0.001 ARG F 21 Details of bonding type rmsd hydrogen bonds : bond 0.04948 ( 1600) hydrogen bonds : angle 4.35982 ( 4728) covalent geometry : bond 0.00437 (32456) covalent geometry : angle 0.66397 (44032) *********************** 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 506 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 408 time to evaluate : 3.507 Fit side-chains revert: symmetry clash REVERT: A 439 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7358 (mp) REVERT: A 580 LYS cc_start: 0.7727 (mmtt) cc_final: 0.7446 (mmpt) REVERT: B 231 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.3926 (mpt) REVERT: B 598 LYS cc_start: 0.7974 (mttt) cc_final: 0.7394 (mtpp) REVERT: B 611 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.7140 (mp10) REVERT: B 634 GLN cc_start: 0.8406 (mt0) cc_final: 0.8016 (mp10) REVERT: C 439 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7345 (mp) REVERT: C 456 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7766 (mm-30) REVERT: C 580 LYS cc_start: 0.7729 (mmtt) cc_final: 0.7374 (mmpt) REVERT: C 700 LYS cc_start: 0.7190 (mtpp) cc_final: 0.6963 (mttm) REVERT: D 231 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.4089 (mpt) REVERT: D 450 PHE cc_start: 0.7376 (OUTLIER) cc_final: 0.6594 (t80) REVERT: D 580 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7276 (mmpt) REVERT: D 598 LYS cc_start: 0.7156 (OUTLIER) cc_final: 0.6744 (mtpp) REVERT: D 611 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.7034 (mp10) REVERT: E 101 LYS cc_start: 0.8182 (ttmt) cc_final: 0.7396 (tmtt) REVERT: E 450 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6522 (t80) REVERT: F 97 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.7173 (ptp) REVERT: F 450 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.6620 (t80) REVERT: F 452 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7040 (mtm-85) REVERT: F 580 LYS cc_start: 0.7655 (mppt) cc_final: 0.7142 (mptm) REVERT: F 598 LYS cc_start: 0.8084 (mttp) cc_final: 0.7604 (mtpm) REVERT: F 611 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.7061 (mp10) REVERT: G 598 LYS cc_start: 0.7909 (mttt) cc_final: 0.7601 (mttm) REVERT: G 700 LYS cc_start: 0.7207 (mtpp) cc_final: 0.6967 (mttm) REVERT: H 450 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.6600 (t80) REVERT: H 598 LYS cc_start: 0.8096 (mttp) cc_final: 0.7606 (mtpm) REVERT: H 611 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.7142 (mp10) outliers start: 98 outliers final: 24 residues processed: 465 average time/residue: 1.3596 time to fit residues: 748.6354 Evaluate side-chains 430 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 390 time to evaluate : 3.211 ------------------------------------------------------------------------------- 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 231 MET Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 611 GLN Chi-restraints excluded: chain C residue 23 ILE 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 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 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 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 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 557 LYS Chi-restraints excluded: chain F residue 611 GLN Chi-restraints excluded: chain F residue 633 SER Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 522 MET Chi-restraints excluded: chain H residue 203 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 43 optimal weight: 4.9990 chunk 342 optimal weight: 0.6980 chunk 301 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 355 optimal weight: 3.9990 chunk 267 optimal weight: 9.9990 chunk 41 optimal weight: 0.0040 chunk 152 optimal weight: 7.9990 chunk 227 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 overall best weight: 2.3398 ------------------------------------------------------------------------------- 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.221638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.169875 restraints weight = 27643.136| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.21 r_work: 0.3420 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32456 Z= 0.164 Angle : 0.655 14.247 44032 Z= 0.319 Chirality : 0.048 0.157 5272 Planarity : 0.004 0.041 5560 Dihedral : 6.590 78.685 4472 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.32 % Allowed : 15.42 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.13), residues: 4056 helix: 1.49 (0.13), residues: 1752 sheet: 1.63 (0.18), residues: 664 loop : -1.24 (0.13), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 631 HIS 0.002 0.000 HIS B 622 PHE 0.011 0.001 PHE A 604 TYR 0.009 0.001 TYR A 658 ARG 0.008 0.001 ARG H 21 Details of bonding type rmsd hydrogen bonds : bond 0.04539 ( 1600) hydrogen bonds : angle 4.25154 ( 4728) covalent geometry : bond 0.00371 (32456) covalent geometry : angle 0.65525 (44032) *********************** 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 497 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 416 time to evaluate : 3.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7426 (mp) REVERT: A 452 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.5701 (mtm-85) REVERT: A 580 LYS cc_start: 0.7741 (mmtt) cc_final: 0.7410 (mmpt) REVERT: B 598 LYS cc_start: 0.7945 (mttt) cc_final: 0.7443 (mtpm) REVERT: B 611 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.7171 (mp10) REVERT: B 634 GLN cc_start: 0.8425 (mt0) cc_final: 0.8043 (mp10) REVERT: C 439 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7417 (mp) REVERT: C 456 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7778 (mm-30) REVERT: C 580 LYS cc_start: 0.7694 (mmtt) cc_final: 0.7364 (mmpt) REVERT: C 700 LYS cc_start: 0.7208 (mtpp) cc_final: 0.6991 (mttm) REVERT: D 23 ILE cc_start: 0.6438 (mm) cc_final: 0.6237 (mp) REVERT: D 450 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.6634 (t80) REVERT: D 522 MET cc_start: 0.7027 (OUTLIER) cc_final: 0.6562 (tpp) REVERT: D 580 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7286 (mmpt) REVERT: D 598 LYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6766 (mtpp) REVERT: D 611 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.7168 (mp10) REVERT: E 101 LYS cc_start: 0.8203 (ttmt) cc_final: 0.7462 (tmtt) REVERT: F 97 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7217 (ptp) REVERT: F 450 PHE cc_start: 0.7477 (OUTLIER) cc_final: 0.6654 (t80) REVERT: F 452 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.6126 (mtm-85) REVERT: F 580 LYS cc_start: 0.7649 (mppt) cc_final: 0.7135 (mptm) REVERT: F 598 LYS cc_start: 0.8076 (mttp) cc_final: 0.7619 (mtpm) REVERT: F 611 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.7165 (mp10) REVERT: G 598 LYS cc_start: 0.7894 (mttt) cc_final: 0.7598 (mttm) REVERT: G 700 LYS cc_start: 0.7228 (mtpp) cc_final: 0.7006 (mttm) REVERT: H 450 PHE cc_start: 0.7472 (OUTLIER) cc_final: 0.6676 (t80) REVERT: H 452 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6063 (mtm-85) REVERT: H 598 LYS cc_start: 0.8077 (mttp) cc_final: 0.7584 (mtpm) REVERT: H 611 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.7176 (mp10) outliers start: 81 outliers final: 26 residues processed: 461 average time/residue: 1.4120 time to fit residues: 767.6580 Evaluate side-chains 436 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 394 time to evaluate : 3.453 ------------------------------------------------------------------------------- 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 452 ARG Chi-restraints excluded: chain B residue 225 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 23 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain D residue 225 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 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 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 225 LEU 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 557 LYS Chi-restraints excluded: chain F residue 611 GLN Chi-restraints excluded: chain F residue 633 SER Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain H residue 450 PHE Chi-restraints excluded: chain H residue 452 ARG Chi-restraints excluded: chain H residue 557 LYS Chi-restraints excluded: chain H residue 611 GLN Chi-restraints excluded: chain H residue 633 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 403 optimal weight: 0.8980 chunk 286 optimal weight: 0.9990 chunk 341 optimal weight: 0.0570 chunk 258 optimal weight: 6.9990 chunk 129 optimal weight: 0.5980 chunk 221 optimal weight: 10.0000 chunk 220 optimal weight: 0.7980 chunk 131 optimal weight: 7.9990 chunk 370 optimal weight: 30.0000 chunk 191 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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 = 0.4398 r_free = 0.4398 target = 0.224580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.173928 restraints weight = 28079.696| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 1.17 r_work: 0.3478 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 32456 Z= 0.103 Angle : 0.576 15.569 44032 Z= 0.277 Chirality : 0.045 0.159 5272 Planarity : 0.003 0.041 5560 Dihedral : 5.568 60.471 4472 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.83 % Allowed : 15.36 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.13), residues: 4056 helix: 1.83 (0.13), residues: 1800 sheet: 1.72 (0.18), residues: 664 loop : -1.30 (0.13), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 631 HIS 0.001 0.000 HIS A 712 PHE 0.010 0.001 PHE F 542 TYR 0.006 0.001 TYR G 255 ARG 0.009 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 1600) hydrogen bonds : angle 3.99276 ( 4728) covalent geometry : bond 0.00209 (32456) covalent geometry : angle 0.57580 (44032) *********************** 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 472 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 408 time to evaluate : 3.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7383 (mp) REVERT: A 580 LYS cc_start: 0.7668 (mmtt) cc_final: 0.7367 (mmpt) REVERT: B 522 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6417 (tpp) REVERT: B 598 LYS cc_start: 0.7958 (mttt) cc_final: 0.7363 (mtpp) REVERT: C 439 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7368 (mp) REVERT: C 456 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7760 (mm-30) REVERT: C 580 LYS cc_start: 0.7623 (mmtt) cc_final: 0.7325 (mmpt) REVERT: D 23 ILE cc_start: 0.6433 (mm) cc_final: 0.6186 (mp) REVERT: D 231 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.4831 (mpt) REVERT: D 450 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.6568 (t80) REVERT: D 452 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.5860 (mtm-85) REVERT: D 456 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7624 (mm-30) REVERT: D 522 MET cc_start: 0.6848 (OUTLIER) cc_final: 0.6463 (tpp) REVERT: D 580 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7185 (mmpt) REVERT: D 598 LYS cc_start: 0.7080 (OUTLIER) cc_final: 0.6746 (mtpp) REVERT: E 101 LYS cc_start: 0.8158 (ttmt) cc_final: 0.7403 (tmtt) REVERT: F 97 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.7065 (ptp) REVERT: F 450 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.6575 (t80) REVERT: F 522 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.6360 (tpp) REVERT: F 598 LYS cc_start: 0.8070 (mttp) cc_final: 0.7503 (mtpp) REVERT: G 242 LYS cc_start: 0.7822 (mtpp) cc_final: 0.7498 (mttp) REVERT: G 522 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6499 (tpp) REVERT: G 598 LYS cc_start: 0.7865 (mttt) cc_final: 0.7582 (mttm) REVERT: H 450 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.6562 (t80) REVERT: H 522 MET cc_start: 0.6861 (mtt) cc_final: 0.6454 (tpp) REVERT: H 594 MET cc_start: 0.7698 (mtp) cc_final: 0.7482 (mmt) REVERT: H 598 LYS cc_start: 0.8023 (mttp) cc_final: 0.7459 (mtpp) outliers start: 64 outliers final: 20 residues processed: 456 average time/residue: 1.3721 time to fit residues: 746.1478 Evaluate side-chains 421 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 387 time to evaluate : 3.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 225 LEU 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 225 LEU Chi-restraints excluded: chain D residue 231 MET 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 633 SER 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 450 PHE Chi-restraints excluded: chain F residue 522 MET Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 522 MET Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 450 PHE Chi-restraints excluded: chain H residue 476 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 214 optimal weight: 8.9990 chunk 381 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 379 optimal weight: 3.9990 chunk 249 optimal weight: 0.8980 chunk 252 optimal weight: 1.9990 chunk 323 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.222421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.171337 restraints weight = 27869.682| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.19 r_work: 0.3440 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32456 Z= 0.146 Angle : 0.636 16.109 44032 Z= 0.306 Chirality : 0.046 0.157 5272 Planarity : 0.004 0.038 5560 Dihedral : 6.253 72.781 4472 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.26 % Allowed : 15.59 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.13), residues: 4056 helix: 1.80 (0.13), residues: 1752 sheet: 1.75 (0.18), residues: 664 loop : -1.16 (0.13), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 631 HIS 0.001 0.000 HIS B 518 PHE 0.012 0.001 PHE F 542 TYR 0.008 0.001 TYR C 658 ARG 0.010 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 1600) hydrogen bonds : angle 4.11454 ( 4728) covalent geometry : bond 0.00327 (32456) covalent geometry : angle 0.63588 (44032) *********************** 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: 79 poor density : 404 time to evaluate : 3.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7368 (mp) REVERT: A 580 LYS cc_start: 0.7736 (mmtt) cc_final: 0.7377 (mmpt) REVERT: B 231 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.4451 (mpt) REVERT: B 456 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7677 (mm-30) REVERT: B 598 LYS cc_start: 0.7942 (mttt) cc_final: 0.7557 (mtpp) REVERT: C 439 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7343 (mp) REVERT: C 456 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7798 (mm-30) REVERT: C 580 LYS cc_start: 0.7637 (mmtt) cc_final: 0.7289 (mmpt) REVERT: D 23 ILE cc_start: 0.6392 (mm) cc_final: 0.6131 (mp) REVERT: D 231 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.4691 (mpt) REVERT: D 450 PHE cc_start: 0.7383 (OUTLIER) cc_final: 0.6596 (t80) REVERT: D 452 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6034 (mtm-85) REVERT: D 580 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7213 (mmpt) REVERT: D 598 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6795 (mtpp) REVERT: E 101 LYS cc_start: 0.8176 (ttmt) cc_final: 0.7408 (tmtt) REVERT: F 97 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.7107 (ptp) REVERT: F 450 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.6582 (t80) REVERT: F 452 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.6431 (mtm-85) REVERT: F 598 LYS cc_start: 0.8072 (mttp) cc_final: 0.7636 (mtpm) REVERT: H 450 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.6590 (t80) REVERT: H 452 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.6203 (mtm-85) REVERT: H 456 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7704 (mm-30) REVERT: H 522 MET cc_start: 0.6929 (mtt) cc_final: 0.6493 (tpp) REVERT: H 611 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.7127 (mp10) outliers start: 79 outliers final: 36 residues processed: 455 average time/residue: 1.3495 time to fit residues: 728.5568 Evaluate side-chains 431 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 381 time to evaluate : 3.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 700 LYS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 444 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 225 LEU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 225 LEU 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 633 SER 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 F residue 97 MET Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 225 LEU 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 633 SER Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 700 LYS Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 243 ARG 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 Chi-restraints excluded: chain H residue 669 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 286 optimal weight: 0.9990 chunk 288 optimal weight: 2.9990 chunk 313 optimal weight: 8.9990 chunk 252 optimal weight: 4.9990 chunk 294 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 312 optimal weight: 1.9990 chunk 402 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 380 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.4382 r_free = 0.4382 target = 0.222867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.170970 restraints weight = 27882.144| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 1.11 r_work: 0.3454 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32456 Z= 0.131 Angle : 0.624 16.787 44032 Z= 0.298 Chirality : 0.046 0.155 5272 Planarity : 0.005 0.204 5560 Dihedral : 6.108 71.330 4472 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.32 % Allowed : 15.88 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.13), residues: 4056 helix: 1.82 (0.13), residues: 1752 sheet: 1.77 (0.18), residues: 664 loop : -1.14 (0.13), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 631 HIS 0.002 0.000 HIS H 246 PHE 0.012 0.001 PHE F 542 TYR 0.007 0.001 TYR A 658 ARG 0.021 0.001 ARG H 243 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 1600) hydrogen bonds : angle 4.07723 ( 4728) covalent geometry : bond 0.00288 (32456) covalent geometry : angle 0.62415 (44032) *********************** 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 474 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 393 time to evaluate : 3.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7362 (mp) REVERT: A 456 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7760 (mm-30) REVERT: A 557 LYS cc_start: 0.8167 (mtmm) cc_final: 0.7910 (mtpt) REVERT: B 231 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.4503 (mpt) REVERT: B 456 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7664 (mm-30) REVERT: B 598 LYS cc_start: 0.7943 (mttt) cc_final: 0.7555 (mtpp) REVERT: B 611 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.7107 (mp10) REVERT: C 439 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7345 (mp) REVERT: C 456 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7775 (mm-30) REVERT: C 580 LYS cc_start: 0.7654 (mmtt) cc_final: 0.7278 (mmpt) REVERT: D 23 ILE cc_start: 0.6413 (mm) cc_final: 0.6162 (mp) REVERT: D 92 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7715 (mm) REVERT: D 231 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.4713 (mpt) REVERT: D 450 PHE cc_start: 0.7367 (OUTLIER) cc_final: 0.6585 (t80) REVERT: D 452 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.5930 (mtm-85) REVERT: D 580 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7207 (mmpt) REVERT: D 598 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6754 (mtpp) REVERT: E 101 LYS cc_start: 0.8172 (ttmt) cc_final: 0.7415 (tmtt) REVERT: E 450 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.6563 (t80) REVERT: F 97 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.7081 (ptp) REVERT: F 450 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.6578 (t80) REVERT: F 452 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.6337 (mtm-85) REVERT: F 522 MET cc_start: 0.6836 (mtt) cc_final: 0.6411 (tpp) REVERT: F 598 LYS cc_start: 0.8080 (mttp) cc_final: 0.7643 (mtpm) REVERT: F 611 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.7069 (mp10) REVERT: H 450 PHE cc_start: 0.7357 (OUTLIER) cc_final: 0.6570 (t80) REVERT: H 452 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.6241 (mtm-85) REVERT: H 456 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7689 (mm-30) REVERT: H 522 MET cc_start: 0.6940 (mtt) cc_final: 0.6515 (tpp) outliers start: 81 outliers final: 36 residues processed: 445 average time/residue: 1.3908 time to fit residues: 733.6849 Evaluate side-chains 433 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 380 time to evaluate : 3.466 ------------------------------------------------------------------------------- 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 700 LYS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 231 MET 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 23 ILE 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 439 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 225 LEU 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 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 414 ASN 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 F residue 633 SER Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 669 GLU Chi-restraints excluded: chain G residue 700 LYS Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 450 PHE Chi-restraints excluded: chain H residue 452 ARG Chi-restraints excluded: chain H residue 476 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 343 optimal weight: 0.4980 chunk 167 optimal weight: 40.0000 chunk 392 optimal weight: 6.9990 chunk 315 optimal weight: 0.7980 chunk 301 optimal weight: 0.0570 chunk 185 optimal weight: 0.9980 chunk 70 optimal weight: 0.0170 chunk 193 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 275 optimal weight: 0.8980 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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 = 0.4406 r_free = 0.4406 target = 0.225427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.175801 restraints weight = 28207.357| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.07 r_work: 0.3508 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 32456 Z= 0.097 Angle : 0.573 17.069 44032 Z= 0.270 Chirality : 0.044 0.154 5272 Planarity : 0.003 0.042 5560 Dihedral : 5.316 55.880 4472 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.54 % Allowed : 16.70 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.13), residues: 4056 helix: 2.00 (0.13), residues: 1808 sheet: 2.02 (0.20), residues: 576 loop : -1.23 (0.13), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 631 HIS 0.001 0.000 HIS D 518 PHE 0.010 0.001 PHE F 542 TYR 0.005 0.001 TYR F 116 ARG 0.011 0.000 ARG E 21 Details of bonding type rmsd hydrogen bonds : bond 0.03233 ( 1600) hydrogen bonds : angle 3.87454 ( 4728) covalent geometry : bond 0.00195 (32456) covalent geometry : angle 0.57306 (44032) *********************** 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 449 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 395 time to evaluate : 3.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 ASN cc_start: 0.8161 (p0) cc_final: 0.7810 (p0) REVERT: A 439 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7369 (mp) REVERT: A 456 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7713 (mm-30) REVERT: B 456 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7612 (mm-30) REVERT: B 522 MET cc_start: 0.6780 (mtt) cc_final: 0.6388 (tpp) REVERT: B 598 LYS cc_start: 0.7962 (mttt) cc_final: 0.7377 (mtpp) REVERT: C 414 ASN cc_start: 0.8215 (p0) cc_final: 0.7748 (p0) REVERT: C 456 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7748 (mm-30) REVERT: C 580 LYS cc_start: 0.7514 (mmtt) cc_final: 0.7222 (mmpt) REVERT: D 92 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7497 (mm) REVERT: D 231 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.4876 (mpt) REVERT: D 450 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.6537 (t80) REVERT: D 452 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.5908 (mtm-85) REVERT: D 456 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7616 (mm-30) REVERT: D 580 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7155 (mmpt) REVERT: D 598 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.6761 (mtpp) REVERT: E 101 LYS cc_start: 0.8133 (ttmt) cc_final: 0.7358 (tmtt) REVERT: F 97 MET cc_start: 0.7215 (ptm) cc_final: 0.6985 (ptp) REVERT: F 450 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.6542 (t80) REVERT: F 522 MET cc_start: 0.6705 (mtt) cc_final: 0.6331 (tpp) REVERT: F 598 LYS cc_start: 0.8051 (mttp) cc_final: 0.7543 (mtpp) REVERT: G 414 ASN cc_start: 0.8204 (p0) cc_final: 0.7781 (p0) REVERT: G 598 LYS cc_start: 0.7810 (mttt) cc_final: 0.7567 (mttm) REVERT: H 450 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.6555 (t80) REVERT: H 456 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7650 (mm-30) REVERT: H 522 MET cc_start: 0.6797 (mtt) cc_final: 0.6422 (tpp) REVERT: H 598 LYS cc_start: 0.7987 (mttp) cc_final: 0.7476 (mtpp) outliers start: 54 outliers final: 30 residues processed: 432 average time/residue: 1.3085 time to fit residues: 675.3896 Evaluate side-chains 412 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 373 time to evaluate : 3.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 700 LYS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 225 LEU 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 225 LEU Chi-restraints excluded: chain D residue 231 MET 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 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 444 LEU Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 450 PHE Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 633 SER Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain G residue 444 LEU 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 225 LEU Chi-restraints excluded: chain H residue 450 PHE Chi-restraints excluded: chain H residue 476 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 162 optimal weight: 20.0000 chunk 213 optimal weight: 7.9990 chunk 388 optimal weight: 0.6980 chunk 169 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 165 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 328 optimal weight: 0.9990 chunk 303 optimal weight: 2.9990 chunk 354 optimal weight: 0.1980 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.4395 r_free = 0.4395 target = 0.224140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.173107 restraints weight = 27904.931| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.15 r_work: 0.3467 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32456 Z= 0.116 Angle : 0.600 17.216 44032 Z= 0.285 Chirality : 0.045 0.155 5272 Planarity : 0.003 0.033 5560 Dihedral : 5.614 60.029 4472 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.34 % Allowed : 17.02 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.13), residues: 4056 helix: 2.06 (0.13), residues: 1752 sheet: 1.97 (0.18), residues: 656 loop : -1.14 (0.13), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 631 HIS 0.001 0.000 HIS A 712 PHE 0.011 0.001 PHE H 542 TYR 0.005 0.001 TYR E 606 ARG 0.008 0.000 ARG H 21 Details of bonding type rmsd hydrogen bonds : bond 0.03684 ( 1600) hydrogen bonds : angle 3.97682 ( 4728) covalent geometry : bond 0.00251 (32456) covalent geometry : angle 0.60044 (44032) ********************** 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 429 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 382 time to evaluate : 3.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 ASN cc_start: 0.8227 (p0) cc_final: 0.7797 (p0) REVERT: A 439 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7404 (mp) REVERT: A 456 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7679 (mm-30) REVERT: A 557 LYS cc_start: 0.8161 (mtmm) cc_final: 0.7896 (mtpt) REVERT: B 456 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7634 (mm-30) REVERT: B 522 MET cc_start: 0.6816 (mtt) cc_final: 0.6396 (tpp) REVERT: B 580 LYS cc_start: 0.7624 (mptm) cc_final: 0.7203 (mmpt) REVERT: B 598 LYS cc_start: 0.7951 (mttt) cc_final: 0.7369 (mtpp) REVERT: C 414 ASN cc_start: 0.8269 (p0) cc_final: 0.7778 (p0) REVERT: C 439 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7423 (mp) REVERT: C 456 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7773 (mm-30) REVERT: D 231 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.4813 (mpt) REVERT: D 450 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.6615 (t80) REVERT: D 452 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.5941 (mtm-85) REVERT: D 456 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7650 (mm-30) REVERT: D 580 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7131 (mmpt) REVERT: D 598 LYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6772 (mtpp) REVERT: E 101 LYS cc_start: 0.8166 (ttmt) cc_final: 0.7388 (tmtt) REVERT: F 97 MET cc_start: 0.7270 (ptm) cc_final: 0.7055 (ptp) REVERT: F 450 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6555 (t80) REVERT: F 522 MET cc_start: 0.6794 (mtt) cc_final: 0.6399 (tpp) REVERT: F 598 LYS cc_start: 0.8046 (mttp) cc_final: 0.7501 (mtpp) REVERT: G 242 LYS cc_start: 0.7841 (mtpp) cc_final: 0.7519 (mttp) REVERT: G 414 ASN cc_start: 0.8264 (p0) cc_final: 0.7808 (p0) REVERT: H 450 PHE cc_start: 0.7361 (OUTLIER) cc_final: 0.6582 (t80) REVERT: H 452 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.6167 (mtm-85) REVERT: H 456 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7664 (mm-30) REVERT: H 522 MET cc_start: 0.6836 (mtt) cc_final: 0.6427 (tpp) REVERT: H 598 LYS cc_start: 0.7981 (mttp) cc_final: 0.7599 (mtpp) outliers start: 47 outliers final: 31 residues processed: 416 average time/residue: 1.4264 time to fit residues: 706.2728 Evaluate side-chains 417 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 376 time to evaluate : 3.430 ------------------------------------------------------------------------------- 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 700 LYS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain C residue 23 ILE 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 439 ILE 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 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 444 LEU Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 444 LEU 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 233 THR Chi-restraints excluded: chain G residue 444 LEU 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 225 LEU Chi-restraints excluded: chain H residue 243 ARG Chi-restraints excluded: chain H residue 450 PHE Chi-restraints excluded: chain H residue 452 ARG Chi-restraints excluded: chain H residue 476 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 73 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 254 optimal weight: 0.0010 chunk 148 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 chunk 8 optimal weight: 0.4980 chunk 194 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 346 optimal weight: 7.9990 chunk 246 optimal weight: 0.9980 chunk 306 optimal weight: 20.0000 overall best weight: 0.7388 ------------------------------------------------------------------------------- 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 = 0.4404 r_free = 0.4404 target = 0.225117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.175234 restraints weight = 28136.874| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.27 r_work: 0.3468 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 32456 Z= 0.102 Angle : 0.588 17.080 44032 Z= 0.276 Chirality : 0.044 0.170 5272 Planarity : 0.003 0.030 5560 Dihedral : 5.364 55.374 4472 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.54 % Allowed : 17.13 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.13), residues: 4056 helix: 2.12 (0.13), residues: 1760 sheet: 2.04 (0.20), residues: 576 loop : -1.09 (0.13), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 631 HIS 0.001 0.000 HIS C 576 PHE 0.010 0.001 PHE F 542 TYR 0.009 0.001 TYR C 658 ARG 0.008 0.000 ARG H 21 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 1600) hydrogen bonds : angle 3.90490 ( 4728) covalent geometry : bond 0.00214 (32456) covalent geometry : angle 0.58776 (44032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28981.10 seconds wall clock time: 500 minutes 12.72 seconds (30012.72 seconds total)