Starting phenix.real_space_refine on Sat Mar 7 00:46:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vcv_31897/03_2026/7vcv_31897.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vcv_31897/03_2026/7vcv_31897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vcv_31897/03_2026/7vcv_31897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vcv_31897/03_2026/7vcv_31897.map" model { file = "/net/cci-nas-00/data/ceres_data/7vcv_31897/03_2026/7vcv_31897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vcv_31897/03_2026/7vcv_31897.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 198 5.16 5 C 22494 2.51 5 N 6372 2.21 5 O 6924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36036 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 5942 Classifications: {'peptide': 758} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 716} Chain: "F" Number of atoms: 5942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 5942 Classifications: {'peptide': 758} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 716} Chain: "E" Number of atoms: 5942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 5942 Classifications: {'peptide': 758} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 716} Chain: "D" Number of atoms: 5942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 5942 Classifications: {'peptide': 758} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 716} Chain: "C" Number of atoms: 5942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 5942 Classifications: {'peptide': 758} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 716} Chain: "B" Number of atoms: 5942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 5942 Classifications: {'peptide': 758} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 716} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.91, per 1000 atoms: 0.22 Number of scatterers: 36036 At special positions: 0 Unit cell: (178.2, 173.88, 117.72, 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 198 16.00 P 36 15.00 Mg 12 11.99 O 6924 8.00 N 6372 7.00 C 22494 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: 2.82 Conformation dependent library (CDL) restraints added in 1.7 seconds 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8496 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 30 sheets defined 46.8% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.605A pdb=" N LYS A 18 " --> pdb=" O ALA A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 49 Processing helix chain 'A' and resid 85 through 92 removed outlier: 3.531A pdb=" N ARG A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.895A pdb=" N PHE A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 198 removed outlier: 3.863A pdb=" N GLU A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 removed outlier: 3.660A pdb=" N GLN A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 226 through 234 removed outlier: 4.210A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 306 through 309 Processing helix chain 'A' and resid 319 through 334 Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.512A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.650A pdb=" N VAL A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 438 through 444 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 483 through 499 removed outlier: 4.649A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 501 through 506 removed outlier: 4.133A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 removed outlier: 4.236A pdb=" N LEU A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 549 Processing helix chain 'A' and resid 556 through 569 removed outlier: 4.392A pdb=" N ARG A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 4.417A pdb=" N ILE A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 610 removed outlier: 3.570A pdb=" N GLY A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 removed outlier: 3.542A pdb=" N LEU A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.756A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 716 Processing helix chain 'A' and resid 734 through 743 removed outlier: 3.599A pdb=" N GLU A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 761 removed outlier: 3.772A pdb=" N THR A 761 " --> pdb=" O MET A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 766 removed outlier: 3.843A pdb=" N ARG A 766 " --> pdb=" O GLN A 763 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 18 removed outlier: 3.605A pdb=" N LYS F 18 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 49 Processing helix chain 'F' and resid 85 through 92 removed outlier: 3.531A pdb=" N ARG F 89 " --> pdb=" O ASN F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 124 Processing helix chain 'F' and resid 130 through 135 Processing helix chain 'F' and resid 135 through 140 removed outlier: 3.895A pdb=" N PHE F 139 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 198 removed outlier: 3.863A pdb=" N GLU F 194 " --> pdb=" O LYS F 190 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 220 removed outlier: 3.659A pdb=" N GLN F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 226 Processing helix chain 'F' and resid 226 through 234 removed outlier: 4.211A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 281 through 296 Processing helix chain 'F' and resid 306 through 309 Processing helix chain 'F' and resid 319 through 334 Processing helix chain 'F' and resid 373 through 385 removed outlier: 3.511A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 403 removed outlier: 3.650A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 425 Processing helix chain 'F' and resid 438 through 444 Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'F' and resid 483 through 499 removed outlier: 4.649A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 501 through 506 removed outlier: 4.134A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 536 removed outlier: 4.236A pdb=" N LEU F 527 " --> pdb=" O GLY F 523 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 549 Processing helix chain 'F' and resid 556 through 569 removed outlier: 4.393A pdb=" N ARG F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 587 removed outlier: 4.418A pdb=" N ILE F 582 " --> pdb=" O GLU F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 610 removed outlier: 3.570A pdb=" N GLY F 610 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 661 removed outlier: 3.541A pdb=" N LEU F 661 " --> pdb=" O LEU F 657 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.755A pdb=" N LEU F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR F 679 " --> pdb=" O LEU F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 716 Processing helix chain 'F' and resid 734 through 743 removed outlier: 3.598A pdb=" N GLU F 738 " --> pdb=" O ASP F 734 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 761 removed outlier: 3.773A pdb=" N THR F 761 " --> pdb=" O MET F 757 " (cutoff:3.500A) Processing helix chain 'F' and resid 762 through 766 removed outlier: 3.844A pdb=" N ARG F 766 " --> pdb=" O GLN F 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 18 removed outlier: 3.604A pdb=" N LYS E 18 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 49 Processing helix chain 'E' and resid 85 through 92 removed outlier: 3.531A pdb=" N ARG E 89 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 124 Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 135 through 140 removed outlier: 3.894A pdb=" N PHE E 139 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 198 removed outlier: 3.863A pdb=" N GLU E 194 " --> pdb=" O LYS E 190 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 220 removed outlier: 3.660A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 226 Processing helix chain 'E' and resid 226 through 234 removed outlier: 4.210A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 281 through 296 Processing helix chain 'E' and resid 306 through 309 Processing helix chain 'E' and resid 319 through 334 Processing helix chain 'E' and resid 373 through 385 removed outlier: 3.512A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 403 removed outlier: 3.650A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 425 Processing helix chain 'E' and resid 438 through 444 Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'E' and resid 483 through 499 removed outlier: 4.649A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 501 through 506 removed outlier: 4.134A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 536 removed outlier: 4.236A pdb=" N LEU E 527 " --> pdb=" O GLY E 523 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 549 Processing helix chain 'E' and resid 556 through 569 removed outlier: 4.392A pdb=" N ARG E 560 " --> pdb=" O GLU E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 587 removed outlier: 4.418A pdb=" N ILE E 582 " --> pdb=" O GLU E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 610 removed outlier: 3.570A pdb=" N GLY E 610 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 661 removed outlier: 3.541A pdb=" N LEU E 661 " --> pdb=" O LEU E 657 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.756A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR E 679 " --> pdb=" O LEU E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 716 Processing helix chain 'E' and resid 734 through 743 removed outlier: 3.598A pdb=" N GLU E 738 " --> pdb=" O ASP E 734 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 761 removed outlier: 3.772A pdb=" N THR E 761 " --> pdb=" O MET E 757 " (cutoff:3.500A) Processing helix chain 'E' and resid 762 through 766 removed outlier: 3.843A pdb=" N ARG E 766 " --> pdb=" O GLN E 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 18 removed outlier: 3.605A pdb=" N LYS D 18 " --> pdb=" O ALA D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 49 Processing helix chain 'D' and resid 85 through 92 removed outlier: 3.531A pdb=" N ARG D 89 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 130 through 135 Processing helix chain 'D' and resid 135 through 140 removed outlier: 3.895A pdb=" N PHE D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 198 removed outlier: 3.863A pdb=" N GLU D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 220 removed outlier: 3.660A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 226 through 234 removed outlier: 4.210A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 281 through 296 Processing helix chain 'D' and resid 306 through 309 Processing helix chain 'D' and resid 319 through 334 Processing helix chain 'D' and resid 373 through 385 removed outlier: 3.512A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 403 removed outlier: 3.650A pdb=" N VAL D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 425 Processing helix chain 'D' and resid 438 through 444 Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 483 through 499 removed outlier: 4.649A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 501 through 506 removed outlier: 4.133A pdb=" N PHE D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 536 removed outlier: 4.236A pdb=" N LEU D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 549 Processing helix chain 'D' and resid 556 through 569 removed outlier: 4.392A pdb=" N ARG D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 587 removed outlier: 4.417A pdb=" N ILE D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 610 removed outlier: 3.570A pdb=" N GLY D 610 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 661 removed outlier: 3.542A pdb=" N LEU D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.756A pdb=" N LEU D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 716 Processing helix chain 'D' and resid 734 through 743 removed outlier: 3.599A pdb=" N GLU D 738 " --> pdb=" O ASP D 734 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 761 removed outlier: 3.772A pdb=" N THR D 761 " --> pdb=" O MET D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 766 removed outlier: 3.843A pdb=" N ARG D 766 " --> pdb=" O GLN D 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 18 removed outlier: 3.605A pdb=" N LYS C 18 " --> pdb=" O ALA C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 85 through 92 removed outlier: 3.530A pdb=" N ARG C 89 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 135 through 140 removed outlier: 3.895A pdb=" N PHE C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 198 removed outlier: 3.863A pdb=" N GLU C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 220 removed outlier: 3.659A pdb=" N GLN C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 226 through 234 removed outlier: 4.210A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 306 through 309 Processing helix chain 'C' and resid 319 through 334 Processing helix chain 'C' and resid 373 through 385 removed outlier: 3.512A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.650A pdb=" N VAL C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 425 Processing helix chain 'C' and resid 438 through 444 Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 483 through 499 removed outlier: 4.650A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 501 through 506 removed outlier: 4.133A pdb=" N PHE C 506 " --> pdb=" O LYS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 536 removed outlier: 4.236A pdb=" N LEU C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 549 Processing helix chain 'C' and resid 556 through 569 removed outlier: 4.392A pdb=" N ARG C 560 " --> pdb=" O GLU C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 587 removed outlier: 4.418A pdb=" N ILE C 582 " --> pdb=" O GLU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 610 removed outlier: 3.570A pdb=" N GLY C 610 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 661 removed outlier: 3.542A pdb=" N LEU C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 679 removed outlier: 3.756A pdb=" N LEU C 675 " --> pdb=" O ASP C 671 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 716 Processing helix chain 'C' and resid 734 through 743 removed outlier: 3.598A pdb=" N GLU C 738 " --> pdb=" O ASP C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 761 removed outlier: 3.773A pdb=" N THR C 761 " --> pdb=" O MET C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 766 removed outlier: 3.839A pdb=" N ARG C 766 " --> pdb=" O GLN C 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.604A pdb=" N LYS B 18 " --> pdb=" O ALA B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 85 through 92 removed outlier: 3.531A pdb=" N ARG B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 135 through 140 removed outlier: 3.894A pdb=" N PHE B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 198 removed outlier: 3.863A pdb=" N GLU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 220 removed outlier: 3.660A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'B' and resid 226 through 234 removed outlier: 4.210A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 281 through 296 Processing helix chain 'B' and resid 306 through 309 Processing helix chain 'B' and resid 319 through 334 Processing helix chain 'B' and resid 373 through 385 removed outlier: 3.512A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.650A pdb=" N VAL B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 438 through 444 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 483 through 499 removed outlier: 4.649A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 501 through 506 removed outlier: 4.134A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 536 removed outlier: 4.236A pdb=" N LEU B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 549 Processing helix chain 'B' and resid 556 through 569 removed outlier: 4.392A pdb=" N ARG B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 587 removed outlier: 4.418A pdb=" N ILE B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 610 removed outlier: 3.570A pdb=" N GLY B 610 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 661 removed outlier: 3.541A pdb=" N LEU B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.756A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 716 Processing helix chain 'B' and resid 734 through 743 removed outlier: 3.598A pdb=" N GLU B 738 " --> pdb=" O ASP B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 761 removed outlier: 3.772A pdb=" N THR B 761 " --> pdb=" O MET B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 766 removed outlier: 3.844A pdb=" N ARG B 766 " --> pdb=" O GLN B 763 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 removed outlier: 3.507A pdb=" N VAL A 57 " --> pdb=" O CYS A 69 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS A 69 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 116 through 118 removed outlier: 4.354A pdb=" N VAL A 161 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 154 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 146 Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.471A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 541 removed outlier: 6.508A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 514 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N THR A 623 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE A 516 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLY A 513 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 25 through 27 removed outlier: 3.507A pdb=" N VAL F 57 " --> pdb=" O CYS F 69 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS F 69 " --> pdb=" O VAL F 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 116 through 118 removed outlier: 4.354A pdb=" N VAL F 161 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL F 154 " --> pdb=" O VAL F 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 145 through 146 Processing sheet with id=AA9, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.470A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY F 240 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 538 through 541 removed outlier: 6.509A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N THR F 623 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE F 516 " --> pdb=" O THR F 623 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLY F 513 " --> pdb=" O GLN F 641 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 25 through 27 removed outlier: 3.507A pdb=" N VAL E 57 " --> pdb=" O CYS E 69 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS E 69 " --> pdb=" O VAL E 57 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 116 through 118 removed outlier: 4.354A pdb=" N VAL E 161 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL E 154 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 145 through 146 Processing sheet with id=AB5, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.470A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 538 through 541 removed outlier: 6.509A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL E 514 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N THR E 623 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE E 516 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLY E 513 " --> pdb=" O GLN E 641 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 25 through 27 removed outlier: 3.507A pdb=" N VAL D 57 " --> pdb=" O CYS D 69 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS D 69 " --> pdb=" O VAL D 57 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 116 through 118 removed outlier: 4.354A pdb=" N VAL D 161 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL D 154 " --> pdb=" O VAL D 161 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 145 through 146 Processing sheet with id=AC1, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.471A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 538 through 541 removed outlier: 6.508A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL D 514 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N THR D 623 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE D 516 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLY D 513 " --> pdb=" O GLN D 641 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.507A pdb=" N VAL C 57 " --> pdb=" O CYS C 69 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS C 69 " --> pdb=" O VAL C 57 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 116 through 118 removed outlier: 4.354A pdb=" N VAL C 161 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL C 154 " --> pdb=" O VAL C 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 145 through 146 Processing sheet with id=AC6, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.470A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 538 through 541 removed outlier: 6.509A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL C 514 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N THR C 623 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE C 516 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLY C 513 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 25 through 27 removed outlier: 3.507A pdb=" N VAL B 57 " --> pdb=" O CYS B 69 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS B 69 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 116 through 118 removed outlier: 4.354A pdb=" N VAL B 161 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL B 154 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 145 through 146 Processing sheet with id=AD2, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.470A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 538 through 541 removed outlier: 6.509A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 514 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N THR B 623 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE B 516 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLY B 513 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) 1326 hydrogen bonds defined for protein. 3906 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.90 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 12625 1.36 - 1.50: 10709 1.50 - 1.65: 12978 1.65 - 1.79: 207 1.79 - 1.94: 105 Bond restraints: 36624 Sorted by residual: bond pdb=" N ARG D 635 " pdb=" CA ARG D 635 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.04e-02 9.25e+03 9.63e+00 bond pdb=" N ARG F 635 " pdb=" CA ARG F 635 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.04e-02 9.25e+03 9.57e+00 bond pdb=" N ARG E 635 " pdb=" CA ARG E 635 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.04e-02 9.25e+03 9.24e+00 bond pdb=" N ARG C 635 " pdb=" CA ARG C 635 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.04e-02 9.25e+03 9.05e+00 bond pdb=" C ARG F 22 " pdb=" N PRO F 23 " ideal model delta sigma weight residual 1.335 1.369 -0.034 1.19e-02 7.06e+03 8.27e+00 ... (remaining 36619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 46669 2.13 - 4.25: 2468 4.25 - 6.38: 333 6.38 - 8.51: 60 8.51 - 10.64: 6 Bond angle restraints: 49536 Sorted by residual: angle pdb=" C ILE F 206 " pdb=" N GLY F 207 " pdb=" CA GLY F 207 " ideal model delta sigma weight residual 122.33 119.13 3.20 7.30e-01 1.88e+00 1.92e+01 angle pdb=" C ILE B 206 " pdb=" N GLY B 207 " pdb=" CA GLY B 207 " ideal model delta sigma weight residual 122.33 119.13 3.20 7.30e-01 1.88e+00 1.92e+01 angle pdb=" C ILE E 206 " pdb=" N GLY E 207 " pdb=" CA GLY E 207 " ideal model delta sigma weight residual 122.33 119.13 3.20 7.30e-01 1.88e+00 1.92e+01 angle pdb=" C ILE C 206 " pdb=" N GLY C 207 " pdb=" CA GLY C 207 " ideal model delta sigma weight residual 122.33 119.16 3.17 7.30e-01 1.88e+00 1.88e+01 angle pdb=" C ILE D 206 " pdb=" N GLY D 207 " pdb=" CA GLY D 207 " ideal model delta sigma weight residual 122.33 119.18 3.15 7.30e-01 1.88e+00 1.87e+01 ... (remaining 49531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.84: 21519 14.84 - 29.68: 961 29.68 - 44.52: 242 44.52 - 59.36: 78 59.36 - 74.20: 18 Dihedral angle restraints: 22818 sinusoidal: 9714 harmonic: 13104 Sorted by residual: dihedral pdb=" CA GLU C 261 " pdb=" C GLU C 261 " pdb=" N THR C 262 " pdb=" CA THR C 262 " ideal model delta harmonic sigma weight residual -180.00 -131.52 -48.48 0 5.00e+00 4.00e-02 9.40e+01 dihedral pdb=" CA GLU F 261 " pdb=" C GLU F 261 " pdb=" N THR F 262 " pdb=" CA THR F 262 " ideal model delta harmonic sigma weight residual -180.00 -131.53 -48.47 0 5.00e+00 4.00e-02 9.40e+01 dihedral pdb=" CA GLU D 261 " pdb=" C GLU D 261 " pdb=" N THR D 262 " pdb=" CA THR D 262 " ideal model delta harmonic sigma weight residual -180.00 -131.54 -48.46 0 5.00e+00 4.00e-02 9.39e+01 ... (remaining 22815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3435 0.049 - 0.099: 1522 0.099 - 0.148: 504 0.148 - 0.198: 99 0.198 - 0.247: 14 Chirality restraints: 5574 Sorted by residual: chirality pdb=" CG LEU C 642 " pdb=" CB LEU C 642 " pdb=" CD1 LEU C 642 " pdb=" CD2 LEU C 642 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CG LEU F 642 " pdb=" CB LEU F 642 " pdb=" CD1 LEU F 642 " pdb=" CD2 LEU F 642 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CG LEU D 642 " pdb=" CB LEU D 642 " pdb=" CD1 LEU D 642 " pdb=" CD2 LEU D 642 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 5571 not shown) Planarity restraints: 6516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 290 " 0.015 2.00e-02 2.50e+03 2.34e-02 9.62e+00 pdb=" CG PHE B 290 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE B 290 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE B 290 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 290 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE B 290 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 290 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 290 " -0.015 2.00e-02 2.50e+03 2.34e-02 9.62e+00 pdb=" CG PHE E 290 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE E 290 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE E 290 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE E 290 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE E 290 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE E 290 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 290 " 0.014 2.00e-02 2.50e+03 2.33e-02 9.52e+00 pdb=" CG PHE C 290 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE C 290 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE C 290 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 290 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE C 290 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE C 290 " 0.000 2.00e-02 2.50e+03 ... (remaining 6513 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 468 2.66 - 3.22: 30987 3.22 - 3.78: 50190 3.78 - 4.34: 68906 4.34 - 4.90: 115196 Nonbonded interactions: 265747 Sorted by model distance: nonbonded pdb=" O2G AGS A 901 " pdb="MG MG A 902 " model vdw 2.097 2.170 nonbonded pdb=" O2G AGS D 901 " pdb="MG MG D 902 " model vdw 2.097 2.170 nonbonded pdb=" O2G AGS F 901 " pdb="MG MG F 902 " model vdw 2.097 2.170 nonbonded pdb=" O2G AGS C 901 " pdb="MG MG C 902 " model vdw 2.097 2.170 nonbonded pdb=" O2G AGS B 901 " pdb="MG MG B 902 " model vdw 2.097 2.170 ... (remaining 265742 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'E' selection = chain 'D' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 32.780 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 : 0.012 0.090 36624 Z= 0.491 Angle : 1.084 10.636 49536 Z= 0.613 Chirality : 0.061 0.247 5574 Planarity : 0.009 0.075 6516 Dihedral : 10.310 74.198 14322 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.10), residues: 4536 helix: -2.80 (0.09), residues: 1908 sheet: -0.92 (0.21), residues: 504 loop : -2.28 (0.11), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 377 TYR 0.034 0.004 TYR B 755 PHE 0.050 0.005 PHE B 290 TRP 0.035 0.006 TRP E 551 HIS 0.020 0.004 HIS F 406 Details of bonding type rmsd covalent geometry : bond 0.01203 (36624) covalent geometry : angle 1.08428 (49536) hydrogen bonds : bond 0.19019 ( 1326) hydrogen bonds : angle 6.97020 ( 3906) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 587 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.6723 (tttt) cc_final: 0.6523 (mtpt) REVERT: A 502 LYS cc_start: 0.7939 (mptt) cc_final: 0.7698 (mmtm) REVERT: F 196 GLU cc_start: 0.6703 (tt0) cc_final: 0.6456 (pp20) REVERT: F 275 MET cc_start: 0.8943 (mmm) cc_final: 0.8728 (mmm) REVERT: F 499 HIS cc_start: 0.8548 (m-70) cc_final: 0.8243 (m90) REVERT: F 542 ILE cc_start: 0.9033 (mm) cc_final: 0.8748 (mt) REVERT: F 564 ASP cc_start: 0.8239 (m-30) cc_final: 0.8026 (m-30) REVERT: F 627 ASP cc_start: 0.8280 (p0) cc_final: 0.8063 (p0) REVERT: E 148 LYS cc_start: 0.6661 (tttt) cc_final: 0.6455 (mtpt) REVERT: E 190 LYS cc_start: 0.7880 (mttt) cc_final: 0.7407 (tptt) REVERT: E 288 LYS cc_start: 0.8611 (mttt) cc_final: 0.8396 (mttm) REVERT: E 580 ASP cc_start: 0.8087 (p0) cc_final: 0.7850 (p0) REVERT: E 679 THR cc_start: 0.5635 (p) cc_final: 0.5251 (p) REVERT: D 502 LYS cc_start: 0.7944 (mptt) cc_final: 0.7697 (mmtm) REVERT: C 196 GLU cc_start: 0.6703 (tt0) cc_final: 0.6443 (pp20) REVERT: C 499 HIS cc_start: 0.8545 (m-70) cc_final: 0.8234 (m90) REVERT: C 564 ASP cc_start: 0.8218 (m-30) cc_final: 0.7983 (m-30) REVERT: C 627 ASP cc_start: 0.8275 (p0) cc_final: 0.8036 (p0) REVERT: B 148 LYS cc_start: 0.6651 (tttt) cc_final: 0.6444 (mtpt) REVERT: B 190 LYS cc_start: 0.7885 (mttt) cc_final: 0.7412 (tptt) REVERT: B 288 LYS cc_start: 0.8625 (mttt) cc_final: 0.8411 (mttm) REVERT: B 580 ASP cc_start: 0.8085 (p0) cc_final: 0.7852 (p0) REVERT: B 679 THR cc_start: 0.5620 (p) cc_final: 0.5232 (p) outliers start: 0 outliers final: 0 residues processed: 587 average time/residue: 0.3092 time to fit residues: 265.6061 Evaluate side-chains 300 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.0970 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 0.6980 chunk 424 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN A 499 HIS F 421 GLN E 398 GLN E 421 GLN E 499 HIS D 421 GLN D 499 HIS C 421 GLN B 398 GLN B 421 GLN B 499 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.194990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.130549 restraints weight = 46434.481| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.80 r_work: 0.3293 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 36624 Z= 0.116 Angle : 0.560 6.283 49536 Z= 0.296 Chirality : 0.043 0.147 5574 Planarity : 0.006 0.058 6516 Dihedral : 8.567 77.203 5190 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.83 % Allowed : 4.59 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.11), residues: 4536 helix: -0.79 (0.11), residues: 1950 sheet: -0.46 (0.22), residues: 486 loop : -1.79 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 256 TYR 0.007 0.001 TYR C 755 PHE 0.015 0.001 PHE F 742 TRP 0.019 0.002 TRP C 551 HIS 0.003 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00246 (36624) covalent geometry : angle 0.55978 (49536) hydrogen bonds : bond 0.05170 ( 1326) hydrogen bonds : angle 5.07747 ( 3906) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 371 time to evaluate : 1.529 Fit side-chains REVERT: A 20 LYS cc_start: 0.6056 (tppt) cc_final: 0.5832 (tptt) REVERT: A 148 LYS cc_start: 0.6564 (tttt) cc_final: 0.6199 (mtpt) REVERT: A 233 ILE cc_start: 0.8213 (tt) cc_final: 0.7964 (tt) REVERT: A 487 ARG cc_start: 0.8508 (ttt180) cc_final: 0.8125 (mtm-85) REVERT: A 757 MET cc_start: 0.8077 (tmm) cc_final: 0.7864 (tmm) REVERT: F 196 GLU cc_start: 0.6574 (tt0) cc_final: 0.6367 (pp20) REVERT: F 627 ASP cc_start: 0.8402 (p0) cc_final: 0.8202 (p0) REVERT: F 678 MET cc_start: 0.6649 (tmm) cc_final: 0.6202 (tmm) REVERT: E 148 LYS cc_start: 0.6400 (tttt) cc_final: 0.6039 (mtpt) REVERT: E 190 LYS cc_start: 0.7774 (mttt) cc_final: 0.7291 (tptt) REVERT: E 678 MET cc_start: 0.6760 (tmm) cc_final: 0.6378 (tmm) REVERT: E 679 THR cc_start: 0.5324 (p) cc_final: 0.5081 (p) REVERT: E 753 ARG cc_start: 0.7853 (ptp-170) cc_final: 0.6790 (mmp80) REVERT: D 20 LYS cc_start: 0.6052 (tppt) cc_final: 0.5831 (tptt) REVERT: D 233 ILE cc_start: 0.8217 (tt) cc_final: 0.7967 (tt) REVERT: D 487 ARG cc_start: 0.8494 (ttt180) cc_final: 0.8128 (mtm-85) REVERT: D 664 SER cc_start: 0.8145 (m) cc_final: 0.7905 (p) REVERT: D 757 MET cc_start: 0.8075 (tmm) cc_final: 0.7863 (tmm) REVERT: C 18 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7417 (mtpt) REVERT: C 196 GLU cc_start: 0.6661 (tt0) cc_final: 0.6414 (pp20) REVERT: C 564 ASP cc_start: 0.8624 (m-30) cc_final: 0.8391 (m-30) REVERT: C 678 MET cc_start: 0.6694 (tmm) cc_final: 0.6217 (tmm) REVERT: C 744 ARG cc_start: 0.6589 (ttp-110) cc_final: 0.6299 (ttm170) REVERT: B 148 LYS cc_start: 0.6402 (tttt) cc_final: 0.6040 (mtpt) REVERT: B 190 LYS cc_start: 0.7773 (mttt) cc_final: 0.7288 (tptt) REVERT: B 678 MET cc_start: 0.6759 (tmm) cc_final: 0.6373 (tmm) REVERT: B 679 THR cc_start: 0.5336 (p) cc_final: 0.5088 (p) REVERT: B 753 ARG cc_start: 0.7858 (ptp-170) cc_final: 0.6796 (mmp80) outliers start: 32 outliers final: 15 residues processed: 389 average time/residue: 0.2580 time to fit residues: 154.5109 Evaluate side-chains 305 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 289 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 584 LYS Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 584 LYS Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain B residue 101 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 180 optimal weight: 7.9990 chunk 240 optimal weight: 20.0000 chunk 265 optimal weight: 0.0870 chunk 289 optimal weight: 9.9990 chunk 49 optimal weight: 0.1980 chunk 438 optimal weight: 0.9990 chunk 236 optimal weight: 5.9990 chunk 360 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 361 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 HIS ** D 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.195598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.133370 restraints weight = 47138.293| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.83 r_work: 0.3316 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36624 Z= 0.115 Angle : 0.511 9.225 49536 Z= 0.266 Chirality : 0.043 0.150 5574 Planarity : 0.005 0.057 6516 Dihedral : 8.170 88.645 5190 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.16 % Allowed : 5.65 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.12), residues: 4536 helix: 0.03 (0.12), residues: 1974 sheet: -0.46 (0.21), residues: 546 loop : -1.31 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 256 TYR 0.008 0.001 TYR D 517 PHE 0.012 0.001 PHE B 290 TRP 0.014 0.002 TRP C 551 HIS 0.003 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00263 (36624) covalent geometry : angle 0.51085 (49536) hydrogen bonds : bond 0.04507 ( 1326) hydrogen bonds : angle 4.48726 ( 3906) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 315 time to evaluate : 1.268 Fit side-chains REVERT: A 20 LYS cc_start: 0.6151 (tppt) cc_final: 0.5885 (tptt) REVERT: A 148 LYS cc_start: 0.6772 (tttt) cc_final: 0.6353 (mtpt) REVERT: A 693 ARG cc_start: 0.7782 (tpp80) cc_final: 0.6963 (tpp80) REVERT: A 757 MET cc_start: 0.8129 (tmm) cc_final: 0.7753 (tmm) REVERT: F 18 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7482 (mtpt) REVERT: F 196 GLU cc_start: 0.6606 (tt0) cc_final: 0.6318 (pp20) REVERT: F 199 ASN cc_start: 0.7761 (m-40) cc_final: 0.7537 (m-40) REVERT: F 627 ASP cc_start: 0.8449 (p0) cc_final: 0.8045 (p0) REVERT: F 693 ARG cc_start: 0.7920 (tpp80) cc_final: 0.7412 (tpp-160) REVERT: E 100 ILE cc_start: 0.7629 (mt) cc_final: 0.7399 (mm) REVERT: E 148 LYS cc_start: 0.6523 (tttt) cc_final: 0.6055 (mtpt) REVERT: E 164 LYS cc_start: 0.4349 (OUTLIER) cc_final: 0.4124 (tttp) REVERT: E 190 LYS cc_start: 0.7800 (mttt) cc_final: 0.7307 (tptt) REVERT: E 753 ARG cc_start: 0.7922 (ptp-170) cc_final: 0.6899 (mmp-170) REVERT: D 20 LYS cc_start: 0.6138 (tppt) cc_final: 0.5872 (tptt) REVERT: D 560 ARG cc_start: 0.7911 (ttm170) cc_final: 0.7711 (ttm170) REVERT: D 564 ASP cc_start: 0.8574 (m-30) cc_final: 0.8351 (m-30) REVERT: D 693 ARG cc_start: 0.7796 (tpp80) cc_final: 0.6979 (tpp80) REVERT: D 757 MET cc_start: 0.8121 (tmm) cc_final: 0.7741 (tmm) REVERT: C 18 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7454 (mtpt) REVERT: C 196 GLU cc_start: 0.6617 (tt0) cc_final: 0.6358 (pp20) REVERT: C 564 ASP cc_start: 0.8572 (m-30) cc_final: 0.8337 (m-30) REVERT: C 678 MET cc_start: 0.6685 (tmm) cc_final: 0.6435 (tmm) REVERT: C 693 ARG cc_start: 0.7931 (tpp80) cc_final: 0.7411 (tpp-160) REVERT: C 753 ARG cc_start: 0.7899 (ptp-170) cc_final: 0.6891 (mmp-170) REVERT: B 100 ILE cc_start: 0.7626 (mt) cc_final: 0.7395 (mm) REVERT: B 148 LYS cc_start: 0.6512 (tttt) cc_final: 0.6046 (mtpt) REVERT: B 164 LYS cc_start: 0.4350 (OUTLIER) cc_final: 0.4123 (tttp) REVERT: B 190 LYS cc_start: 0.7801 (mttt) cc_final: 0.7303 (tptt) REVERT: B 753 ARG cc_start: 0.7924 (ptp-170) cc_final: 0.6900 (mmp-170) outliers start: 45 outliers final: 21 residues processed: 345 average time/residue: 0.2340 time to fit residues: 128.7508 Evaluate side-chains 301 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 276 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 630 ASP Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 164 LYS Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 642 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 286 optimal weight: 0.3980 chunk 339 optimal weight: 5.9990 chunk 431 optimal weight: 0.9980 chunk 406 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 420 optimal weight: 7.9990 chunk 229 optimal weight: 30.0000 chunk 340 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 352 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 GLN ** D 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.193322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.126882 restraints weight = 46989.037| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.69 r_work: 0.3266 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 36624 Z= 0.164 Angle : 0.540 7.736 49536 Z= 0.278 Chirality : 0.045 0.145 5574 Planarity : 0.005 0.052 6516 Dihedral : 8.157 97.622 5190 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.70 % Allowed : 5.70 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.12), residues: 4536 helix: 0.28 (0.12), residues: 1974 sheet: 0.02 (0.23), residues: 474 loop : -1.12 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 625 TYR 0.011 0.001 TYR C 517 PHE 0.020 0.002 PHE F 516 TRP 0.011 0.002 TRP C 551 HIS 0.005 0.001 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.00398 (36624) covalent geometry : angle 0.53980 (49536) hydrogen bonds : bond 0.05140 ( 1326) hydrogen bonds : angle 4.39763 ( 3906) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 292 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.6759 (tttt) cc_final: 0.6401 (mtpt) REVERT: A 433 GLU cc_start: 0.7111 (pt0) cc_final: 0.6592 (tm-30) REVERT: F 18 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7390 (mtpt) REVERT: F 84 MET cc_start: 0.6071 (OUTLIER) cc_final: 0.5785 (ptm) REVERT: F 196 GLU cc_start: 0.6691 (tt0) cc_final: 0.6450 (pp20) REVERT: F 199 ASN cc_start: 0.7759 (m-40) cc_final: 0.7535 (m-40) REVERT: F 753 ARG cc_start: 0.7902 (ptp-170) cc_final: 0.6914 (mmp-170) REVERT: E 100 ILE cc_start: 0.7613 (mt) cc_final: 0.7374 (mm) REVERT: E 148 LYS cc_start: 0.6502 (tttt) cc_final: 0.5967 (mtmt) REVERT: E 164 LYS cc_start: 0.4367 (OUTLIER) cc_final: 0.4163 (tttp) REVERT: E 190 LYS cc_start: 0.7765 (mttt) cc_final: 0.7304 (tptp) REVERT: E 564 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8352 (m-30) REVERT: E 678 MET cc_start: 0.6978 (tmm) cc_final: 0.6752 (tmm) REVERT: E 740 MET cc_start: 0.8123 (mmm) cc_final: 0.7649 (mmm) REVERT: E 753 ARG cc_start: 0.7894 (ptp-170) cc_final: 0.6950 (mmp-170) REVERT: D 433 GLU cc_start: 0.7142 (pt0) cc_final: 0.6613 (tm-30) REVERT: C 18 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7365 (mtpt) REVERT: C 196 GLU cc_start: 0.6700 (tt0) cc_final: 0.6493 (pp20) REVERT: C 564 ASP cc_start: 0.8644 (m-30) cc_final: 0.8385 (m-30) REVERT: C 678 MET cc_start: 0.6702 (tmm) cc_final: 0.6421 (tmm) REVERT: C 753 ARG cc_start: 0.7918 (ptp-170) cc_final: 0.6963 (mmp-170) REVERT: B 100 ILE cc_start: 0.7608 (mt) cc_final: 0.7372 (mm) REVERT: B 148 LYS cc_start: 0.6499 (tttt) cc_final: 0.5959 (mtmt) REVERT: B 164 LYS cc_start: 0.4366 (OUTLIER) cc_final: 0.4162 (tttp) REVERT: B 190 LYS cc_start: 0.7760 (mttt) cc_final: 0.7297 (tptp) REVERT: B 564 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8359 (m-30) REVERT: B 678 MET cc_start: 0.6972 (tmm) cc_final: 0.6745 (tmm) REVERT: B 740 MET cc_start: 0.8109 (mmm) cc_final: 0.7632 (mmm) REVERT: B 753 ARG cc_start: 0.7894 (ptp-170) cc_final: 0.6943 (mmp-170) outliers start: 66 outliers final: 42 residues processed: 343 average time/residue: 0.2465 time to fit residues: 134.8466 Evaluate side-chains 317 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 268 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain F residue 630 ASP Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 164 LYS Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 647 LEU Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 699 ILE Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 699 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 326 optimal weight: 0.4980 chunk 173 optimal weight: 0.7980 chunk 333 optimal weight: 2.9990 chunk 304 optimal weight: 40.0000 chunk 266 optimal weight: 5.9990 chunk 161 optimal weight: 0.0470 chunk 434 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 299 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 268 optimal weight: 10.0000 overall best weight: 1.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 763 GLN F 421 GLN D 763 GLN C 421 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.194584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.131030 restraints weight = 47143.190| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.81 r_work: 0.3269 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36624 Z= 0.116 Angle : 0.493 6.464 49536 Z= 0.254 Chirality : 0.043 0.145 5574 Planarity : 0.004 0.050 6516 Dihedral : 8.035 103.618 5190 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.44 % Allowed : 6.73 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.12), residues: 4536 helix: 0.64 (0.12), residues: 1962 sheet: 0.17 (0.25), residues: 414 loop : -0.97 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 65 TYR 0.008 0.001 TYR A 517 PHE 0.012 0.001 PHE C 516 TRP 0.011 0.001 TRP C 551 HIS 0.002 0.001 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.00274 (36624) covalent geometry : angle 0.49276 (49536) hydrogen bonds : bond 0.04337 ( 1326) hydrogen bonds : angle 4.19773 ( 3906) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 289 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.6758 (tttt) cc_final: 0.6384 (mtpt) REVERT: A 433 GLU cc_start: 0.7116 (pt0) cc_final: 0.6574 (tm-30) REVERT: A 584 LYS cc_start: 0.4934 (OUTLIER) cc_final: 0.4401 (mttm) REVERT: F 18 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7333 (mtpt) REVERT: F 84 MET cc_start: 0.6136 (ptm) cc_final: 0.5825 (ptm) REVERT: F 196 GLU cc_start: 0.6698 (tt0) cc_final: 0.6457 (pp20) REVERT: F 753 ARG cc_start: 0.7936 (ptp-170) cc_final: 0.6916 (mmp-170) REVERT: E 100 ILE cc_start: 0.7591 (mt) cc_final: 0.7339 (mm) REVERT: E 148 LYS cc_start: 0.6502 (tttt) cc_final: 0.5969 (mtmt) REVERT: E 190 LYS cc_start: 0.7683 (mttt) cc_final: 0.7232 (tptp) REVERT: E 578 GLU cc_start: 0.7847 (pt0) cc_final: 0.7535 (pt0) REVERT: E 740 MET cc_start: 0.8069 (mmm) cc_final: 0.7562 (mmm) REVERT: E 753 ARG cc_start: 0.7861 (ptp-170) cc_final: 0.6951 (mmp-170) REVERT: D 433 GLU cc_start: 0.7122 (pt0) cc_final: 0.6588 (tm-30) REVERT: D 584 LYS cc_start: 0.4957 (OUTLIER) cc_final: 0.4432 (mttm) REVERT: C 18 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7317 (mtpt) REVERT: C 196 GLU cc_start: 0.6712 (tt0) cc_final: 0.6448 (pp20) REVERT: C 564 ASP cc_start: 0.8640 (m-30) cc_final: 0.8381 (m-30) REVERT: C 753 ARG cc_start: 0.7938 (ptp-170) cc_final: 0.6964 (mmp-170) REVERT: B 100 ILE cc_start: 0.7589 (mt) cc_final: 0.7341 (mm) REVERT: B 148 LYS cc_start: 0.6499 (tttt) cc_final: 0.5963 (mtmt) REVERT: B 190 LYS cc_start: 0.7673 (mttt) cc_final: 0.7223 (tptp) REVERT: B 578 GLU cc_start: 0.7844 (pt0) cc_final: 0.7533 (pt0) REVERT: B 740 MET cc_start: 0.8074 (mmm) cc_final: 0.7567 (mmm) REVERT: B 753 ARG cc_start: 0.7859 (ptp-170) cc_final: 0.6954 (mmp-170) outliers start: 56 outliers final: 30 residues processed: 338 average time/residue: 0.2513 time to fit residues: 134.8217 Evaluate side-chains 318 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 284 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 630 ASP Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 699 ILE Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 584 LYS Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 699 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 55 optimal weight: 2.9990 chunk 412 optimal weight: 5.9990 chunk 356 optimal weight: 0.9990 chunk 409 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 241 optimal weight: 20.0000 chunk 440 optimal weight: 7.9990 chunk 423 optimal weight: 0.9990 chunk 404 optimal weight: 0.2980 chunk 392 optimal weight: 5.9990 chunk 207 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN F 33 ASN F 199 ASN D 33 ASN C 33 ASN C 199 ASN B 33 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.196127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.130996 restraints weight = 47173.699| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.71 r_work: 0.3337 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 36624 Z= 0.094 Angle : 0.462 8.055 49536 Z= 0.237 Chirality : 0.043 0.141 5574 Planarity : 0.004 0.048 6516 Dihedral : 7.837 109.823 5190 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.14 % Allowed : 7.53 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.13), residues: 4536 helix: 0.87 (0.12), residues: 1980 sheet: -0.11 (0.23), residues: 486 loop : -0.78 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 359 TYR 0.007 0.001 TYR F 517 PHE 0.008 0.001 PHE B 290 TRP 0.010 0.001 TRP F 551 HIS 0.002 0.000 HIS F 406 Details of bonding type rmsd covalent geometry : bond 0.00215 (36624) covalent geometry : angle 0.46225 (49536) hydrogen bonds : bond 0.03567 ( 1326) hydrogen bonds : angle 3.89972 ( 3906) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 311 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.6747 (tttt) cc_final: 0.6372 (mtpt) REVERT: A 433 GLU cc_start: 0.6996 (pt0) cc_final: 0.6556 (tm-30) REVERT: A 584 LYS cc_start: 0.5097 (OUTLIER) cc_final: 0.4782 (mttt) REVERT: A 744 ARG cc_start: 0.7484 (ttm170) cc_final: 0.7212 (mtp180) REVERT: F 18 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7254 (mtpt) REVERT: F 84 MET cc_start: 0.6105 (OUTLIER) cc_final: 0.5857 (ptm) REVERT: F 196 GLU cc_start: 0.6696 (tt0) cc_final: 0.6411 (pp20) REVERT: F 630 ASP cc_start: 0.6857 (OUTLIER) cc_final: 0.6495 (t70) REVERT: F 753 ARG cc_start: 0.7903 (ptp-170) cc_final: 0.6919 (mmp-170) REVERT: E 100 ILE cc_start: 0.7671 (mt) cc_final: 0.7408 (mm) REVERT: E 148 LYS cc_start: 0.6483 (tttt) cc_final: 0.5949 (mtmt) REVERT: E 190 LYS cc_start: 0.7542 (mttt) cc_final: 0.7098 (tptp) REVERT: E 550 MET cc_start: 0.4486 (ttp) cc_final: 0.3880 (tpt) REVERT: E 753 ARG cc_start: 0.7845 (ptp-170) cc_final: 0.6982 (mmp-170) REVERT: D 20 LYS cc_start: 0.6391 (tppt) cc_final: 0.6180 (tptt) REVERT: D 190 LYS cc_start: 0.7580 (mttt) cc_final: 0.7152 (tptt) REVERT: D 433 GLU cc_start: 0.7008 (pt0) cc_final: 0.6571 (tm-30) REVERT: D 584 LYS cc_start: 0.5111 (OUTLIER) cc_final: 0.4803 (mttt) REVERT: D 678 MET cc_start: 0.6584 (tmm) cc_final: 0.6049 (tmm) REVERT: C 18 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7234 (mtpt) REVERT: C 196 GLU cc_start: 0.6671 (tt0) cc_final: 0.6442 (pp20) REVERT: C 564 ASP cc_start: 0.8557 (m-30) cc_final: 0.8313 (m-30) REVERT: C 630 ASP cc_start: 0.6837 (OUTLIER) cc_final: 0.6542 (t70) REVERT: C 753 ARG cc_start: 0.7949 (ptp-170) cc_final: 0.6962 (mmp-170) REVERT: B 100 ILE cc_start: 0.7667 (mt) cc_final: 0.7404 (mm) REVERT: B 148 LYS cc_start: 0.6481 (tttt) cc_final: 0.5947 (mtmt) REVERT: B 190 LYS cc_start: 0.7543 (mttt) cc_final: 0.7094 (tptp) REVERT: B 550 MET cc_start: 0.4465 (ttp) cc_final: 0.3850 (tpt) REVERT: B 753 ARG cc_start: 0.7843 (ptp-170) cc_final: 0.6981 (mmp-170) outliers start: 44 outliers final: 29 residues processed: 347 average time/residue: 0.2524 time to fit residues: 138.8329 Evaluate side-chains 326 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 290 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 630 ASP Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 630 ASP Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 647 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 584 LYS Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 341 optimal weight: 4.9990 chunk 271 optimal weight: 2.9990 chunk 314 optimal weight: 0.0010 chunk 58 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 347 optimal weight: 8.9990 chunk 423 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 447 optimal weight: 2.9990 chunk 369 optimal weight: 10.0000 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 199 ASN F 33 ASN E 199 ASN D 33 ASN D 199 ASN C 33 ASN B 33 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.194755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.130020 restraints weight = 47191.164| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.61 r_work: 0.3279 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36624 Z= 0.117 Angle : 0.479 8.020 49536 Z= 0.245 Chirality : 0.043 0.162 5574 Planarity : 0.004 0.048 6516 Dihedral : 7.837 110.432 5190 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.37 % Allowed : 7.77 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.13), residues: 4536 helix: 0.90 (0.12), residues: 1980 sheet: 0.32 (0.24), residues: 438 loop : -0.66 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 359 TYR 0.008 0.001 TYR F 517 PHE 0.013 0.001 PHE C 516 TRP 0.008 0.001 TRP C 551 HIS 0.002 0.001 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.00280 (36624) covalent geometry : angle 0.47913 (49536) hydrogen bonds : bond 0.04013 ( 1326) hydrogen bonds : angle 3.86872 ( 3906) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 292 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.6822 (tttt) cc_final: 0.6322 (mtpt) REVERT: A 433 GLU cc_start: 0.7169 (pt0) cc_final: 0.6631 (tm-30) REVERT: A 561 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8318 (mm-30) REVERT: A 582 ILE cc_start: 0.7603 (mt) cc_final: 0.7377 (tt) REVERT: A 584 LYS cc_start: 0.5146 (OUTLIER) cc_final: 0.4753 (mttt) REVERT: A 678 MET cc_start: 0.6831 (tmm) cc_final: 0.6324 (tmm) REVERT: A 744 ARG cc_start: 0.7396 (ttm170) cc_final: 0.7119 (mtp180) REVERT: F 18 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7189 (mtpt) REVERT: F 84 MET cc_start: 0.5993 (OUTLIER) cc_final: 0.5655 (ptm) REVERT: F 196 GLU cc_start: 0.6702 (tt0) cc_final: 0.6432 (pp20) REVERT: F 630 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6760 (t70) REVERT: F 753 ARG cc_start: 0.7947 (ptp-170) cc_final: 0.6928 (mmp-170) REVERT: E 100 ILE cc_start: 0.7675 (mt) cc_final: 0.7405 (mm) REVERT: E 148 LYS cc_start: 0.6577 (tttt) cc_final: 0.6004 (mtmt) REVERT: E 190 LYS cc_start: 0.7413 (mttt) cc_final: 0.6986 (tptp) REVERT: E 550 MET cc_start: 0.4779 (ttp) cc_final: 0.4009 (tpt) REVERT: E 578 GLU cc_start: 0.7969 (pt0) cc_final: 0.7758 (pt0) REVERT: E 753 ARG cc_start: 0.7855 (ptp-170) cc_final: 0.6948 (mmp-170) REVERT: D 433 GLU cc_start: 0.7165 (pt0) cc_final: 0.6634 (tm-30) REVERT: D 582 ILE cc_start: 0.7600 (mt) cc_final: 0.7377 (tt) REVERT: D 584 LYS cc_start: 0.5195 (OUTLIER) cc_final: 0.4809 (mttt) REVERT: D 678 MET cc_start: 0.6867 (tmm) cc_final: 0.6389 (tmm) REVERT: C 18 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7171 (mtpt) REVERT: C 196 GLU cc_start: 0.6697 (tt0) cc_final: 0.6423 (pp20) REVERT: C 564 ASP cc_start: 0.8802 (m-30) cc_final: 0.8564 (m-30) REVERT: C 630 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6871 (t70) REVERT: C 753 ARG cc_start: 0.7944 (ptp-170) cc_final: 0.6903 (mmp-170) REVERT: B 100 ILE cc_start: 0.7671 (mt) cc_final: 0.7404 (mm) REVERT: B 148 LYS cc_start: 0.6570 (tttt) cc_final: 0.6007 (mtmt) REVERT: B 190 LYS cc_start: 0.7403 (mttt) cc_final: 0.6976 (tptp) REVERT: B 550 MET cc_start: 0.4748 (ttp) cc_final: 0.3984 (tpt) REVERT: B 578 GLU cc_start: 0.7972 (pt0) cc_final: 0.7765 (pt0) REVERT: B 753 ARG cc_start: 0.7848 (ptp-170) cc_final: 0.6944 (mmp-170) outliers start: 53 outliers final: 33 residues processed: 333 average time/residue: 0.2349 time to fit residues: 125.0673 Evaluate side-chains 321 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 281 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 630 ASP Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 630 ASP Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 584 LYS Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 630 ASP Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 642 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 354 optimal weight: 10.0000 chunk 198 optimal weight: 0.9980 chunk 280 optimal weight: 4.9990 chunk 250 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 chunk 385 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 421 GLN F 33 ASN D 421 GLN C 33 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.192608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.127580 restraints weight = 47113.685| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.76 r_work: 0.3233 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 36624 Z= 0.172 Angle : 0.537 8.487 49536 Z= 0.273 Chirality : 0.045 0.161 5574 Planarity : 0.004 0.048 6516 Dihedral : 8.022 109.858 5190 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.60 % Allowed : 8.13 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.13), residues: 4536 helix: 0.84 (0.12), residues: 1962 sheet: 0.26 (0.24), residues: 438 loop : -0.70 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 711 TYR 0.012 0.001 TYR D 203 PHE 0.016 0.002 PHE A 516 TRP 0.007 0.002 TRP C 551 HIS 0.004 0.001 HIS F 406 Details of bonding type rmsd covalent geometry : bond 0.00424 (36624) covalent geometry : angle 0.53736 (49536) hydrogen bonds : bond 0.04992 ( 1326) hydrogen bonds : angle 4.03393 ( 3906) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 283 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.6733 (tttt) cc_final: 0.6324 (mtpt) REVERT: A 433 GLU cc_start: 0.7038 (pt0) cc_final: 0.6617 (tm-30) REVERT: A 561 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8098 (mm-30) REVERT: A 582 ILE cc_start: 0.7525 (mt) cc_final: 0.7325 (tt) REVERT: A 584 LYS cc_start: 0.5030 (OUTLIER) cc_final: 0.4536 (mttm) REVERT: F 18 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7308 (mtpt) REVERT: F 84 MET cc_start: 0.5976 (OUTLIER) cc_final: 0.5704 (ptm) REVERT: F 196 GLU cc_start: 0.6729 (tt0) cc_final: 0.6515 (pp20) REVERT: F 630 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.6934 (t70) REVERT: F 753 ARG cc_start: 0.7934 (ptp-170) cc_final: 0.6935 (mmp-170) REVERT: E 100 ILE cc_start: 0.7614 (mt) cc_final: 0.7330 (mm) REVERT: E 148 LYS cc_start: 0.6506 (tttt) cc_final: 0.5958 (mtmt) REVERT: E 190 LYS cc_start: 0.7441 (mttt) cc_final: 0.7023 (tptp) REVERT: E 550 MET cc_start: 0.4551 (OUTLIER) cc_final: 0.3880 (tpt) REVERT: E 753 ARG cc_start: 0.7842 (ptp-170) cc_final: 0.7059 (mmp-170) REVERT: D 433 GLU cc_start: 0.7034 (pt0) cc_final: 0.6625 (tm-30) REVERT: D 561 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8109 (mm-30) REVERT: D 584 LYS cc_start: 0.5068 (OUTLIER) cc_final: 0.4717 (mttt) REVERT: D 625 ARG cc_start: 0.7848 (tpp80) cc_final: 0.7579 (tpt-90) REVERT: C 18 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7322 (mtpt) REVERT: C 196 GLU cc_start: 0.6586 (tt0) cc_final: 0.6361 (pp20) REVERT: C 564 ASP cc_start: 0.8578 (m-30) cc_final: 0.8323 (m-30) REVERT: C 630 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6869 (t70) REVERT: C 753 ARG cc_start: 0.7958 (ptp-170) cc_final: 0.6931 (mmp-170) REVERT: B 100 ILE cc_start: 0.7614 (mt) cc_final: 0.7333 (mm) REVERT: B 148 LYS cc_start: 0.6495 (tttt) cc_final: 0.5955 (mtmt) REVERT: B 190 LYS cc_start: 0.7435 (mttt) cc_final: 0.7019 (tptp) REVERT: B 550 MET cc_start: 0.4525 (OUTLIER) cc_final: 0.3862 (tpt) REVERT: B 753 ARG cc_start: 0.7842 (ptp-170) cc_final: 0.7064 (mmp-170) outliers start: 62 outliers final: 41 residues processed: 323 average time/residue: 0.2371 time to fit residues: 123.4932 Evaluate side-chains 328 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 278 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain F residue 630 ASP Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 699 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 584 LYS Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 630 ASP Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 699 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 387 optimal weight: 4.9990 chunk 23 optimal weight: 0.0670 chunk 195 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 368 optimal weight: 5.9990 chunk 200 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN F 33 ASN D 33 ASN C 33 ASN B 33 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.193579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.129971 restraints weight = 46829.328| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.82 r_work: 0.3204 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36624 Z= 0.136 Angle : 0.500 8.436 49536 Z= 0.256 Chirality : 0.044 0.172 5574 Planarity : 0.004 0.047 6516 Dihedral : 7.963 111.138 5190 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.24 % Allowed : 8.57 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.13), residues: 4536 helix: 0.98 (0.12), residues: 1950 sheet: -0.10 (0.22), residues: 510 loop : -0.65 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 359 TYR 0.009 0.001 TYR F 517 PHE 0.014 0.001 PHE C 516 TRP 0.008 0.001 TRP C 551 HIS 0.003 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00330 (36624) covalent geometry : angle 0.49988 (49536) hydrogen bonds : bond 0.04409 ( 1326) hydrogen bonds : angle 3.95632 ( 3906) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 282 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.6716 (tttt) cc_final: 0.6338 (mtpt) REVERT: A 433 GLU cc_start: 0.7104 (pt0) cc_final: 0.6644 (tm-30) REVERT: A 561 GLU cc_start: 0.8247 (mm-30) cc_final: 0.8007 (mm-30) REVERT: A 584 LYS cc_start: 0.4775 (OUTLIER) cc_final: 0.4397 (mttt) REVERT: A 625 ARG cc_start: 0.7748 (tpp80) cc_final: 0.7468 (tpt-90) REVERT: F 18 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7220 (mtpt) REVERT: F 84 MET cc_start: 0.5842 (OUTLIER) cc_final: 0.5550 (ptm) REVERT: F 196 GLU cc_start: 0.6702 (tt0) cc_final: 0.6443 (pp20) REVERT: F 753 ARG cc_start: 0.7857 (ptp-170) cc_final: 0.6878 (mmp-170) REVERT: E 100 ILE cc_start: 0.7529 (mt) cc_final: 0.7255 (mm) REVERT: E 148 LYS cc_start: 0.6474 (tttt) cc_final: 0.5924 (mtmt) REVERT: E 190 LYS cc_start: 0.7470 (mttt) cc_final: 0.7030 (tptp) REVERT: E 550 MET cc_start: 0.4613 (OUTLIER) cc_final: 0.3885 (tpt) REVERT: E 608 MET cc_start: 0.8496 (ttm) cc_final: 0.8073 (mtp) REVERT: E 753 ARG cc_start: 0.7737 (ptp-170) cc_final: 0.6980 (mmp-170) REVERT: D 433 GLU cc_start: 0.7102 (pt0) cc_final: 0.6652 (tm-30) REVERT: D 561 GLU cc_start: 0.8268 (mm-30) cc_final: 0.8021 (mm-30) REVERT: D 584 LYS cc_start: 0.4667 (OUTLIER) cc_final: 0.4441 (mttt) REVERT: D 625 ARG cc_start: 0.7739 (tpp80) cc_final: 0.7387 (tpt-90) REVERT: C 18 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7235 (mtpt) REVERT: C 196 GLU cc_start: 0.6580 (tt0) cc_final: 0.6327 (pp20) REVERT: C 564 ASP cc_start: 0.8516 (m-30) cc_final: 0.8268 (m-30) REVERT: C 630 ASP cc_start: 0.6955 (OUTLIER) cc_final: 0.6678 (t70) REVERT: C 753 ARG cc_start: 0.7809 (ptp-170) cc_final: 0.6812 (mmp-170) REVERT: B 100 ILE cc_start: 0.7525 (mt) cc_final: 0.7254 (mm) REVERT: B 148 LYS cc_start: 0.6466 (tttt) cc_final: 0.5921 (mtmt) REVERT: B 190 LYS cc_start: 0.7463 (mttt) cc_final: 0.7025 (tptp) REVERT: B 550 MET cc_start: 0.4719 (OUTLIER) cc_final: 0.3963 (tpt) REVERT: B 608 MET cc_start: 0.8490 (ttm) cc_final: 0.8066 (mtp) REVERT: B 753 ARG cc_start: 0.7744 (ptp-170) cc_final: 0.6988 (mmp-170) outliers start: 48 outliers final: 38 residues processed: 314 average time/residue: 0.2322 time to fit residues: 115.7421 Evaluate side-chains 325 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 279 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 584 LYS Chi-restraints excluded: chain E residue 699 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 584 LYS Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 630 ASP Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 699 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 93 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 312 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 271 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 318 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN D 33 ASN B 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.188877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.121748 restraints weight = 47010.278| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.72 r_work: 0.3164 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 36624 Z= 0.360 Angle : 0.719 9.262 49536 Z= 0.365 Chirality : 0.052 0.188 5574 Planarity : 0.006 0.054 6516 Dihedral : 8.453 106.339 5190 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.47 % Allowed : 8.49 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.12), residues: 4536 helix: 0.29 (0.12), residues: 1968 sheet: -0.53 (0.22), residues: 510 loop : -1.01 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 424 TYR 0.021 0.002 TYR D 203 PHE 0.028 0.003 PHE C 516 TRP 0.009 0.002 TRP E 551 HIS 0.010 0.002 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.00895 (36624) covalent geometry : angle 0.71863 (49536) hydrogen bonds : bond 0.07090 ( 1326) hydrogen bonds : angle 4.51542 ( 3906) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 284 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.6511 (tppt) cc_final: 0.6287 (tptt) REVERT: A 148 LYS cc_start: 0.6765 (tttt) cc_final: 0.6207 (mtpt) REVERT: A 233 ILE cc_start: 0.8119 (tt) cc_final: 0.7813 (tt) REVERT: A 433 GLU cc_start: 0.7093 (pt0) cc_final: 0.6730 (tm-30) REVERT: A 561 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8249 (mm-30) REVERT: A 584 LYS cc_start: 0.4705 (OUTLIER) cc_final: 0.4105 (mttt) REVERT: A 753 ARG cc_start: 0.7655 (ptp-170) cc_final: 0.6830 (mmp-170) REVERT: F 18 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7296 (mtpt) REVERT: F 196 GLU cc_start: 0.6761 (tt0) cc_final: 0.6458 (pp20) REVERT: F 753 ARG cc_start: 0.7959 (ptp-170) cc_final: 0.6955 (mmp-170) REVERT: E 20 LYS cc_start: 0.6896 (tppt) cc_final: 0.5801 (ttpt) REVERT: E 100 ILE cc_start: 0.7544 (mt) cc_final: 0.7270 (mm) REVERT: E 148 LYS cc_start: 0.6516 (tttt) cc_final: 0.5934 (mtmt) REVERT: E 190 LYS cc_start: 0.7401 (mttt) cc_final: 0.6962 (tptp) REVERT: E 550 MET cc_start: 0.4953 (OUTLIER) cc_final: 0.4313 (tpt) REVERT: E 608 MET cc_start: 0.8756 (ttm) cc_final: 0.8320 (mtp) REVERT: E 753 ARG cc_start: 0.7831 (ptp-170) cc_final: 0.6999 (mmp-170) REVERT: D 20 LYS cc_start: 0.6514 (tppt) cc_final: 0.6289 (tptt) REVERT: D 233 ILE cc_start: 0.8110 (tt) cc_final: 0.7805 (tt) REVERT: D 433 GLU cc_start: 0.7093 (pt0) cc_final: 0.6736 (tm-30) REVERT: D 561 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8288 (mm-30) REVERT: D 584 LYS cc_start: 0.4842 (OUTLIER) cc_final: 0.4311 (mttt) REVERT: D 753 ARG cc_start: 0.7669 (ptp-170) cc_final: 0.6840 (mmp-170) REVERT: C 18 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7278 (mtpt) REVERT: C 196 GLU cc_start: 0.6768 (tt0) cc_final: 0.6477 (pp20) REVERT: C 564 ASP cc_start: 0.8753 (m-30) cc_final: 0.8536 (m-30) REVERT: C 753 ARG cc_start: 0.7967 (ptp-170) cc_final: 0.6917 (mmp-170) REVERT: B 20 LYS cc_start: 0.6889 (tppt) cc_final: 0.5802 (ttpt) REVERT: B 100 ILE cc_start: 0.7530 (mt) cc_final: 0.7260 (mm) REVERT: B 148 LYS cc_start: 0.6500 (tttt) cc_final: 0.5923 (mtmt) REVERT: B 190 LYS cc_start: 0.7393 (mttt) cc_final: 0.6957 (tptp) REVERT: B 550 MET cc_start: 0.4957 (OUTLIER) cc_final: 0.4318 (tpt) REVERT: B 608 MET cc_start: 0.8768 (ttm) cc_final: 0.8331 (mtp) REVERT: B 709 ARG cc_start: 0.6888 (mmt90) cc_final: 0.6516 (mmp80) REVERT: B 753 ARG cc_start: 0.7816 (ptp-170) cc_final: 0.6992 (mmp-170) outliers start: 57 outliers final: 36 residues processed: 323 average time/residue: 0.2501 time to fit residues: 126.5464 Evaluate side-chains 317 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 275 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 699 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 584 LYS Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 699 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 447 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 chunk 215 optimal weight: 9.9990 chunk 354 optimal weight: 0.9990 chunk 281 optimal weight: 0.6980 chunk 314 optimal weight: 7.9990 chunk 401 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 224 optimal weight: 0.4980 chunk 210 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN F 33 ASN D 33 ASN C 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.193917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.132560 restraints weight = 46631.569| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.88 r_work: 0.3285 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36624 Z= 0.110 Angle : 0.502 8.500 49536 Z= 0.259 Chirality : 0.043 0.171 5574 Planarity : 0.004 0.045 6516 Dihedral : 8.061 111.898 5190 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.95 % Allowed : 9.16 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.13), residues: 4536 helix: 0.93 (0.12), residues: 1950 sheet: -0.28 (0.22), residues: 510 loop : -0.74 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 709 TYR 0.009 0.001 TYR F 517 PHE 0.011 0.001 PHE C 516 TRP 0.012 0.001 TRP B 551 HIS 0.003 0.001 HIS F 406 Details of bonding type rmsd covalent geometry : bond 0.00251 (36624) covalent geometry : angle 0.50222 (49536) hydrogen bonds : bond 0.04238 ( 1326) hydrogen bonds : angle 4.02140 ( 3906) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10129.58 seconds wall clock time: 173 minutes 13.93 seconds (10393.93 seconds total)