Starting phenix.real_space_refine on Mon Jul 6 14:24:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vcv_31897/07_2026/7vcv_31897.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vcv_31897/07_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_31897/07_2026/7vcv_31897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vcv_31897/07_2026/7vcv_31897.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7vcv_31897/07_2026/7vcv_31897.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vcv_31897/07_2026/7vcv_31897.cif" model { file = "/net/cci-nas-00/data/ceres_data/7vcv_31897/07_2026/7vcv_31897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vcv_31897/07_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.11, per 1000 atoms: 0.20 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: 3.31 Conformation dependent library (CDL) restraints added in 1.4 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: 1.17 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: 7.03 Time building geometry restraints manager: 4.35 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: 21478 14.84 - 29.68: 948 29.68 - 44.52: 200 44.52 - 59.36: 42 59.36 - 74.20: 18 Dihedral angle restraints: 22686 sinusoidal: 9582 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 22683 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: 0.13 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: 1.650 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: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.520 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.080 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:1.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 9.724 74.198 14190 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/Z covalent geometry : bond 0.01203 / 0.49 (36624) covalent geometry : angle 1.08428 / 0.61 (49536) hydrogen bonds : bond 0.19019 / 12.29 ( 1326) hydrogen bonds : angle 6.97020 / 4.80 ( 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 : 1.479 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: 0.2760 time to fit residues: 239.8725 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 : 1.381 ------------------------------------------------------------------------------- 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... 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 = 0.4290 r_free = 0.4290 target = 0.195252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.132899 restraints weight = 46440.306| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.73 r_work: 0.3308 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36624 Z= 0.117 Angle : 0.558 6.304 49536 Z= 0.294 Chirality : 0.043 0.144 5574 Planarity : 0.006 0.057 6516 Dihedral : 6.967 69.228 5058 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.77 % Allowed : 4.49 % Favored : 94.74 % 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: -1.88 (0.11), residues: 4536 helix: -0.80 (0.11), residues: 1962 sheet: -0.46 (0.22), residues: 486 loop : -1.83 (0.12), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 256 TYR 0.006 0.001 TYR C 755 PHE 0.015 0.001 PHE F 742 TRP 0.019 0.002 TRP F 551 HIS 0.003 0.001 HIS B 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (36624) covalent geometry : angle 0.55791 / 0.29 (49536) hydrogen bonds : bond 0.05022 / 3.27 ( 1326) hydrogen bonds : angle 5.02705 / 3.44 ( 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 411 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 381 time to evaluate : 1.052 Fit side-chains REVERT: A 20 LYS cc_start: 0.6019 (tppt) cc_final: 0.5782 (tptt) REVERT: A 148 LYS cc_start: 0.6602 (tttt) cc_final: 0.6217 (mtpt) REVERT: A 190 LYS cc_start: 0.7921 (mttt) cc_final: 0.7477 (tptt) REVERT: A 233 ILE cc_start: 0.8233 (tt) cc_final: 0.7980 (tt) REVERT: A 487 ARG cc_start: 0.8474 (ttt180) cc_final: 0.8116 (mtm-85) REVERT: A 564 ASP cc_start: 0.8488 (m-30) cc_final: 0.8280 (m-30) REVERT: A 757 MET cc_start: 0.8133 (tmm) cc_final: 0.7904 (tmm) REVERT: F 584 LYS cc_start: 0.4553 (OUTLIER) cc_final: 0.3937 (mttt) REVERT: F 678 MET cc_start: 0.6660 (tmm) cc_final: 0.6320 (tmm) REVERT: E 148 LYS cc_start: 0.6446 (tttt) cc_final: 0.6071 (mtpt) REVERT: E 190 LYS cc_start: 0.7786 (mttt) cc_final: 0.7306 (tptt) REVERT: E 678 MET cc_start: 0.6766 (tmm) cc_final: 0.6374 (tmm) REVERT: E 679 THR cc_start: 0.5364 (p) cc_final: 0.5116 (p) REVERT: E 753 ARG cc_start: 0.7858 (ptp-170) cc_final: 0.6802 (mmp80) REVERT: D 20 LYS cc_start: 0.6011 (tppt) cc_final: 0.5774 (tptt) REVERT: D 190 LYS cc_start: 0.7924 (mttt) cc_final: 0.7480 (tptt) REVERT: D 233 ILE cc_start: 0.8233 (tt) cc_final: 0.7978 (tt) REVERT: D 487 ARG cc_start: 0.8463 (ttt180) cc_final: 0.8121 (mtm-85) REVERT: D 757 MET cc_start: 0.8130 (tmm) cc_final: 0.7900 (tmm) REVERT: C 18 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7433 (mtpt) REVERT: C 196 GLU cc_start: 0.6584 (tt0) cc_final: 0.6382 (pp20) REVERT: C 275 MET cc_start: 0.9059 (mmm) cc_final: 0.8853 (mmm) REVERT: C 564 ASP cc_start: 0.8615 (m-30) cc_final: 0.8381 (m-30) REVERT: C 627 ASP cc_start: 0.8357 (p0) cc_final: 0.8123 (p0) REVERT: C 678 MET cc_start: 0.6685 (tmm) cc_final: 0.6183 (tmm) REVERT: C 744 ARG cc_start: 0.6781 (ttp-110) cc_final: 0.6430 (ttm170) REVERT: B 148 LYS cc_start: 0.6445 (tttt) cc_final: 0.6074 (mtpt) REVERT: B 190 LYS cc_start: 0.7785 (mttt) cc_final: 0.7304 (tptt) REVERT: B 678 MET cc_start: 0.6754 (tmm) cc_final: 0.6359 (tmm) REVERT: B 679 THR cc_start: 0.5374 (p) cc_final: 0.5120 (p) REVERT: B 753 ARG cc_start: 0.7865 (ptp-170) cc_final: 0.6809 (mmp80) outliers start: 30 outliers final: 14 residues processed: 399 average time/residue: 0.2320 time to fit residues: 144.0692 Evaluate side-chains 310 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 294 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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: 2.9990 chunk 240 optimal weight: 20.0000 chunk 265 optimal weight: 0.7980 chunk 289 optimal weight: 10.0000 chunk 49 optimal weight: 0.1980 chunk 438 optimal weight: 0.8980 chunk 236 optimal weight: 4.9990 chunk 360 optimal weight: 0.3980 chunk 120 optimal weight: 3.9990 chunk 361 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 499 HIS C 499 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.196165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.134201 restraints weight = 47152.210| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.71 r_work: 0.3329 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 36624 Z= 0.106 Angle : 0.503 8.940 49536 Z= 0.262 Chirality : 0.043 0.183 5574 Planarity : 0.005 0.057 6516 Dihedral : 6.503 66.952 5058 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.14 % Allowed : 5.75 % Favored : 93.11 % 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: -0.92 (0.12), residues: 4536 helix: 0.06 (0.12), residues: 1974 sheet: -0.41 (0.21), residues: 546 loop : -1.28 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 256 TYR 0.008 0.001 TYR C 517 PHE 0.012 0.001 PHE B 290 TRP 0.014 0.002 TRP A 551 HIS 0.003 0.001 HIS F 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (36624) covalent geometry : angle 0.50264 / 0.26 (49536) hydrogen bonds : bond 0.04337 / 2.82 ( 1326) hydrogen bonds : angle 4.46308 / 3.06 ( 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 370 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 326 time to evaluate : 1.413 Fit side-chains REVERT: A 20 LYS cc_start: 0.6020 (tppt) cc_final: 0.5753 (tptt) REVERT: A 148 LYS cc_start: 0.6732 (tttt) cc_final: 0.6350 (mtpt) REVERT: A 190 LYS cc_start: 0.7920 (mttt) cc_final: 0.7486 (tptt) REVERT: A 564 ASP cc_start: 0.8548 (m-30) cc_final: 0.8332 (m-30) REVERT: A 693 ARG cc_start: 0.7762 (tpp80) cc_final: 0.7254 (tpp-160) REVERT: A 757 MET cc_start: 0.8135 (tmm) cc_final: 0.7765 (tmm) REVERT: F 18 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7457 (mtpt) REVERT: F 199 ASN cc_start: 0.7748 (m-40) cc_final: 0.7544 (m110) REVERT: F 693 ARG cc_start: 0.7932 (tpp80) cc_final: 0.7427 (tpp-160) REVERT: E 148 LYS cc_start: 0.6488 (tttt) cc_final: 0.6027 (mtpt) REVERT: E 190 LYS cc_start: 0.7809 (mttt) cc_final: 0.7322 (tptt) REVERT: E 753 ARG cc_start: 0.7922 (ptp-170) cc_final: 0.6907 (mmp-170) REVERT: D 20 LYS cc_start: 0.6007 (tppt) cc_final: 0.5741 (tptt) REVERT: D 190 LYS cc_start: 0.7928 (mttt) cc_final: 0.7495 (tptt) REVERT: D 564 ASP cc_start: 0.8494 (m-30) cc_final: 0.8272 (m-30) REVERT: D 693 ARG cc_start: 0.7761 (tpp80) cc_final: 0.7261 (tpp-160) REVERT: D 757 MET cc_start: 0.8127 (tmm) cc_final: 0.7759 (tmm) REVERT: C 18 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7444 (mtpt) REVERT: C 196 GLU cc_start: 0.6621 (tt0) cc_final: 0.6359 (pp20) REVERT: C 564 ASP cc_start: 0.8585 (m-30) cc_final: 0.8324 (m-30) REVERT: C 627 ASP cc_start: 0.8461 (p0) cc_final: 0.8043 (p0) REVERT: C 693 ARG cc_start: 0.7946 (tpp80) cc_final: 0.7432 (tpp-160) REVERT: B 148 LYS cc_start: 0.6485 (tttt) cc_final: 0.6028 (mtpt) REVERT: B 190 LYS cc_start: 0.7803 (mttt) cc_final: 0.7312 (tptt) REVERT: B 753 ARG cc_start: 0.7925 (ptp-170) cc_final: 0.6907 (mmp-170) outliers start: 44 outliers final: 25 residues processed: 357 average time/residue: 0.2403 time to fit residues: 137.2758 Evaluate side-chains 317 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 290 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 336 LYS Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 601 ILE 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 314 GLU Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 601 ILE 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: 8.9990 chunk 339 optimal weight: 1.9990 chunk 431 optimal weight: 2.9990 chunk 406 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 420 optimal weight: 7.9990 chunk 229 optimal weight: 30.0000 chunk 340 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 352 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 421 GLN B 421 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.193342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.131555 restraints weight = 47014.933| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.05 r_work: 0.3297 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 36624 Z= 0.171 Angle : 0.550 7.529 49536 Z= 0.282 Chirality : 0.045 0.151 5574 Planarity : 0.005 0.052 6516 Dihedral : 6.420 62.624 5058 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.47 % Allowed : 6.09 % Favored : 92.44 % 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: -0.59 (0.12), residues: 4536 helix: 0.28 (0.12), residues: 1974 sheet: 0.10 (0.23), residues: 474 loop : -1.11 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 256 TYR 0.010 0.001 TYR C 517 PHE 0.020 0.002 PHE E 290 TRP 0.012 0.002 TRP C 551 HIS 0.005 0.001 HIS E 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.17 (36624) covalent geometry : angle 0.55043 / 0.28 (49536) hydrogen bonds : bond 0.05196 / 3.39 ( 1326) hydrogen bonds : angle 4.39572 / 3.02 ( 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 347 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 290 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.6761 (tttt) cc_final: 0.6395 (mtpt) REVERT: A 433 GLU cc_start: 0.7075 (pt0) cc_final: 0.6565 (tm-30) REVERT: F 18 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7416 (mtpt) REVERT: F 84 MET cc_start: 0.5985 (OUTLIER) cc_final: 0.5710 (ptm) REVERT: F 753 ARG cc_start: 0.7940 (ptp-170) cc_final: 0.6938 (mmp-170) REVERT: E 148 LYS cc_start: 0.6501 (tttt) cc_final: 0.5957 (mtmt) REVERT: E 190 LYS cc_start: 0.7733 (mttt) cc_final: 0.7275 (tptp) REVERT: E 564 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8343 (m-30) REVERT: E 678 MET cc_start: 0.6991 (tmm) cc_final: 0.6775 (tmm) REVERT: E 740 MET cc_start: 0.8158 (mmm) cc_final: 0.7653 (mmm) REVERT: E 753 ARG cc_start: 0.7914 (ptp-170) cc_final: 0.6899 (mmp-170) REVERT: D 433 GLU cc_start: 0.7094 (pt0) cc_final: 0.6581 (tm-30) REVERT: C 18 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7401 (mtpt) REVERT: C 196 GLU cc_start: 0.6718 (tt0) cc_final: 0.6513 (pp20) REVERT: C 564 ASP cc_start: 0.8646 (m-30) cc_final: 0.8394 (m-30) REVERT: C 753 ARG cc_start: 0.7939 (ptp-170) cc_final: 0.6982 (mmp-170) REVERT: B 148 LYS cc_start: 0.6503 (tttt) cc_final: 0.5953 (mtmt) REVERT: B 190 LYS cc_start: 0.7729 (mttt) cc_final: 0.7270 (tptp) REVERT: B 564 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8360 (m-30) REVERT: B 678 MET cc_start: 0.6985 (tmm) cc_final: 0.6767 (tmm) REVERT: B 740 MET cc_start: 0.8136 (mmm) cc_final: 0.7628 (mmm) REVERT: B 753 ARG cc_start: 0.7914 (ptp-170) cc_final: 0.6960 (mmp-170) outliers start: 57 outliers final: 43 residues processed: 332 average time/residue: 0.2350 time to fit residues: 125.2218 Evaluate side-chains 314 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 266 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 535 CYS 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 314 GLU 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 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 535 CYS Chi-restraints excluded: chain D residue 598 ASP 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 598 ASP Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain B residue 101 SER 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: 0.8980 chunk 173 optimal weight: 0.7980 chunk 333 optimal weight: 1.9990 chunk 304 optimal weight: 30.0000 chunk 266 optimal weight: 5.9990 chunk 161 optimal weight: 0.0570 chunk 434 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 299 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 268 optimal weight: 8.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 199 ASN F 421 GLN C 421 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.195425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.131764 restraints weight = 47228.934| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.80 r_work: 0.3289 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 36624 Z= 0.103 Angle : 0.479 6.956 49536 Z= 0.247 Chirality : 0.043 0.152 5574 Planarity : 0.004 0.050 6516 Dihedral : 6.173 58.689 5058 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.26 % Allowed : 6.73 % Favored : 92.00 % 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 (0.13), residues: 4536 helix: 0.67 (0.12), residues: 1968 sheet: -0.19 (0.23), residues: 486 loop : -0.94 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 65 TYR 0.007 0.001 TYR C 517 PHE 0.010 0.001 PHE C 516 TRP 0.010 0.001 TRP E 551 HIS 0.002 0.000 HIS C 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (36624) covalent geometry : angle 0.47853 / 0.25 (49536) hydrogen bonds : bond 0.03990 / 2.61 ( 1326) hydrogen bonds : angle 4.11108 / 2.81 ( 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 346 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 297 time to evaluate : 1.373 Fit side-chains REVERT: A 148 LYS cc_start: 0.6756 (tttt) cc_final: 0.6373 (mtpt) REVERT: A 433 GLU cc_start: 0.7083 (pt0) cc_final: 0.6544 (tm-30) REVERT: A 584 LYS cc_start: 0.4938 (OUTLIER) cc_final: 0.4433 (mttm) REVERT: F 18 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7318 (mtpt) REVERT: F 84 MET cc_start: 0.6192 (ptm) cc_final: 0.5898 (ptm) REVERT: F 753 ARG cc_start: 0.7908 (ptp-170) cc_final: 0.6908 (mmp-170) REVERT: E 148 LYS cc_start: 0.6496 (tttt) cc_final: 0.5954 (mtmt) REVERT: E 190 LYS cc_start: 0.7710 (mttt) cc_final: 0.7260 (tptt) REVERT: E 578 GLU cc_start: 0.7578 (pt0) cc_final: 0.7054 (pt0) REVERT: E 740 MET cc_start: 0.8158 (mmm) cc_final: 0.7641 (mmm) REVERT: E 753 ARG cc_start: 0.7858 (ptp-170) cc_final: 0.6953 (mmp-170) REVERT: D 433 GLU cc_start: 0.7074 (pt0) cc_final: 0.6550 (tm-30) REVERT: D 584 LYS cc_start: 0.4960 (OUTLIER) cc_final: 0.4457 (mttm) REVERT: C 18 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7315 (mtpt) REVERT: C 196 GLU cc_start: 0.6720 (tt0) cc_final: 0.6432 (pp20) REVERT: C 564 ASP cc_start: 0.8622 (m-30) cc_final: 0.8382 (m-30) REVERT: C 753 ARG cc_start: 0.7984 (ptp-170) cc_final: 0.6974 (mmp-170) REVERT: B 148 LYS cc_start: 0.6499 (tttt) cc_final: 0.5956 (mtmt) REVERT: B 190 LYS cc_start: 0.7705 (mttt) cc_final: 0.7253 (tptt) REVERT: B 578 GLU cc_start: 0.7577 (pt0) cc_final: 0.7048 (pt0) REVERT: B 740 MET cc_start: 0.8144 (mmm) cc_final: 0.7625 (mmm) REVERT: B 753 ARG cc_start: 0.7851 (ptp-170) cc_final: 0.6950 (mmp-170) outliers start: 49 outliers final: 28 residues processed: 335 average time/residue: 0.2489 time to fit residues: 132.1798 Evaluate side-chains 318 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 286 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 535 CYS 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 101 SER Chi-restraints excluded: chain F residue 344 MET 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 601 ILE 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 535 CYS 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 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 630 ASP 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 601 ILE Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 642 LEU 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: 1.9990 chunk 409 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 241 optimal weight: 3.9990 chunk 440 optimal weight: 0.8980 chunk 423 optimal weight: 1.9990 chunk 404 optimal weight: 3.9990 chunk 392 optimal weight: 30.0000 chunk 207 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN A 199 ASN F 33 ASN D 199 ASN C 33 ASN C 199 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.194909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.132585 restraints weight = 47179.096| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.00 r_work: 0.3288 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2718 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= 0.113 Angle : 0.480 7.894 49536 Z= 0.246 Chirality : 0.043 0.146 5574 Planarity : 0.004 0.048 6516 Dihedral : 6.030 58.827 5058 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.55 % Allowed : 7.15 % Favored : 91.31 % 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: -0.00 (0.13), residues: 4536 helix: 0.79 (0.12), residues: 1980 sheet: 0.39 (0.25), residues: 414 loop : -0.79 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 359 TYR 0.008 0.001 TYR D 517 PHE 0.013 0.001 PHE C 516 TRP 0.009 0.001 TRP B 551 HIS 0.002 0.001 HIS F 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (36624) covalent geometry : angle 0.48047 / 0.25 (49536) hydrogen bonds : bond 0.04056 / 2.65 ( 1326) hydrogen bonds : angle 3.95987 / 2.71 ( 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 350 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 290 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.6749 (tttt) cc_final: 0.6371 (mtpt) REVERT: A 433 GLU cc_start: 0.7042 (pt0) cc_final: 0.6576 (tm-30) REVERT: A 584 LYS cc_start: 0.5044 (OUTLIER) cc_final: 0.4642 (mttt) REVERT: A 678 MET cc_start: 0.6787 (tmm) cc_final: 0.6273 (tmm) REVERT: A 744 ARG cc_start: 0.7500 (ttm170) cc_final: 0.7232 (mtp180) REVERT: F 18 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7287 (mtpt) REVERT: F 84 MET cc_start: 0.5968 (OUTLIER) cc_final: 0.5626 (ptm) REVERT: F 753 ARG cc_start: 0.7911 (ptp-170) cc_final: 0.6915 (mmp-170) REVERT: E 148 LYS cc_start: 0.6488 (tttt) cc_final: 0.5953 (mtmt) REVERT: E 190 LYS cc_start: 0.7533 (mttt) cc_final: 0.7079 (tptp) REVERT: E 753 ARG cc_start: 0.7861 (ptp-170) cc_final: 0.6983 (mmp-170) REVERT: D 433 GLU cc_start: 0.7036 (pt0) cc_final: 0.6604 (tm-30) REVERT: D 584 LYS cc_start: 0.5049 (OUTLIER) cc_final: 0.4675 (mttt) REVERT: D 678 MET cc_start: 0.6775 (tmm) cc_final: 0.6262 (tmm) REVERT: C 18 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7267 (mtpt) REVERT: C 196 GLU cc_start: 0.6693 (tt0) cc_final: 0.6458 (pp20) REVERT: C 564 ASP cc_start: 0.8604 (m-30) cc_final: 0.8358 (m-30) REVERT: C 630 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6709 (t70) REVERT: C 753 ARG cc_start: 0.8000 (ptp-170) cc_final: 0.6999 (mmp-170) REVERT: B 148 LYS cc_start: 0.6491 (tttt) cc_final: 0.5955 (mtmt) REVERT: B 190 LYS cc_start: 0.7534 (mttt) cc_final: 0.7080 (tptp) REVERT: B 753 ARG cc_start: 0.7864 (ptp-170) cc_final: 0.6985 (mmp-170) outliers start: 60 outliers final: 37 residues processed: 338 average time/residue: 0.2267 time to fit residues: 124.6480 Evaluate side-chains 321 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 278 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 535 CYS 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 535 CYS 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 601 ILE Chi-restraints excluded: chain E residue 642 LEU 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 535 CYS 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 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 601 ILE Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 699 ILE 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: 3.9990 chunk 314 optimal weight: 0.0000 chunk 58 optimal weight: 0.0470 chunk 33 optimal weight: 4.9990 chunk 347 optimal weight: 7.9990 chunk 423 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 447 optimal weight: 5.9990 chunk 369 optimal weight: 10.0000 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN A 421 GLN F 33 ASN D 33 ASN D 421 GLN B 33 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.194172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.131834 restraints weight = 47193.952| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.76 r_work: 0.3242 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2798 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= 0.128 Angle : 0.493 8.273 49536 Z= 0.252 Chirality : 0.044 0.152 5574 Planarity : 0.004 0.048 6516 Dihedral : 5.977 59.288 5058 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.65 % Allowed : 7.53 % Favored : 90.82 % 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: 0.10 (0.13), residues: 4536 helix: 0.84 (0.12), residues: 1986 sheet: 0.33 (0.24), residues: 438 loop : -0.68 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 359 TYR 0.009 0.001 TYR F 517 PHE 0.014 0.001 PHE C 516 TRP 0.008 0.001 TRP A 551 HIS 0.003 0.001 HIS F 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (36624) covalent geometry : angle 0.49280 / 0.25 (49536) hydrogen bonds : bond 0.04277 / 2.80 ( 1326) hydrogen bonds : angle 3.93136 / 2.69 ( 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 353 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 289 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.6742 (tttt) cc_final: 0.6355 (mtpt) REVERT: A 283 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: A 433 GLU cc_start: 0.7051 (pt0) cc_final: 0.6611 (tm-30) REVERT: A 582 ILE cc_start: 0.7437 (mt) cc_final: 0.7230 (tt) REVERT: A 584 LYS cc_start: 0.5115 (OUTLIER) cc_final: 0.4836 (mttt) REVERT: A 625 ARG cc_start: 0.7756 (tpp80) cc_final: 0.7447 (tpt-90) REVERT: F 18 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7300 (mtpt) REVERT: F 84 MET cc_start: 0.6034 (ptm) cc_final: 0.5735 (ptm) REVERT: F 753 ARG cc_start: 0.7899 (ptp-170) cc_final: 0.6906 (mmp-170) REVERT: E 148 LYS cc_start: 0.6509 (tttt) cc_final: 0.5990 (mtmt) REVERT: E 190 LYS cc_start: 0.7442 (mttt) cc_final: 0.7024 (tptp) REVERT: E 550 MET cc_start: 0.4617 (OUTLIER) cc_final: 0.3937 (tpt) REVERT: E 753 ARG cc_start: 0.7823 (ptp-170) cc_final: 0.6958 (mmp-170) REVERT: D 283 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: D 433 GLU cc_start: 0.7043 (pt0) cc_final: 0.6619 (tm-30) REVERT: D 582 ILE cc_start: 0.7429 (mt) cc_final: 0.7224 (tt) REVERT: D 584 LYS cc_start: 0.5125 (OUTLIER) cc_final: 0.4747 (mttt) REVERT: C 18 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7287 (mtpt) REVERT: C 196 GLU cc_start: 0.6721 (tt0) cc_final: 0.6494 (pp20) REVERT: C 564 ASP cc_start: 0.8606 (m-30) cc_final: 0.8355 (m-30) REVERT: C 630 ASP cc_start: 0.7047 (OUTLIER) cc_final: 0.6773 (t70) REVERT: C 753 ARG cc_start: 0.7908 (ptp-170) cc_final: 0.6888 (mmp-170) REVERT: B 148 LYS cc_start: 0.6512 (tttt) cc_final: 0.5994 (mtmt) REVERT: B 190 LYS cc_start: 0.7446 (mttt) cc_final: 0.7027 (tptp) REVERT: B 550 MET cc_start: 0.4571 (OUTLIER) cc_final: 0.3910 (tpt) REVERT: B 608 MET cc_start: 0.8469 (ttm) cc_final: 0.8066 (mtp) REVERT: B 753 ARG cc_start: 0.7828 (ptp-170) cc_final: 0.6946 (mmp-170) outliers start: 64 outliers final: 47 residues processed: 337 average time/residue: 0.2230 time to fit residues: 121.8451 Evaluate side-chains 336 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 280 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 535 CYS 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 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 535 CYS Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 601 ILE 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 E residue 699 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 535 CYS 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 229 LEU 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 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 550 MET Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 699 ILE 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: 0.0970 chunk 280 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 277 optimal weight: 4.9990 chunk 385 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN F 33 ASN D 33 ASN B 33 ASN 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 = 0.194532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.132168 restraints weight = 47186.459| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.73 r_work: 0.3249 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2893 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 : 0.479 8.260 49536 Z= 0.246 Chirality : 0.043 0.171 5574 Planarity : 0.004 0.047 6516 Dihedral : 5.920 59.964 5058 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.75 % Allowed : 7.69 % Favored : 90.56 % 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: 0.19 (0.13), residues: 4536 helix: 0.98 (0.12), residues: 1968 sheet: -0.03 (0.22), residues: 510 loop : -0.61 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 359 TYR 0.008 0.001 TYR F 517 PHE 0.012 0.001 PHE C 516 TRP 0.009 0.001 TRP F 551 HIS 0.002 0.001 HIS C 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (36624) covalent geometry : angle 0.47939 / 0.25 (49536) hydrogen bonds : bond 0.04039 / 2.65 ( 1326) hydrogen bonds : angle 3.87423 / 2.66 ( 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 353 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 285 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.6727 (tttt) cc_final: 0.6353 (mtpt) REVERT: A 283 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: A 433 GLU cc_start: 0.7090 (pt0) cc_final: 0.6652 (tm-30) REVERT: A 582 ILE cc_start: 0.7431 (mt) cc_final: 0.7229 (tt) REVERT: A 584 LYS cc_start: 0.4961 (OUTLIER) cc_final: 0.4647 (mttt) REVERT: A 625 ARG cc_start: 0.7729 (tpp80) cc_final: 0.7449 (tpt-90) REVERT: F 18 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7278 (mtpt) REVERT: F 84 MET cc_start: 0.5944 (OUTLIER) cc_final: 0.5630 (ptm) REVERT: F 753 ARG cc_start: 0.7901 (ptp-170) cc_final: 0.6919 (mmp-170) REVERT: E 148 LYS cc_start: 0.6527 (tttt) cc_final: 0.5963 (mtmt) REVERT: E 190 LYS cc_start: 0.7508 (mttt) cc_final: 0.7063 (tptp) REVERT: E 550 MET cc_start: 0.4492 (OUTLIER) cc_final: 0.3820 (tpt) REVERT: E 608 MET cc_start: 0.8484 (ttm) cc_final: 0.8043 (mtp) REVERT: E 753 ARG cc_start: 0.7783 (ptp-170) cc_final: 0.7029 (mmp-170) REVERT: D 283 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: D 433 GLU cc_start: 0.7078 (pt0) cc_final: 0.6667 (tm-30) REVERT: D 582 ILE cc_start: 0.7428 (mt) cc_final: 0.7226 (tt) REVERT: D 584 LYS cc_start: 0.4961 (OUTLIER) cc_final: 0.4642 (mttt) REVERT: D 625 ARG cc_start: 0.7722 (tpp80) cc_final: 0.7419 (tpt-90) REVERT: C 18 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7263 (mtpt) REVERT: C 196 GLU cc_start: 0.6717 (tt0) cc_final: 0.6457 (pp20) REVERT: C 564 ASP cc_start: 0.8599 (m-30) cc_final: 0.8344 (m-30) REVERT: C 630 ASP cc_start: 0.6951 (OUTLIER) cc_final: 0.6687 (t70) REVERT: C 753 ARG cc_start: 0.7889 (ptp-170) cc_final: 0.6878 (mmp-170) REVERT: B 148 LYS cc_start: 0.6539 (tttt) cc_final: 0.5970 (mtmt) REVERT: B 190 LYS cc_start: 0.7502 (mttt) cc_final: 0.7058 (tptp) REVERT: B 550 MET cc_start: 0.4465 (OUTLIER) cc_final: 0.3799 (tpt) REVERT: B 608 MET cc_start: 0.8440 (ttm) cc_final: 0.8047 (mtp) REVERT: B 753 ARG cc_start: 0.7794 (ptp-170) cc_final: 0.6936 (mmp-170) outliers start: 68 outliers final: 48 residues processed: 333 average time/residue: 0.2187 time to fit residues: 117.6166 Evaluate side-chains 337 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 279 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 535 CYS 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 229 LEU 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 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 601 ILE 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 E residue 647 LEU Chi-restraints excluded: chain E residue 699 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 535 CYS 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 229 LEU 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 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 314 GLU 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 601 ILE Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 647 LEU 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: 9.9990 chunk 23 optimal weight: 0.0050 chunk 195 optimal weight: 6.9990 chunk 261 optimal weight: 0.2980 chunk 368 optimal weight: 6.9990 chunk 200 optimal weight: 0.0980 chunk 67 optimal weight: 4.9990 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: 1.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN F 33 ASN D 33 ASN B 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.194840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.130336 restraints weight = 46926.607| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.76 r_work: 0.3264 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2975 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= 0.112 Angle : 0.476 8.415 49536 Z= 0.244 Chirality : 0.043 0.182 5574 Planarity : 0.004 0.047 6516 Dihedral : 5.868 59.899 5058 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.60 % Allowed : 8.08 % Favored : 90.33 % 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: 0.28 (0.13), residues: 4536 helix: 1.02 (0.12), residues: 1980 sheet: 0.05 (0.22), residues: 510 loop : -0.53 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 359 TYR 0.008 0.001 TYR C 517 PHE 0.012 0.001 PHE C 516 TRP 0.008 0.001 TRP C 551 HIS 0.002 0.000 HIS C 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (36624) covalent geometry : angle 0.47570 / 0.24 (49536) hydrogen bonds : bond 0.03937 / 2.58 ( 1326) hydrogen bonds : angle 3.81400 / 2.62 ( 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 348 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 286 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.6735 (tttt) cc_final: 0.6290 (mtpt) REVERT: A 283 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: A 433 GLU cc_start: 0.7086 (pt0) cc_final: 0.6683 (tm-30) REVERT: A 584 LYS cc_start: 0.4688 (OUTLIER) cc_final: 0.4308 (mttt) REVERT: A 625 ARG cc_start: 0.7758 (tpp80) cc_final: 0.7526 (tpt-90) REVERT: F 18 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7278 (mtpt) REVERT: F 84 MET cc_start: 0.6032 (OUTLIER) cc_final: 0.5705 (ptm) REVERT: F 753 ARG cc_start: 0.7890 (ptp-170) cc_final: 0.6906 (mmp-170) REVERT: E 148 LYS cc_start: 0.6520 (tttt) cc_final: 0.5972 (mtmt) REVERT: E 190 LYS cc_start: 0.7503 (mttt) cc_final: 0.7058 (tptp) REVERT: E 608 MET cc_start: 0.8501 (ttm) cc_final: 0.8062 (mtp) REVERT: E 753 ARG cc_start: 0.7826 (ptp-170) cc_final: 0.7044 (mmp-170) REVERT: D 283 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: D 433 GLU cc_start: 0.7058 (pt0) cc_final: 0.6679 (tm-30) REVERT: D 442 MET cc_start: 0.8043 (mmm) cc_final: 0.7838 (mmm) REVERT: D 584 LYS cc_start: 0.4811 (OUTLIER) cc_final: 0.4408 (mttt) REVERT: D 625 ARG cc_start: 0.7752 (tpp80) cc_final: 0.7505 (tpt-90) REVERT: C 18 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7264 (mtpt) REVERT: C 196 GLU cc_start: 0.6733 (tt0) cc_final: 0.6464 (pp20) REVERT: C 564 ASP cc_start: 0.8527 (m-30) cc_final: 0.8272 (m-30) REVERT: C 753 ARG cc_start: 0.7891 (ptp-170) cc_final: 0.6905 (mmp-170) REVERT: B 148 LYS cc_start: 0.6525 (tttt) cc_final: 0.5978 (mtmt) REVERT: B 190 LYS cc_start: 0.7504 (mttt) cc_final: 0.7060 (tptp) REVERT: B 608 MET cc_start: 0.8461 (ttm) cc_final: 0.8096 (mtp) REVERT: B 753 ARG cc_start: 0.7825 (ptp-170) cc_final: 0.7051 (mmp-170) outliers start: 62 outliers final: 48 residues processed: 328 average time/residue: 0.2236 time to fit residues: 117.3014 Evaluate side-chains 334 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 279 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 535 CYS 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 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 601 ILE 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 E residue 647 LEU Chi-restraints excluded: chain E residue 699 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 535 CYS 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 229 LEU 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 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 314 GLU Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 630 ASP 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: 7.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 312 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 271 optimal weight: 0.0060 chunk 89 optimal weight: 4.9990 chunk 318 optimal weight: 7.9990 overall best weight: 3.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN F 33 ASN D 33 ASN B 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.191105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126168 restraints weight = 46951.874| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.78 r_work: 0.3214 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 36624 Z= 0.251 Angle : 0.608 9.028 49536 Z= 0.310 Chirality : 0.047 0.181 5574 Planarity : 0.005 0.049 6516 Dihedral : 6.206 59.401 5058 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.63 % Allowed : 8.10 % 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: -0.17 (0.12), residues: 4536 helix: 0.65 (0.12), residues: 1968 sheet: -0.20 (0.22), residues: 510 loop : -0.76 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 711 TYR 0.015 0.002 TYR A 203 PHE 0.021 0.002 PHE C 516 TRP 0.007 0.002 TRP B 476 HIS 0.006 0.001 HIS F 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.25 (36624) covalent geometry : angle 0.60790 / 0.31 (49536) hydrogen bonds : bond 0.05897 / 3.85 ( 1326) hydrogen bonds : angle 4.19050 / 2.88 ( 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 347 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 284 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.6820 (tttt) cc_final: 0.6315 (mtpt) REVERT: A 433 GLU cc_start: 0.7067 (pt0) cc_final: 0.6848 (tm-30) REVERT: A 584 LYS cc_start: 0.4960 (OUTLIER) cc_final: 0.4453 (mttt) REVERT: A 753 ARG cc_start: 0.7853 (ptp-170) cc_final: 0.7049 (mmp-170) REVERT: F 18 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7372 (mtpt) REVERT: F 84 MET cc_start: 0.6033 (OUTLIER) cc_final: 0.5828 (ptm) REVERT: F 753 ARG cc_start: 0.8012 (ptp-170) cc_final: 0.7061 (mmp-170) REVERT: E 148 LYS cc_start: 0.6462 (tttt) cc_final: 0.5929 (mtmt) REVERT: E 190 LYS cc_start: 0.7484 (mttt) cc_final: 0.7045 (tptp) REVERT: E 753 ARG cc_start: 0.7883 (ptp-170) cc_final: 0.7085 (mmp-170) REVERT: D 433 GLU cc_start: 0.7052 (pt0) cc_final: 0.6852 (tm-30) REVERT: D 584 LYS cc_start: 0.4942 (OUTLIER) cc_final: 0.4320 (mttm) REVERT: C 18 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7373 (mtpt) REVERT: C 196 GLU cc_start: 0.6757 (tt0) cc_final: 0.6493 (pp20) REVERT: C 564 ASP cc_start: 0.8604 (m-30) cc_final: 0.8374 (m-30) REVERT: C 753 ARG cc_start: 0.8010 (ptp-170) cc_final: 0.6970 (mmp-170) REVERT: B 148 LYS cc_start: 0.6464 (tttt) cc_final: 0.5934 (mtmt) REVERT: B 190 LYS cc_start: 0.7486 (mttt) cc_final: 0.7049 (tptp) REVERT: B 442 MET cc_start: 0.8286 (mmm) cc_final: 0.8003 (mmm) REVERT: B 753 ARG cc_start: 0.7880 (ptp-170) cc_final: 0.7090 (mmp-170) outliers start: 63 outliers final: 41 residues processed: 326 average time/residue: 0.2395 time to fit residues: 125.9576 Evaluate side-chains 321 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 275 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 535 CYS 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 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 535 CYS 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 314 GLU Chi-restraints excluded: chain E residue 344 MET 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 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 535 CYS 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 229 LEU 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 728 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 535 CYS 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: 5.9990 chunk 48 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 354 optimal weight: 3.9990 chunk 281 optimal weight: 0.6980 chunk 314 optimal weight: 0.9990 chunk 401 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 chunk 224 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN F 33 ASN D 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.193704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.127216 restraints weight = 46619.580| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.72 r_work: 0.3287 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2974 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= 0.126 Angle : 0.501 8.651 49536 Z= 0.258 Chirality : 0.044 0.183 5574 Planarity : 0.004 0.046 6516 Dihedral : 6.022 59.247 5058 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.24 % Allowed : 8.44 % Favored : 90.33 % 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: 0.17 (0.13), residues: 4536 helix: 0.99 (0.12), residues: 1956 sheet: -0.09 (0.22), residues: 510 loop : -0.64 (0.14), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 711 TYR 0.009 0.001 TYR F 517 PHE 0.013 0.001 PHE C 516 TRP 0.009 0.001 TRP B 551 HIS 0.003 0.001 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (36624) covalent geometry : angle 0.50106 / 0.26 (49536) hydrogen bonds : bond 0.04397 / 2.88 ( 1326) hydrogen bonds : angle 3.96285 / 2.72 ( 3906) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8919.28 seconds wall clock time: 153 minutes 5.65 seconds (9185.65 seconds total)