Starting phenix.real_space_refine on Fri Mar 6 23:49:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bpb_30150/03_2026/7bpb_30150.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bpb_30150/03_2026/7bpb_30150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bpb_30150/03_2026/7bpb_30150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bpb_30150/03_2026/7bpb_30150.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bpb_30150/03_2026/7bpb_30150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bpb_30150/03_2026/7bpb_30150.map" } resolution = 4.3 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= 0.070 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: 5 Type Number sf(0) Gaussians P 30 5.49 5 S 180 5.16 5 C 22008 2.51 5 N 6252 2.21 5 O 6768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35238 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "B" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "C" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "D" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "E" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "F" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5815 Classifications: {'peptide': 740} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 699} Chain breaks: 1 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {'ADP': 1, 'ANP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.53, per 1000 atoms: 0.24 Number of scatterers: 35238 At special positions: 0 Unit cell: (169.534, 185.629, 101.935, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 30 15.00 O 6768 8.00 N 6252 7.00 C 22008 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=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.5 seconds 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8304 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 30 sheets defined 47.6% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 130 through 139 removed outlier: 3.669A pdb=" N TYR A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 209 through 226 removed outlier: 3.617A pdb=" N VAL A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 278 through 296 removed outlier: 3.746A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 319 through 334 removed outlier: 3.617A pdb=" N ARG A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.854A pdb=" N ILE A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 407 through 426 removed outlier: 3.506A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 433 removed outlier: 4.019A pdb=" N GLU A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.582A pdb=" N SER A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.671A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 removed outlier: 3.834A 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 499 through 507 removed outlier: 4.010A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 535 Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.683A pdb=" N LEU A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 580 through 586 removed outlier: 4.137A pdb=" N ARG A 586 " --> pdb=" O ILE A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 610 removed outlier: 3.896A pdb=" N GLY A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.953A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 662 Processing helix chain 'A' and resid 672 through 679 Processing helix chain 'A' and resid 685 through 714 removed outlier: 4.998A pdb=" N CYS A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN A 692 " --> pdb=" O THR A 688 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG A 713 " --> pdb=" O ARG A 709 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 742 removed outlier: 4.016A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 762 removed outlier: 4.020A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE A 758 " --> pdb=" O LYS A 754 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 759 " --> pdb=" O TYR A 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 130 through 139 removed outlier: 3.668A pdb=" N TYR B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 209 through 226 removed outlier: 3.617A pdb=" N VAL B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 278 through 296 removed outlier: 3.746A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 309 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 319 through 334 removed outlier: 3.618A pdb=" N ARG B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.854A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 407 through 426 removed outlier: 3.838A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 removed outlier: 4.018A pdb=" N GLU B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 445 removed outlier: 3.581A pdb=" N SER B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 removed outlier: 3.672A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 removed outlier: 3.834A 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 499 through 507 removed outlier: 4.009A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 535 Processing helix chain 'B' and resid 543 through 552 removed outlier: 3.683A pdb=" N LEU B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 569 Processing helix chain 'B' and resid 580 through 586 removed outlier: 4.137A pdb=" N ARG B 586 " --> pdb=" O ILE B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 610 removed outlier: 3.895A pdb=" N GLY B 610 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.953A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 662 Processing helix chain 'B' and resid 672 through 679 Processing helix chain 'B' and resid 685 through 714 removed outlier: 4.998A pdb=" N CYS B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN B 692 " --> pdb=" O THR B 688 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG B 713 " --> pdb=" O ARG B 709 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 742 removed outlier: 4.016A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 762 removed outlier: 4.020A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE B 758 " --> pdb=" O LYS B 754 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 759 " --> pdb=" O TYR B 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 50 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 130 through 139 removed outlier: 3.669A pdb=" N TYR C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS C 136 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix Processing helix chain 'C' and resid 209 through 226 removed outlier: 3.617A pdb=" N VAL C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 278 through 296 removed outlier: 3.746A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 309 Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 319 through 334 removed outlier: 3.618A pdb=" N ARG C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.854A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 407 through 426 removed outlier: 3.879A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 433 removed outlier: 4.018A pdb=" N GLU C 433 " --> pdb=" O LEU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 445 removed outlier: 3.581A pdb=" N SER C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.671A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 removed outlier: 3.834A 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 499 through 507 removed outlier: 4.010A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 535 Processing helix chain 'C' and resid 543 through 552 removed outlier: 3.683A pdb=" N LEU C 547 " --> pdb=" O LYS C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 580 through 586 removed outlier: 4.137A pdb=" N ARG C 586 " --> pdb=" O ILE C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 610 removed outlier: 3.895A pdb=" N GLY C 610 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.953A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 662 Processing helix chain 'C' and resid 672 through 679 Processing helix chain 'C' and resid 685 through 714 removed outlier: 4.998A pdb=" N CYS C 691 " --> pdb=" O LEU C 687 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN C 692 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG C 713 " --> pdb=" O ARG C 709 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 742 removed outlier: 4.016A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 762 removed outlier: 4.020A pdb=" N ILE C 752 " --> pdb=" O SER C 748 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE C 758 " --> pdb=" O LYS C 754 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA C 759 " --> pdb=" O TYR C 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 50 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 130 through 139 removed outlier: 3.669A pdb=" N TYR D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 209 through 226 removed outlier: 3.617A pdb=" N VAL D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 278 through 296 removed outlier: 3.746A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 309 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 319 through 334 removed outlier: 3.618A pdb=" N ARG D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.854A pdb=" N ILE D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 407 through 426 removed outlier: 3.814A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 433 removed outlier: 4.019A pdb=" N GLU D 433 " --> pdb=" O LEU D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 445 removed outlier: 3.582A pdb=" N SER D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.671A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 499 removed outlier: 3.834A 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 499 through 507 removed outlier: 4.010A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 535 Processing helix chain 'D' and resid 543 through 552 removed outlier: 3.684A pdb=" N LEU D 547 " --> pdb=" O LYS D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 569 Processing helix chain 'D' and resid 580 through 586 removed outlier: 4.136A pdb=" N ARG D 586 " --> pdb=" O ILE D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 610 removed outlier: 3.895A pdb=" N GLY D 610 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.953A pdb=" N ARG D 635 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 662 Processing helix chain 'D' and resid 672 through 679 Processing helix chain 'D' and resid 685 through 714 removed outlier: 4.999A pdb=" N CYS D 691 " --> pdb=" O LEU D 687 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN D 692 " --> pdb=" O THR D 688 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG D 713 " --> pdb=" O ARG D 709 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 742 removed outlier: 4.016A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 762 removed outlier: 4.020A pdb=" N ILE D 752 " --> pdb=" O SER D 748 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE D 758 " --> pdb=" O LYS D 754 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA D 759 " --> pdb=" O TYR D 755 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 50 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 130 through 139 removed outlier: 3.668A pdb=" N TYR E 134 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LYS E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Proline residue: E 137 - end of helix Processing helix chain 'E' and resid 209 through 226 removed outlier: 3.617A pdb=" N VAL E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 278 through 296 removed outlier: 3.745A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 309 Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 319 through 334 removed outlier: 3.618A pdb=" N ARG E 323 " --> pdb=" O GLU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.853A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 397 through 402 Processing helix chain 'E' and resid 407 through 426 removed outlier: 3.842A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 433 removed outlier: 4.019A pdb=" N GLU E 433 " --> pdb=" O LEU E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 445 removed outlier: 3.582A pdb=" N SER E 444 " --> pdb=" O GLU E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 458 removed outlier: 3.672A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 499 removed outlier: 3.834A 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 499 through 507 removed outlier: 4.009A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 535 Processing helix chain 'E' and resid 543 through 552 removed outlier: 3.684A pdb=" N LEU E 547 " --> pdb=" O LYS E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 569 Processing helix chain 'E' and resid 580 through 586 removed outlier: 4.137A pdb=" N ARG E 586 " --> pdb=" O ILE E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 610 removed outlier: 3.895A pdb=" N GLY E 610 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.953A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 662 Processing helix chain 'E' and resid 672 through 679 Processing helix chain 'E' and resid 685 through 714 removed outlier: 4.998A pdb=" N CYS E 691 " --> pdb=" O LEU E 687 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN E 692 " --> pdb=" O THR E 688 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG E 713 " --> pdb=" O ARG E 709 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN E 714 " --> pdb=" O GLU E 710 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 742 removed outlier: 4.017A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 762 removed outlier: 4.019A pdb=" N ILE E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE E 758 " --> pdb=" O LYS E 754 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA E 759 " --> pdb=" O TYR E 755 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 50 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 85 through 92 Processing helix chain 'F' and resid 130 through 139 removed outlier: 3.669A pdb=" N TYR F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Proline residue: F 137 - end of helix Processing helix chain 'F' and resid 209 through 226 removed outlier: 3.617A pdb=" N VAL F 220 " --> pdb=" O ILE F 216 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 278 through 296 removed outlier: 3.746A pdb=" N ASN F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 309 Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 319 through 334 removed outlier: 3.618A pdb=" N ARG F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.854A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 397 through 402 Processing helix chain 'F' and resid 407 through 426 removed outlier: 3.787A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 433 removed outlier: 4.018A pdb=" N GLU F 433 " --> pdb=" O LEU F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 445 removed outlier: 3.581A pdb=" N SER F 444 " --> pdb=" O GLU F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.672A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 removed outlier: 3.834A 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 499 through 507 removed outlier: 4.010A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 535 Processing helix chain 'F' and resid 543 through 552 removed outlier: 3.683A pdb=" N LEU F 547 " --> pdb=" O LYS F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 569 Processing helix chain 'F' and resid 580 through 586 removed outlier: 4.137A pdb=" N ARG F 586 " --> pdb=" O ILE F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 610 removed outlier: 3.895A pdb=" N GLY F 610 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.953A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 662 Processing helix chain 'F' and resid 672 through 679 Processing helix chain 'F' and resid 685 through 714 removed outlier: 4.998A pdb=" N CYS F 691 " --> pdb=" O LEU F 687 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN F 692 " --> pdb=" O THR F 688 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG F 713 " --> pdb=" O ARG F 709 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN F 714 " --> pdb=" O GLU F 710 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 742 removed outlier: 4.016A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 762 removed outlier: 4.020A pdb=" N ILE F 752 " --> pdb=" O SER F 748 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE F 758 " --> pdb=" O LYS F 754 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA F 759 " --> pdb=" O TYR F 755 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 117 removed outlier: 7.073A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 144 through 147 Processing sheet with id=AA4, first strand: chain 'A' and resid 268 through 270 removed outlier: 7.090A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 241 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 345 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR A 347 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 542 removed outlier: 3.767A pdb=" N ILE A 540 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 514 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 623 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 643 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 517 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 25 through 27 Processing sheet with id=AA7, first strand: chain 'B' and resid 114 through 117 removed outlier: 7.073A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 144 through 147 Processing sheet with id=AA9, first strand: chain 'B' and resid 268 through 270 removed outlier: 7.089A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B 241 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA B 345 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR B 347 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 538 through 542 removed outlier: 3.769A pdb=" N ILE B 540 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B 514 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B 623 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 643 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR B 517 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 25 through 27 Processing sheet with id=AB3, first strand: chain 'C' and resid 114 through 117 removed outlier: 7.072A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 144 through 147 Processing sheet with id=AB5, first strand: chain 'C' and resid 268 through 270 removed outlier: 7.090A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 241 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C 345 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR C 347 " --> pdb=" O LEU C 243 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 538 through 542 removed outlier: 3.768A pdb=" N ILE C 540 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 514 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR C 623 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE C 643 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR C 517 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 25 through 27 Processing sheet with id=AB8, first strand: chain 'D' and resid 114 through 117 removed outlier: 7.073A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 144 through 147 Processing sheet with id=AC1, first strand: chain 'D' and resid 268 through 270 removed outlier: 7.089A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE D 241 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA D 345 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR D 347 " --> pdb=" O LEU D 243 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 538 through 542 removed outlier: 3.768A pdb=" N ILE D 540 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL D 514 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR D 623 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE D 643 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR D 517 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 25 through 27 Processing sheet with id=AC4, first strand: chain 'E' and resid 114 through 117 removed outlier: 7.073A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 144 through 147 Processing sheet with id=AC6, first strand: chain 'E' and resid 268 through 270 removed outlier: 7.089A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE E 241 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA E 345 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR E 347 " --> pdb=" O LEU E 243 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 538 through 542 removed outlier: 3.768A pdb=" N ILE E 540 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL E 514 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR E 623 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE E 643 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR E 517 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 25 through 27 Processing sheet with id=AC9, first strand: chain 'F' and resid 114 through 117 removed outlier: 7.073A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 144 through 147 Processing sheet with id=AD2, first strand: chain 'F' and resid 268 through 270 removed outlier: 7.090A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE F 241 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA F 345 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR F 347 " --> pdb=" O LEU F 243 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 538 through 542 removed outlier: 3.767A pdb=" N ILE F 540 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL F 514 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR F 623 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE F 643 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR F 517 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1386 hydrogen bonds defined for protein. 3924 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: 7.71 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6660 1.32 - 1.45: 8002 1.45 - 1.57: 20828 1.57 - 1.70: 36 1.70 - 1.82: 294 Bond restraints: 35820 Sorted by residual: bond pdb=" O3A ANP E 901 " pdb=" PB ANP E 901 " ideal model delta sigma weight residual 1.700 1.549 0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" O3A ANP D 901 " pdb=" PB ANP D 901 " ideal model delta sigma weight residual 1.700 1.549 0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" O3A ANP A 902 " pdb=" PB ANP A 902 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" O3A ANP C 901 " pdb=" PB ANP C 901 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" O3A ANP E 903 " pdb=" PB ANP E 903 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.63e+01 ... (remaining 35815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 47020 2.84 - 5.68: 1207 5.68 - 8.52: 141 8.52 - 11.36: 28 11.36 - 14.19: 30 Bond angle restraints: 48426 Sorted by residual: angle pdb=" PB ANP D 901 " pdb=" N3B ANP D 901 " pdb=" PG ANP D 901 " ideal model delta sigma weight residual 126.95 112.76 14.19 3.00e+00 1.11e-01 2.24e+01 angle pdb=" PB ANP E 901 " pdb=" N3B ANP E 901 " pdb=" PG ANP E 901 " ideal model delta sigma weight residual 126.95 112.78 14.17 3.00e+00 1.11e-01 2.23e+01 angle pdb=" PB ANP C 901 " pdb=" N3B ANP C 901 " pdb=" PG ANP C 901 " ideal model delta sigma weight residual 126.95 112.79 14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" PB ANP E 903 " pdb=" N3B ANP E 903 " pdb=" PG ANP E 903 " ideal model delta sigma weight residual 126.95 112.80 14.15 3.00e+00 1.11e-01 2.23e+01 angle pdb=" PB ANP A 902 " pdb=" N3B ANP A 902 " pdb=" PG ANP A 902 " ideal model delta sigma weight residual 126.95 112.80 14.15 3.00e+00 1.11e-01 2.23e+01 ... (remaining 48421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.85: 21778 34.85 - 69.71: 542 69.71 - 104.56: 36 104.56 - 139.41: 0 139.41 - 174.27: 6 Dihedral angle restraints: 22362 sinusoidal: 9564 harmonic: 12798 Sorted by residual: dihedral pdb=" C5' ADP B 902 " pdb=" O5' ADP B 902 " pdb=" PA ADP B 902 " pdb=" O2A ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 31.62 -91.62 1 2.00e+01 2.50e-03 2.47e+01 dihedral pdb=" C5' ADP C 902 " pdb=" O5' ADP C 902 " pdb=" PA ADP C 902 " pdb=" O2A ADP C 902 " ideal model delta sinusoidal sigma weight residual -60.00 31.60 -91.60 1 2.00e+01 2.50e-03 2.47e+01 dihedral pdb=" C5' ADP D 902 " pdb=" O5' ADP D 902 " pdb=" PA ADP D 902 " pdb=" O2A ADP D 902 " ideal model delta sinusoidal sigma weight residual -60.00 31.59 -91.59 1 2.00e+01 2.50e-03 2.47e+01 ... (remaining 22359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3795 0.057 - 0.114: 1143 0.114 - 0.170: 355 0.170 - 0.227: 84 0.227 - 0.284: 41 Chirality restraints: 5418 Sorted by residual: chirality pdb=" C3' ANP A 902 " pdb=" C2' ANP A 902 " pdb=" C4' ANP A 902 " pdb=" O3' ANP A 902 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' ANP B 901 " pdb=" C2' ANP B 901 " pdb=" C4' ANP B 901 " pdb=" O3' ANP B 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' ANP E 903 " pdb=" C2' ANP E 903 " pdb=" C4' ANP E 903 " pdb=" O3' ANP E 903 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 5415 not shown) Planarity restraints: 6378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 544 " 0.062 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO B 545 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO B 545 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 545 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 544 " -0.062 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO E 545 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO E 545 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 545 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 544 " -0.062 5.00e-02 4.00e+02 9.30e-02 1.39e+01 pdb=" N PRO D 545 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO D 545 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 545 " -0.050 5.00e-02 4.00e+02 ... (remaining 6375 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 312 2.54 - 3.13: 24711 3.13 - 3.72: 55189 3.72 - 4.31: 68815 4.31 - 4.90: 110366 Nonbonded interactions: 259393 Sorted by model distance: nonbonded pdb=" CG ARG E 744 " pdb=" OE1 GLN F 763 " model vdw 1.956 3.440 nonbonded pdb=" OE1 GLN A 763 " pdb=" O ARG F 745 " model vdw 2.033 3.040 nonbonded pdb=" O ARG D 745 " pdb=" OE1 GLN E 763 " model vdw 2.038 3.040 nonbonded pdb=" CG ARG C 744 " pdb=" OE1 GLN D 763 " model vdw 2.071 3.440 nonbonded pdb=" O ARG C 745 " pdb=" OE1 GLN D 763 " model vdw 2.126 3.040 ... (remaining 259388 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 20 through 766) selection = (chain 'B' and resid 20 through 766) selection = (chain 'C' and resid 20 through 766) selection = (chain 'D' and resid 20 through 766) selection = (chain 'E' and resid 20 through 766) selection = (chain 'F' and resid 20 through 766) } 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 group one per residue 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: 3.150 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 32.870 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 : 0.007 0.151 35838 Z= 0.333 Angle : 1.118 14.194 48426 Z= 0.584 Chirality : 0.065 0.284 5418 Planarity : 0.009 0.093 6378 Dihedral : 16.099 174.269 14058 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.09 % Favored : 93.82 % Rotamer: Outliers : 0.05 % Allowed : 8.89 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -4.20 (0.10), residues: 4416 helix: -3.32 (0.07), residues: 1890 sheet: -2.08 (0.17), residues: 774 loop : -2.21 (0.13), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 83 TYR 0.014 0.002 TYR E 244 PHE 0.016 0.002 PHE A 152 TRP 0.006 0.002 TRP B 454 HIS 0.015 0.002 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00693 (35820) covalent geometry : angle 1.11832 (48426) hydrogen bonds : bond 0.16144 ( 1386) hydrogen bonds : angle 6.72534 ( 3924) Misc. bond : bond 0.01846 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 811 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8794 (mp) cc_final: 0.8484 (tp) REVERT: A 147 ARG cc_start: 0.6807 (ptp-110) cc_final: 0.6588 (ptp-170) REVERT: A 221 GLU cc_start: 0.8818 (pt0) cc_final: 0.8572 (pt0) REVERT: A 364 ASP cc_start: 0.8189 (p0) cc_final: 0.7914 (p0) REVERT: A 395 ASP cc_start: 0.7784 (t70) cc_final: 0.7303 (t0) REVERT: A 431 ASP cc_start: 0.8022 (t70) cc_final: 0.7691 (t0) REVERT: A 440 GLU cc_start: 0.9012 (tt0) cc_final: 0.8636 (tp30) REVERT: B 203 TYR cc_start: 0.7468 (m-10) cc_final: 0.7255 (m-10) REVERT: B 231 LYS cc_start: 0.9262 (mmmm) cc_final: 0.8746 (ttpt) REVERT: B 244 TYR cc_start: 0.8086 (p90) cc_final: 0.7450 (p90) REVERT: B 261 GLU cc_start: 0.8727 (tm-30) cc_final: 0.7458 (tm-30) REVERT: B 364 ASP cc_start: 0.8226 (p0) cc_final: 0.7752 (p0) REVERT: B 388 MET cc_start: 0.8616 (tpt) cc_final: 0.8396 (tpt) REVERT: B 440 GLU cc_start: 0.9047 (tt0) cc_final: 0.8531 (tp30) REVERT: B 449 MET cc_start: 0.7647 (ppp) cc_final: 0.7059 (ppp) REVERT: B 454 TRP cc_start: 0.9040 (t60) cc_final: 0.8798 (t60) REVERT: B 543 LYS cc_start: 0.8847 (mppt) cc_final: 0.8616 (mtmt) REVERT: C 221 GLU cc_start: 0.8799 (pt0) cc_final: 0.8578 (pt0) REVERT: C 231 LYS cc_start: 0.9261 (mmmm) cc_final: 0.9054 (mmmm) REVERT: C 364 ASP cc_start: 0.7994 (p0) cc_final: 0.7615 (p0) REVERT: C 395 ASP cc_start: 0.7824 (t70) cc_final: 0.7202 (t0) REVERT: C 431 ASP cc_start: 0.7851 (t70) cc_final: 0.7505 (t0) REVERT: C 440 GLU cc_start: 0.9102 (tt0) cc_final: 0.8672 (tp30) REVERT: C 445 LEU cc_start: 0.8602 (tp) cc_final: 0.8271 (pp) REVERT: C 449 MET cc_start: 0.7682 (ppp) cc_final: 0.7081 (ppp) REVERT: C 517 TYR cc_start: 0.8922 (p90) cc_final: 0.8412 (p90) REVERT: C 550 MET cc_start: 0.8685 (mtm) cc_final: 0.8441 (mtm) REVERT: C 709 ARG cc_start: 0.8222 (ttt180) cc_final: 0.7996 (mmp80) REVERT: D 124 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8466 (mp0) REVERT: D 130 LEU cc_start: 0.8863 (mp) cc_final: 0.8566 (tp) REVERT: D 196 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6755 (mm-30) REVERT: D 221 GLU cc_start: 0.8789 (pt0) cc_final: 0.8395 (pm20) REVERT: D 231 LYS cc_start: 0.9196 (mmmm) cc_final: 0.8726 (ttpt) REVERT: D 364 ASP cc_start: 0.8090 (p0) cc_final: 0.7632 (p0) REVERT: D 431 ASP cc_start: 0.7884 (t70) cc_final: 0.7473 (t0) REVERT: D 440 GLU cc_start: 0.8990 (tt0) cc_final: 0.8591 (tp30) REVERT: D 449 MET cc_start: 0.7719 (ppp) cc_final: 0.7419 (tmm) REVERT: D 508 MET cc_start: 0.7033 (tmm) cc_final: 0.6386 (tpp) REVERT: E 147 ARG cc_start: 0.6837 (ptp-110) cc_final: 0.6620 (ptp-170) REVERT: E 203 TYR cc_start: 0.7512 (m-10) cc_final: 0.7187 (m-10) REVERT: E 231 LYS cc_start: 0.9280 (mmmm) cc_final: 0.8717 (ttpt) REVERT: E 244 TYR cc_start: 0.8098 (p90) cc_final: 0.7494 (p90) REVERT: E 261 GLU cc_start: 0.8635 (tm-30) cc_final: 0.7354 (tm-30) REVERT: E 364 ASP cc_start: 0.8095 (p0) cc_final: 0.7637 (p0) REVERT: E 395 ASP cc_start: 0.7829 (t70) cc_final: 0.7286 (t0) REVERT: E 440 GLU cc_start: 0.9051 (tt0) cc_final: 0.8520 (tp30) REVERT: E 449 MET cc_start: 0.7654 (ppp) cc_final: 0.7085 (ppp) REVERT: E 454 TRP cc_start: 0.9085 (t60) cc_final: 0.8711 (t60) REVERT: E 517 TYR cc_start: 0.8970 (p90) cc_final: 0.8176 (p90) REVERT: F 58 LEU cc_start: 0.9066 (tt) cc_final: 0.8772 (pp) REVERT: F 221 GLU cc_start: 0.8864 (pt0) cc_final: 0.8633 (pm20) REVERT: F 231 LYS cc_start: 0.9286 (mmmm) cc_final: 0.8807 (ttpt) REVERT: F 302 PHE cc_start: 0.8968 (t80) cc_final: 0.8717 (t80) REVERT: F 344 MET cc_start: 0.8506 (mtp) cc_final: 0.7993 (mtp) REVERT: F 364 ASP cc_start: 0.8108 (p0) cc_final: 0.7646 (p0) REVERT: F 388 MET cc_start: 0.8763 (tpt) cc_final: 0.8506 (tpp) REVERT: F 431 ASP cc_start: 0.7549 (t70) cc_final: 0.7288 (t0) REVERT: F 440 GLU cc_start: 0.9045 (tt0) cc_final: 0.8673 (tp30) REVERT: F 449 MET cc_start: 0.7796 (ppp) cc_final: 0.7453 (tmm) REVERT: F 508 MET cc_start: 0.6695 (tmm) cc_final: 0.6243 (tpp) REVERT: F 517 TYR cc_start: 0.8940 (p90) cc_final: 0.8253 (p90) REVERT: F 550 MET cc_start: 0.8595 (mtm) cc_final: 0.8394 (mtm) outliers start: 2 outliers final: 0 residues processed: 812 average time/residue: 0.2786 time to fit residues: 336.7000 Evaluate side-chains 541 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 541 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 3.9990 chunk 424 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN B 327 GLN B 499 HIS C 327 GLN D 327 GLN E 327 GLN F 327 GLN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.143079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.119456 restraints weight = 77505.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.122766 restraints weight = 44026.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.125008 restraints weight = 29279.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.126529 restraints weight = 21796.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.127452 restraints weight = 17694.719| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 35838 Z= 0.158 Angle : 0.697 8.006 48426 Z= 0.349 Chirality : 0.046 0.177 5418 Planarity : 0.007 0.079 6378 Dihedral : 10.953 169.843 5094 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -2.29 (0.12), residues: 4416 helix: -1.16 (0.11), residues: 1890 sheet: -1.48 (0.18), residues: 720 loop : -1.76 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 635 TYR 0.017 0.001 TYR A 244 PHE 0.022 0.001 PHE F 139 TRP 0.016 0.002 TRP D 454 HIS 0.008 0.001 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.00353 (35820) covalent geometry : angle 0.69684 (48426) hydrogen bonds : bond 0.04305 ( 1386) hydrogen bonds : angle 4.99652 ( 3924) Misc. bond : bond 0.00104 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 679 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8534 (ptt) cc_final: 0.8331 (tpp) REVERT: A 130 LEU cc_start: 0.8782 (mp) cc_final: 0.8517 (tp) REVERT: A 196 GLU cc_start: 0.7630 (mt-10) cc_final: 0.6993 (mm-30) REVERT: A 244 TYR cc_start: 0.7932 (p90) cc_final: 0.7695 (p90) REVERT: A 364 ASP cc_start: 0.7896 (p0) cc_final: 0.7620 (p0) REVERT: A 431 ASP cc_start: 0.7837 (t70) cc_final: 0.7603 (t0) REVERT: A 440 GLU cc_start: 0.8836 (tt0) cc_final: 0.8527 (tp30) REVERT: A 508 MET cc_start: 0.8419 (ptp) cc_final: 0.7747 (ptm) REVERT: A 709 ARG cc_start: 0.8203 (ttt180) cc_final: 0.7274 (ttp80) REVERT: A 740 MET cc_start: 0.5580 (ptt) cc_final: 0.5338 (ptt) REVERT: A 750 ASN cc_start: 0.8740 (p0) cc_final: 0.8518 (p0) REVERT: B 131 PHE cc_start: 0.8656 (t80) cc_final: 0.8454 (t80) REVERT: B 147 ARG cc_start: 0.6794 (ptp-110) cc_final: 0.6414 (ptp-170) REVERT: B 154 VAL cc_start: 0.8431 (m) cc_final: 0.8230 (m) REVERT: B 163 PHE cc_start: 0.8729 (m-80) cc_final: 0.8444 (m-80) REVERT: B 364 ASP cc_start: 0.8097 (p0) cc_final: 0.7838 (p0) REVERT: B 368 ASP cc_start: 0.7509 (t0) cc_final: 0.7308 (p0) REVERT: B 373 ASP cc_start: 0.7357 (p0) cc_final: 0.7127 (p0) REVERT: B 388 MET cc_start: 0.8351 (tpt) cc_final: 0.8136 (tpt) REVERT: B 440 GLU cc_start: 0.8983 (tt0) cc_final: 0.8493 (tp30) REVERT: B 449 MET cc_start: 0.7771 (ppp) cc_final: 0.7213 (ppp) REVERT: B 508 MET cc_start: 0.7929 (ptp) cc_final: 0.7440 (ptp) REVERT: B 543 LYS cc_start: 0.8813 (mppt) cc_final: 0.8597 (mtmt) REVERT: B 750 ASN cc_start: 0.8494 (p0) cc_final: 0.8235 (p0) REVERT: C 196 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6284 (mm-30) REVERT: C 364 ASP cc_start: 0.7848 (p0) cc_final: 0.7539 (p0) REVERT: C 368 ASP cc_start: 0.7987 (t0) cc_final: 0.7644 (t0) REVERT: C 431 ASP cc_start: 0.7939 (t70) cc_final: 0.7643 (t0) REVERT: C 440 GLU cc_start: 0.8891 (tt0) cc_final: 0.8533 (tp30) REVERT: C 449 MET cc_start: 0.7812 (ppp) cc_final: 0.7164 (ppp) REVERT: C 517 TYR cc_start: 0.8759 (p90) cc_final: 0.8265 (p90) REVERT: C 550 MET cc_start: 0.8594 (mtm) cc_final: 0.8303 (mtm) REVERT: D 46 MET cc_start: 0.8415 (ptt) cc_final: 0.8161 (tpp) REVERT: D 124 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8420 (mp0) REVERT: D 130 LEU cc_start: 0.8745 (mp) cc_final: 0.8506 (tp) REVERT: D 147 ARG cc_start: 0.6728 (ptp-110) cc_final: 0.6475 (ptp-170) REVERT: D 196 GLU cc_start: 0.7440 (mt-10) cc_final: 0.6846 (mm-30) REVERT: D 244 TYR cc_start: 0.8025 (p90) cc_final: 0.7509 (p90) REVERT: D 431 ASP cc_start: 0.7818 (t70) cc_final: 0.7484 (t0) REVERT: D 440 GLU cc_start: 0.8770 (tt0) cc_final: 0.8473 (tp30) REVERT: D 508 MET cc_start: 0.7071 (tmm) cc_final: 0.6731 (ptm) REVERT: E 113 ARG cc_start: 0.6437 (ttt180) cc_final: 0.6178 (mtt-85) REVERT: E 147 ARG cc_start: 0.6834 (ptp-110) cc_final: 0.6632 (ptp-170) REVERT: E 154 VAL cc_start: 0.8427 (m) cc_final: 0.8199 (m) REVERT: E 231 LYS cc_start: 0.9136 (mmmm) cc_final: 0.8603 (ttpt) REVERT: E 364 ASP cc_start: 0.8015 (p0) cc_final: 0.7759 (p0) REVERT: E 368 ASP cc_start: 0.7524 (t0) cc_final: 0.7237 (p0) REVERT: E 440 GLU cc_start: 0.9008 (tt0) cc_final: 0.8468 (tp30) REVERT: E 449 MET cc_start: 0.7747 (ppp) cc_final: 0.7242 (ppp) REVERT: E 517 TYR cc_start: 0.8759 (p90) cc_final: 0.8218 (p90) REVERT: E 712 GLU cc_start: 0.6772 (tt0) cc_final: 0.6202 (tt0) REVERT: E 744 ARG cc_start: 0.5701 (mmt-90) cc_final: 0.5317 (mmt-90) REVERT: F 130 LEU cc_start: 0.8488 (mp) cc_final: 0.8285 (tp) REVERT: F 203 TYR cc_start: 0.7529 (m-10) cc_final: 0.6452 (m-10) REVERT: F 364 ASP cc_start: 0.7894 (p0) cc_final: 0.7639 (p0) REVERT: F 388 MET cc_start: 0.8438 (tpt) cc_final: 0.8199 (tpt) REVERT: F 426 LYS cc_start: 0.9300 (tmtt) cc_final: 0.9066 (tptt) REVERT: F 431 ASP cc_start: 0.7706 (t70) cc_final: 0.7472 (t0) REVERT: F 440 GLU cc_start: 0.8935 (tt0) cc_final: 0.8599 (tp30) REVERT: F 517 TYR cc_start: 0.8805 (p90) cc_final: 0.8221 (p90) REVERT: F 550 MET cc_start: 0.8537 (mtm) cc_final: 0.8301 (mtm) REVERT: F 750 ASN cc_start: 0.8693 (p0) cc_final: 0.8461 (p0) outliers start: 0 outliers final: 0 residues processed: 679 average time/residue: 0.2505 time to fit residues: 261.0900 Evaluate side-chains 521 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 521 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 344 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 436 optimal weight: 3.9990 chunk 383 optimal weight: 8.9990 chunk 396 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 374 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS D 43 GLN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 ASN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.140959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.117796 restraints weight = 78492.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.121039 restraints weight = 44582.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.123195 restraints weight = 29621.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.124638 restraints weight = 22099.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.125607 restraints weight = 17967.325| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35838 Z= 0.179 Angle : 0.684 10.639 48426 Z= 0.343 Chirality : 0.046 0.140 5418 Planarity : 0.006 0.076 6378 Dihedral : 10.967 175.890 5094 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.12), residues: 4416 helix: -0.40 (0.12), residues: 1926 sheet: -1.07 (0.19), residues: 690 loop : -1.87 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 635 TYR 0.018 0.001 TYR A 755 PHE 0.017 0.002 PHE F 302 TRP 0.012 0.002 TRP F 454 HIS 0.009 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00404 (35820) covalent geometry : angle 0.68436 (48426) hydrogen bonds : bond 0.04152 ( 1386) hydrogen bonds : angle 4.81563 ( 3924) Misc. bond : bond 0.00160 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 648 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8544 (t80) cc_final: 0.8329 (t80) REVERT: A 196 GLU cc_start: 0.7448 (mt-10) cc_final: 0.6877 (mm-30) REVERT: A 221 GLU cc_start: 0.8915 (pt0) cc_final: 0.8686 (pm20) REVERT: A 364 ASP cc_start: 0.8029 (p0) cc_final: 0.7760 (p0) REVERT: A 431 ASP cc_start: 0.7862 (t70) cc_final: 0.7651 (t0) REVERT: A 440 GLU cc_start: 0.8705 (tt0) cc_final: 0.8483 (tp30) REVERT: A 674 PHE cc_start: 0.5726 (m-10) cc_final: 0.5314 (m-10) REVERT: A 709 ARG cc_start: 0.8299 (ttt180) cc_final: 0.7557 (ttp80) REVERT: A 750 ASN cc_start: 0.8656 (p0) cc_final: 0.8446 (p0) REVERT: B 131 PHE cc_start: 0.8570 (t80) cc_final: 0.8310 (t80) REVERT: B 147 ARG cc_start: 0.7045 (ptp-110) cc_final: 0.6813 (ptp-170) REVERT: B 163 PHE cc_start: 0.8771 (m-80) cc_final: 0.8346 (m-80) REVERT: B 231 LYS cc_start: 0.9080 (mmmm) cc_final: 0.8597 (ttpt) REVERT: B 244 TYR cc_start: 0.8141 (p90) cc_final: 0.7023 (p90) REVERT: B 364 ASP cc_start: 0.8219 (p0) cc_final: 0.7927 (p0) REVERT: B 440 GLU cc_start: 0.8957 (tt0) cc_final: 0.8476 (tp30) REVERT: B 449 MET cc_start: 0.7858 (ppp) cc_final: 0.7276 (ppp) REVERT: B 508 MET cc_start: 0.7493 (ptp) cc_final: 0.6618 (tpp) REVERT: C 196 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6402 (mm-30) REVERT: C 244 TYR cc_start: 0.8259 (p90) cc_final: 0.7249 (p90) REVERT: C 364 ASP cc_start: 0.7879 (p0) cc_final: 0.7580 (p0) REVERT: C 431 ASP cc_start: 0.7972 (t70) cc_final: 0.7700 (t0) REVERT: C 440 GLU cc_start: 0.8838 (tt0) cc_final: 0.8505 (tp30) REVERT: C 517 TYR cc_start: 0.8746 (p90) cc_final: 0.8272 (p90) REVERT: C 550 MET cc_start: 0.8629 (mtm) cc_final: 0.8299 (mtm) REVERT: C 740 MET cc_start: 0.5606 (ptt) cc_final: 0.5399 (ptt) REVERT: D 131 PHE cc_start: 0.8567 (t80) cc_final: 0.8363 (t80) REVERT: D 147 ARG cc_start: 0.6799 (ptp-110) cc_final: 0.6582 (ptp-170) REVERT: D 196 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6797 (mm-30) REVERT: D 364 ASP cc_start: 0.7930 (p0) cc_final: 0.7616 (p0) REVERT: D 431 ASP cc_start: 0.7805 (t70) cc_final: 0.7556 (t0) REVERT: D 440 GLU cc_start: 0.8602 (tt0) cc_final: 0.8397 (tp30) REVERT: D 449 MET cc_start: 0.7636 (ppp) cc_final: 0.7412 (ppp) REVERT: D 674 PHE cc_start: 0.5879 (m-10) cc_final: 0.5414 (m-10) REVERT: E 163 PHE cc_start: 0.8770 (m-80) cc_final: 0.8344 (m-80) REVERT: E 244 TYR cc_start: 0.8140 (p90) cc_final: 0.7128 (p90) REVERT: E 364 ASP cc_start: 0.8128 (p0) cc_final: 0.7806 (p0) REVERT: E 431 ASP cc_start: 0.7752 (t70) cc_final: 0.7524 (t0) REVERT: E 440 GLU cc_start: 0.8948 (tt0) cc_final: 0.8466 (tp30) REVERT: E 750 ASN cc_start: 0.8590 (p0) cc_final: 0.8298 (p0) REVERT: F 163 PHE cc_start: 0.8744 (m-80) cc_final: 0.8415 (m-80) REVERT: F 364 ASP cc_start: 0.7999 (p0) cc_final: 0.7634 (p0) REVERT: F 368 ASP cc_start: 0.7914 (t0) cc_final: 0.7373 (p0) REVERT: F 426 LYS cc_start: 0.9379 (tmtt) cc_final: 0.9158 (tptt) REVERT: F 440 GLU cc_start: 0.8906 (tt0) cc_final: 0.8561 (tp30) REVERT: F 517 TYR cc_start: 0.8801 (p90) cc_final: 0.8225 (p90) REVERT: F 550 MET cc_start: 0.8565 (mtm) cc_final: 0.8316 (mtm) outliers start: 0 outliers final: 0 residues processed: 648 average time/residue: 0.2387 time to fit residues: 243.2385 Evaluate side-chains 507 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 507 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 300 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 218 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 377 optimal weight: 20.0000 chunk 182 optimal weight: 9.9990 chunk 235 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 HIS ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 ASN E 763 GLN F 91 ASN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.136746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.113546 restraints weight = 79811.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.116601 restraints weight = 46582.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.118633 restraints weight = 31495.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.119989 restraints weight = 23718.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.120844 restraints weight = 19469.051| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 35838 Z= 0.268 Angle : 0.784 7.790 48426 Z= 0.397 Chirality : 0.049 0.166 5418 Planarity : 0.006 0.076 6378 Dihedral : 11.258 177.400 5094 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.12), residues: 4416 helix: -0.51 (0.11), residues: 1926 sheet: -1.12 (0.19), residues: 690 loop : -1.92 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 744 TYR 0.021 0.002 TYR E 203 PHE 0.023 0.002 PHE A 363 TRP 0.010 0.002 TRP F 454 HIS 0.007 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00601 (35820) covalent geometry : angle 0.78388 (48426) hydrogen bonds : bond 0.04841 ( 1386) hydrogen bonds : angle 5.27528 ( 3924) Misc. bond : bond 0.00112 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 611 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8686 (t80) cc_final: 0.8384 (t80) REVERT: A 196 GLU cc_start: 0.7612 (mt-10) cc_final: 0.6899 (mm-30) REVERT: A 221 GLU cc_start: 0.9024 (pt0) cc_final: 0.8701 (pm20) REVERT: A 316 THR cc_start: 0.8608 (m) cc_final: 0.8247 (p) REVERT: A 364 ASP cc_start: 0.8043 (p0) cc_final: 0.7722 (p0) REVERT: A 431 ASP cc_start: 0.7904 (t70) cc_final: 0.7681 (t0) REVERT: A 709 ARG cc_start: 0.8457 (ttt180) cc_final: 0.7617 (ttp80) REVERT: A 750 ASN cc_start: 0.8695 (p0) cc_final: 0.8475 (p0) REVERT: B 147 ARG cc_start: 0.7014 (ptp-110) cc_final: 0.6708 (ptp-170) REVERT: B 163 PHE cc_start: 0.8838 (m-80) cc_final: 0.8382 (m-80) REVERT: B 231 LYS cc_start: 0.9129 (mmmm) cc_final: 0.8608 (ttpt) REVERT: B 316 THR cc_start: 0.8692 (m) cc_final: 0.8338 (p) REVERT: B 431 ASP cc_start: 0.7796 (t70) cc_final: 0.7549 (t0) REVERT: B 440 GLU cc_start: 0.8923 (tt0) cc_final: 0.8497 (tp30) REVERT: C 203 TYR cc_start: 0.7172 (m-10) cc_final: 0.5973 (m-10) REVERT: C 218 GLU cc_start: 0.8805 (pp20) cc_final: 0.8388 (pp20) REVERT: C 364 ASP cc_start: 0.8035 (p0) cc_final: 0.7756 (p0) REVERT: C 368 ASP cc_start: 0.7941 (t70) cc_final: 0.7570 (t0) REVERT: C 431 ASP cc_start: 0.7894 (t70) cc_final: 0.7665 (t0) REVERT: C 440 GLU cc_start: 0.8838 (tt0) cc_final: 0.8516 (tp30) REVERT: C 508 MET cc_start: 0.8303 (ptp) cc_final: 0.7969 (ptm) REVERT: C 517 TYR cc_start: 0.8789 (p90) cc_final: 0.8306 (p90) REVERT: C 550 MET cc_start: 0.8620 (mtm) cc_final: 0.8378 (mtm) REVERT: C 740 MET cc_start: 0.5668 (ptt) cc_final: 0.5438 (ptt) REVERT: D 131 PHE cc_start: 0.8654 (t80) cc_final: 0.8398 (t80) REVERT: D 134 TYR cc_start: 0.7673 (m-80) cc_final: 0.7473 (m-80) REVERT: D 147 ARG cc_start: 0.6794 (ptp-110) cc_final: 0.6552 (ptp-170) REVERT: D 196 GLU cc_start: 0.7566 (mt-10) cc_final: 0.6830 (mm-30) REVERT: D 364 ASP cc_start: 0.7990 (p0) cc_final: 0.7670 (p0) REVERT: D 431 ASP cc_start: 0.7862 (t70) cc_final: 0.7610 (t0) REVERT: D 440 GLU cc_start: 0.8626 (tt0) cc_final: 0.8347 (tp30) REVERT: E 131 PHE cc_start: 0.8615 (t80) cc_final: 0.8302 (t80) REVERT: E 231 LYS cc_start: 0.9119 (mmmm) cc_final: 0.8601 (ttpt) REVERT: E 316 THR cc_start: 0.8727 (m) cc_final: 0.8341 (p) REVERT: E 364 ASP cc_start: 0.8148 (p0) cc_final: 0.7866 (p0) REVERT: E 431 ASP cc_start: 0.7713 (t70) cc_final: 0.7496 (t0) REVERT: E 440 GLU cc_start: 0.8921 (tt0) cc_final: 0.8480 (tp30) REVERT: E 744 ARG cc_start: 0.5537 (mmt-90) cc_final: 0.5294 (mmt-90) REVERT: E 750 ASN cc_start: 0.8650 (p0) cc_final: 0.8353 (p0) REVERT: F 131 PHE cc_start: 0.8615 (t80) cc_final: 0.8380 (t80) REVERT: F 163 PHE cc_start: 0.8847 (m-80) cc_final: 0.8465 (m-80) REVERT: F 203 TYR cc_start: 0.7370 (m-10) cc_final: 0.6343 (m-10) REVERT: F 219 MET cc_start: 0.8315 (ttm) cc_final: 0.8046 (ttm) REVERT: F 231 LYS cc_start: 0.9142 (mmmm) cc_final: 0.8727 (mmtp) REVERT: F 364 ASP cc_start: 0.8101 (p0) cc_final: 0.7730 (p0) REVERT: F 426 LYS cc_start: 0.9403 (tmtt) cc_final: 0.9176 (tptt) REVERT: F 440 GLU cc_start: 0.8917 (tt0) cc_final: 0.8553 (tp30) REVERT: F 517 TYR cc_start: 0.8831 (p90) cc_final: 0.8334 (p90) REVERT: F 550 MET cc_start: 0.8633 (mtm) cc_final: 0.8396 (mtm) outliers start: 0 outliers final: 0 residues processed: 611 average time/residue: 0.2290 time to fit residues: 221.8296 Evaluate side-chains 487 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 487 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 220 optimal weight: 9.9990 chunk 340 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 313 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 294 optimal weight: 0.9990 chunk 428 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN B 340 HIS B 558 ASN C 226 HIS C 340 HIS C 398 GLN D 226 HIS E 340 HIS F 91 ASN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.142368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.121265 restraints weight = 78237.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.124240 restraints weight = 48798.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.126119 restraints weight = 32282.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.126650 restraints weight = 26343.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.128164 restraints weight = 22028.243| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35838 Z= 0.130 Angle : 0.656 10.289 48426 Z= 0.323 Chirality : 0.046 0.147 5418 Planarity : 0.006 0.076 6378 Dihedral : 10.663 170.795 5094 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.13), residues: 4416 helix: 0.01 (0.12), residues: 1926 sheet: -0.89 (0.20), residues: 672 loop : -1.63 (0.15), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 711 TYR 0.016 0.001 TYR C 755 PHE 0.011 0.001 PHE D 363 TRP 0.006 0.002 TRP F 454 HIS 0.008 0.001 HIS C 340 Details of bonding type rmsd covalent geometry : bond 0.00294 (35820) covalent geometry : angle 0.65563 (48426) hydrogen bonds : bond 0.03709 ( 1386) hydrogen bonds : angle 4.54415 ( 3924) Misc. bond : bond 0.00061 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 649 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8602 (t80) cc_final: 0.8356 (t80) REVERT: A 196 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6607 (mm-30) REVERT: A 221 GLU cc_start: 0.8883 (pt0) cc_final: 0.8603 (pt0) REVERT: A 231 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8579 (ttpt) REVERT: A 316 THR cc_start: 0.8473 (m) cc_final: 0.8092 (p) REVERT: A 364 ASP cc_start: 0.8021 (p0) cc_final: 0.7694 (p0) REVERT: A 431 ASP cc_start: 0.7830 (t70) cc_final: 0.7577 (t0) REVERT: A 674 PHE cc_start: 0.5365 (m-10) cc_final: 0.4939 (m-10) REVERT: A 709 ARG cc_start: 0.8354 (ttt180) cc_final: 0.7317 (ttp80) REVERT: A 750 ASN cc_start: 0.8713 (p0) cc_final: 0.8417 (p0) REVERT: B 155 ARG cc_start: 0.7338 (mtp85) cc_final: 0.7104 (mmt90) REVERT: B 163 PHE cc_start: 0.8786 (m-80) cc_final: 0.8465 (m-80) REVERT: B 219 MET cc_start: 0.8065 (ttm) cc_final: 0.7850 (ttm) REVERT: B 231 LYS cc_start: 0.9148 (mmmm) cc_final: 0.8621 (ttpt) REVERT: B 244 TYR cc_start: 0.7989 (p90) cc_final: 0.7447 (p90) REVERT: B 316 THR cc_start: 0.8592 (m) cc_final: 0.8242 (p) REVERT: B 431 ASP cc_start: 0.7653 (t70) cc_final: 0.7425 (t0) REVERT: B 440 GLU cc_start: 0.8824 (tt0) cc_final: 0.8467 (tp30) REVERT: B 517 TYR cc_start: 0.8696 (p90) cc_final: 0.8309 (p90) REVERT: B 709 ARG cc_start: 0.8727 (mmp80) cc_final: 0.8484 (mmp80) REVERT: B 712 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6224 (mt-10) REVERT: C 163 PHE cc_start: 0.8697 (m-80) cc_final: 0.8344 (m-80) REVERT: C 218 GLU cc_start: 0.8712 (pp20) cc_final: 0.8175 (pp20) REVERT: C 219 MET cc_start: 0.8313 (ttm) cc_final: 0.7999 (ttm) REVERT: C 244 TYR cc_start: 0.8122 (p90) cc_final: 0.7067 (p90) REVERT: C 302 PHE cc_start: 0.8813 (t80) cc_final: 0.8417 (t80) REVERT: C 364 ASP cc_start: 0.7905 (p0) cc_final: 0.7513 (p0) REVERT: C 431 ASP cc_start: 0.7765 (t70) cc_final: 0.7527 (t0) REVERT: C 440 GLU cc_start: 0.8769 (tt0) cc_final: 0.8467 (tp30) REVERT: C 517 TYR cc_start: 0.8734 (p90) cc_final: 0.8180 (p90) REVERT: C 550 MET cc_start: 0.8609 (mtm) cc_final: 0.8334 (mtm) REVERT: C 712 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6494 (mt-10) REVERT: C 740 MET cc_start: 0.5320 (ptt) cc_final: 0.5060 (ptt) REVERT: C 744 ARG cc_start: 0.6288 (mmt-90) cc_final: 0.6011 (mmt-90) REVERT: D 147 ARG cc_start: 0.6605 (ptp-110) cc_final: 0.6250 (ptp-170) REVERT: D 196 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6579 (mm-30) REVERT: D 364 ASP cc_start: 0.7987 (p0) cc_final: 0.7728 (p0) REVERT: D 395 ASP cc_start: 0.7682 (t70) cc_final: 0.6938 (t0) REVERT: D 431 ASP cc_start: 0.7798 (t70) cc_final: 0.7569 (t0) REVERT: D 440 GLU cc_start: 0.8521 (tt0) cc_final: 0.8261 (tp30) REVERT: D 674 PHE cc_start: 0.5362 (m-10) cc_final: 0.4921 (m-10) REVERT: E 131 PHE cc_start: 0.8595 (t80) cc_final: 0.8327 (t80) REVERT: E 163 PHE cc_start: 0.8816 (m-80) cc_final: 0.8509 (m-80) REVERT: E 231 LYS cc_start: 0.9124 (mmmm) cc_final: 0.8602 (ttpt) REVERT: E 244 TYR cc_start: 0.8179 (p90) cc_final: 0.7195 (p90) REVERT: E 316 THR cc_start: 0.8604 (m) cc_final: 0.8229 (p) REVERT: E 364 ASP cc_start: 0.8128 (p0) cc_final: 0.7750 (p0) REVERT: E 427 MET cc_start: 0.6859 (ttt) cc_final: 0.6563 (tpt) REVERT: E 431 ASP cc_start: 0.7619 (t70) cc_final: 0.7392 (t0) REVERT: E 440 GLU cc_start: 0.8874 (tt0) cc_final: 0.8404 (tp30) REVERT: E 712 GLU cc_start: 0.6880 (tt0) cc_final: 0.6552 (tt0) REVERT: E 750 ASN cc_start: 0.8642 (p0) cc_final: 0.8359 (p0) REVERT: F 49 LEU cc_start: 0.9449 (mt) cc_final: 0.9228 (tt) REVERT: F 163 PHE cc_start: 0.8797 (m-80) cc_final: 0.8477 (m-80) REVERT: F 219 MET cc_start: 0.8305 (ttm) cc_final: 0.7953 (ttm) REVERT: F 231 LYS cc_start: 0.9129 (mmmm) cc_final: 0.8670 (ttpt) REVERT: F 316 THR cc_start: 0.8498 (m) cc_final: 0.8139 (p) REVERT: F 364 ASP cc_start: 0.7911 (p0) cc_final: 0.7452 (p0) REVERT: F 426 LYS cc_start: 0.9309 (tmtt) cc_final: 0.9106 (tptt) REVERT: F 440 GLU cc_start: 0.8848 (tt0) cc_final: 0.8483 (tp30) REVERT: F 517 TYR cc_start: 0.8771 (p90) cc_final: 0.8149 (p90) REVERT: F 550 MET cc_start: 0.8506 (mtm) cc_final: 0.8217 (mtm) outliers start: 0 outliers final: 0 residues processed: 649 average time/residue: 0.2285 time to fit residues: 236.2418 Evaluate side-chains 503 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 503 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 81 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 182 optimal weight: 0.9990 chunk 342 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 330 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 397 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN B 327 GLN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 HIS C 398 GLN ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.140589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.117361 restraints weight = 82891.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.120208 restraints weight = 48859.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.122133 restraints weight = 33307.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.123278 restraints weight = 25507.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.124253 restraints weight = 21301.011| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 35838 Z= 0.230 Angle : 0.740 8.202 48426 Z= 0.373 Chirality : 0.048 0.185 5418 Planarity : 0.006 0.076 6378 Dihedral : 11.074 176.487 5094 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.12), residues: 4416 helix: -0.10 (0.12), residues: 1926 sheet: -0.96 (0.20), residues: 684 loop : -1.87 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 635 TYR 0.020 0.002 TYR A 244 PHE 0.022 0.002 PHE C 563 TRP 0.009 0.002 TRP B 476 HIS 0.004 0.001 HIS F 406 Details of bonding type rmsd covalent geometry : bond 0.00523 (35820) covalent geometry : angle 0.73955 (48426) hydrogen bonds : bond 0.04444 ( 1386) hydrogen bonds : angle 4.94189 ( 3924) Misc. bond : bond 0.00073 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 615 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8691 (t80) cc_final: 0.8432 (t80) REVERT: A 138 TYR cc_start: 0.8740 (t80) cc_final: 0.8534 (t80) REVERT: A 196 GLU cc_start: 0.7456 (mt-10) cc_final: 0.6778 (mm-30) REVERT: A 221 GLU cc_start: 0.9000 (pt0) cc_final: 0.8670 (pt0) REVERT: A 316 THR cc_start: 0.8529 (m) cc_final: 0.8200 (p) REVERT: A 364 ASP cc_start: 0.8156 (p0) cc_final: 0.7786 (p0) REVERT: A 709 ARG cc_start: 0.8282 (ttt180) cc_final: 0.7762 (ttp80) REVERT: A 750 ASN cc_start: 0.8818 (p0) cc_final: 0.8555 (p0) REVERT: B 46 MET cc_start: 0.7855 (ptt) cc_final: 0.7557 (ptt) REVERT: B 147 ARG cc_start: 0.6985 (ptp-110) cc_final: 0.6773 (ptm160) REVERT: B 163 PHE cc_start: 0.8952 (m-80) cc_final: 0.8552 (m-80) REVERT: B 231 LYS cc_start: 0.9156 (mmmm) cc_final: 0.8610 (ttpt) REVERT: B 316 THR cc_start: 0.8705 (m) cc_final: 0.8363 (p) REVERT: B 344 MET cc_start: 0.8558 (mtm) cc_final: 0.8348 (mtp) REVERT: B 364 ASP cc_start: 0.8105 (p0) cc_final: 0.7807 (p0) REVERT: B 388 MET cc_start: 0.8305 (tpt) cc_final: 0.7849 (tpp) REVERT: B 438 ASP cc_start: 0.7758 (p0) cc_final: 0.7016 (t70) REVERT: B 440 GLU cc_start: 0.8859 (tt0) cc_final: 0.8484 (tp30) REVERT: B 712 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6745 (mp0) REVERT: B 750 ASN cc_start: 0.8784 (p0) cc_final: 0.8451 (p0) REVERT: C 219 MET cc_start: 0.8368 (ttm) cc_final: 0.8014 (ttm) REVERT: C 244 TYR cc_start: 0.8181 (p90) cc_final: 0.7389 (p90) REVERT: C 364 ASP cc_start: 0.8043 (p0) cc_final: 0.7670 (p0) REVERT: C 431 ASP cc_start: 0.7808 (t70) cc_final: 0.7584 (t0) REVERT: C 440 GLU cc_start: 0.8875 (tt0) cc_final: 0.8564 (tp30) REVERT: C 517 TYR cc_start: 0.8827 (p90) cc_final: 0.8305 (p90) REVERT: C 550 MET cc_start: 0.8646 (mtm) cc_final: 0.8391 (mtm) REVERT: C 712 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6650 (mt-10) REVERT: C 740 MET cc_start: 0.5518 (ptt) cc_final: 0.5250 (ptt) REVERT: C 744 ARG cc_start: 0.6339 (mmt-90) cc_final: 0.6058 (mmt-90) REVERT: D 131 PHE cc_start: 0.8746 (t80) cc_final: 0.8525 (t80) REVERT: D 147 ARG cc_start: 0.6677 (ptp-110) cc_final: 0.6417 (ptp-170) REVERT: D 196 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6777 (mm-30) REVERT: D 244 TYR cc_start: 0.8165 (p90) cc_final: 0.7006 (p90) REVERT: D 316 THR cc_start: 0.8662 (m) cc_final: 0.8257 (p) REVERT: D 364 ASP cc_start: 0.8065 (p0) cc_final: 0.7698 (p0) REVERT: D 431 ASP cc_start: 0.7849 (t70) cc_final: 0.7598 (t0) REVERT: D 440 GLU cc_start: 0.8678 (tt0) cc_final: 0.8394 (tp30) REVERT: E 147 ARG cc_start: 0.6588 (ptp-110) cc_final: 0.6383 (ptm160) REVERT: E 163 PHE cc_start: 0.8909 (m-80) cc_final: 0.8456 (m-80) REVERT: E 231 LYS cc_start: 0.9100 (mmmm) cc_final: 0.8557 (ttpt) REVERT: E 244 TYR cc_start: 0.8349 (p90) cc_final: 0.7374 (p90) REVERT: E 316 THR cc_start: 0.8699 (m) cc_final: 0.8355 (p) REVERT: E 431 ASP cc_start: 0.7751 (t70) cc_final: 0.7525 (t0) REVERT: E 440 GLU cc_start: 0.8917 (tt0) cc_final: 0.8470 (tp30) REVERT: E 712 GLU cc_start: 0.7024 (tt0) cc_final: 0.6743 (tt0) REVERT: E 744 ARG cc_start: 0.5588 (mmt-90) cc_final: 0.5235 (mmt-90) REVERT: E 750 ASN cc_start: 0.8726 (p0) cc_final: 0.8468 (p0) REVERT: F 163 PHE cc_start: 0.8850 (m-80) cc_final: 0.8510 (m-80) REVERT: F 203 TYR cc_start: 0.7526 (m-10) cc_final: 0.6804 (m-10) REVERT: F 219 MET cc_start: 0.8113 (ttm) cc_final: 0.7843 (ttm) REVERT: F 231 LYS cc_start: 0.9129 (mmmm) cc_final: 0.8656 (mmtp) REVERT: F 244 TYR cc_start: 0.8027 (p90) cc_final: 0.7099 (p90) REVERT: F 316 THR cc_start: 0.8559 (m) cc_final: 0.8168 (p) REVERT: F 364 ASP cc_start: 0.8029 (p0) cc_final: 0.7647 (p0) REVERT: F 426 LYS cc_start: 0.9398 (tmtt) cc_final: 0.9170 (tptt) REVERT: F 440 GLU cc_start: 0.8911 (tt0) cc_final: 0.8559 (tp30) REVERT: F 517 TYR cc_start: 0.8810 (p90) cc_final: 0.8220 (p90) REVERT: F 550 MET cc_start: 0.8630 (mtm) cc_final: 0.8372 (mtm) REVERT: F 740 MET cc_start: 0.5837 (ptt) cc_final: 0.5558 (ptt) outliers start: 0 outliers final: 0 residues processed: 615 average time/residue: 0.2403 time to fit residues: 233.6966 Evaluate side-chains 486 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 191 optimal weight: 2.9990 chunk 343 optimal weight: 0.9990 chunk 418 optimal weight: 10.0000 chunk 15 optimal weight: 0.0870 chunk 316 optimal weight: 0.8980 chunk 227 optimal weight: 20.0000 chunk 310 optimal weight: 2.9990 chunk 398 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS B 340 HIS B 406 HIS C 340 HIS C 398 GLN C 406 HIS D 398 GLN D 404 HIS D 406 HIS E 340 HIS E 406 HIS ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.143818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.120930 restraints weight = 77762.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.124248 restraints weight = 43818.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.126467 restraints weight = 28966.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.127913 restraints weight = 21487.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.128907 restraints weight = 17435.085| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35838 Z= 0.120 Angle : 0.676 12.692 48426 Z= 0.329 Chirality : 0.046 0.225 5418 Planarity : 0.005 0.076 6378 Dihedral : 10.291 167.843 5094 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.03 % Allowed : 1.40 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.13), residues: 4416 helix: 0.18 (0.12), residues: 1944 sheet: -0.67 (0.20), residues: 678 loop : -1.54 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 225 TYR 0.015 0.001 TYR C 755 PHE 0.009 0.001 PHE D 131 TRP 0.010 0.002 TRP D 551 HIS 0.018 0.002 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00264 (35820) covalent geometry : angle 0.67620 (48426) hydrogen bonds : bond 0.03344 ( 1386) hydrogen bonds : angle 4.38548 ( 3924) Misc. bond : bond 0.00057 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 654 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.7513 (m-80) cc_final: 0.7312 (m-80) REVERT: A 163 PHE cc_start: 0.8786 (m-80) cc_final: 0.8505 (m-80) REVERT: A 196 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6591 (mm-30) REVERT: A 219 MET cc_start: 0.8506 (ttm) cc_final: 0.8280 (ttm) REVERT: A 221 GLU cc_start: 0.8901 (pt0) cc_final: 0.8489 (pm20) REVERT: A 231 LYS cc_start: 0.9060 (mmmm) cc_final: 0.8582 (ttpt) REVERT: A 316 THR cc_start: 0.8385 (m) cc_final: 0.8087 (p) REVERT: A 364 ASP cc_start: 0.7968 (p0) cc_final: 0.7641 (p0) REVERT: A 438 ASP cc_start: 0.7540 (p0) cc_final: 0.7289 (t70) REVERT: A 567 ARG cc_start: 0.8481 (ttp-110) cc_final: 0.8108 (ttm-80) REVERT: A 674 PHE cc_start: 0.5523 (m-10) cc_final: 0.5123 (m-10) REVERT: A 709 ARG cc_start: 0.8061 (ttt180) cc_final: 0.7511 (ttp80) REVERT: A 750 ASN cc_start: 0.8795 (p0) cc_final: 0.8485 (p0) REVERT: B 163 PHE cc_start: 0.8799 (m-80) cc_final: 0.8503 (m-80) REVERT: B 219 MET cc_start: 0.8231 (ttm) cc_final: 0.8012 (ttm) REVERT: B 231 LYS cc_start: 0.9169 (mmmm) cc_final: 0.8612 (ttpt) REVERT: B 244 TYR cc_start: 0.7955 (p90) cc_final: 0.7652 (p90) REVERT: B 316 THR cc_start: 0.8577 (m) cc_final: 0.8228 (p) REVERT: B 426 LYS cc_start: 0.9242 (tmtt) cc_final: 0.9005 (tmmt) REVERT: B 438 ASP cc_start: 0.7397 (p0) cc_final: 0.6908 (t70) REVERT: B 440 GLU cc_start: 0.8803 (tt0) cc_final: 0.8426 (tp30) REVERT: B 517 TYR cc_start: 0.8663 (p90) cc_final: 0.8339 (p90) REVERT: B 709 ARG cc_start: 0.8772 (mmp80) cc_final: 0.8467 (mmp80) REVERT: B 712 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6262 (mt-10) REVERT: C 163 PHE cc_start: 0.8628 (m-80) cc_final: 0.8303 (m-80) REVERT: C 244 TYR cc_start: 0.7922 (p90) cc_final: 0.7163 (p90) REVERT: C 302 PHE cc_start: 0.8956 (t80) cc_final: 0.8670 (t80) REVERT: C 364 ASP cc_start: 0.7819 (p0) cc_final: 0.7389 (p0) REVERT: C 431 ASP cc_start: 0.7782 (t70) cc_final: 0.7558 (t0) REVERT: C 440 GLU cc_start: 0.8794 (tt0) cc_final: 0.8495 (tp30) REVERT: C 517 TYR cc_start: 0.8720 (p90) cc_final: 0.8166 (p90) REVERT: C 550 MET cc_start: 0.8520 (mtm) cc_final: 0.8220 (mtm) REVERT: C 740 MET cc_start: 0.5349 (ptt) cc_final: 0.5087 (ptt) REVERT: C 744 ARG cc_start: 0.6036 (mmt-90) cc_final: 0.5708 (mmt-90) REVERT: D 46 MET cc_start: 0.8191 (ptt) cc_final: 0.7928 (ptt) REVERT: D 113 ARG cc_start: 0.6875 (ttt180) cc_final: 0.6668 (tpt170) REVERT: D 131 PHE cc_start: 0.8490 (t80) cc_final: 0.8233 (t80) REVERT: D 147 ARG cc_start: 0.6537 (ptp-110) cc_final: 0.6230 (ptp-170) REVERT: D 163 PHE cc_start: 0.8830 (m-80) cc_final: 0.8532 (m-80) REVERT: D 196 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6604 (mm-30) REVERT: D 316 THR cc_start: 0.8412 (m) cc_final: 0.7972 (p) REVERT: D 364 ASP cc_start: 0.7915 (p0) cc_final: 0.7541 (p0) REVERT: D 431 ASP cc_start: 0.7748 (t70) cc_final: 0.7508 (t0) REVERT: D 440 GLU cc_start: 0.8605 (tt0) cc_final: 0.8313 (tp30) REVERT: D 449 MET cc_start: 0.7356 (ppp) cc_final: 0.7088 (ppp) REVERT: D 674 PHE cc_start: 0.5365 (m-10) cc_final: 0.4958 (m-10) REVERT: E 163 PHE cc_start: 0.8826 (m-80) cc_final: 0.8560 (m-80) REVERT: E 231 LYS cc_start: 0.9086 (mmmm) cc_final: 0.8563 (ttpt) REVERT: E 244 TYR cc_start: 0.8055 (p90) cc_final: 0.7302 (p90) REVERT: E 316 THR cc_start: 0.8551 (m) cc_final: 0.8188 (p) REVERT: E 426 LYS cc_start: 0.9212 (tmtt) cc_final: 0.8957 (tmmt) REVERT: E 427 MET cc_start: 0.6747 (ttt) cc_final: 0.6392 (tpt) REVERT: E 431 ASP cc_start: 0.7592 (t70) cc_final: 0.7303 (t0) REVERT: E 440 GLU cc_start: 0.8889 (tt0) cc_final: 0.8463 (tp30) REVERT: E 711 ARG cc_start: 0.8383 (ttt-90) cc_final: 0.8171 (mmm-85) REVERT: E 712 GLU cc_start: 0.6955 (tt0) cc_final: 0.6676 (tt0) REVERT: F 124 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8515 (mp0) REVERT: F 163 PHE cc_start: 0.8859 (m-80) cc_final: 0.8569 (m-80) REVERT: F 218 GLU cc_start: 0.8434 (pp20) cc_final: 0.8189 (pp20) REVERT: F 219 MET cc_start: 0.8140 (ttm) cc_final: 0.7891 (ttm) REVERT: F 231 LYS cc_start: 0.9142 (mmmm) cc_final: 0.8717 (ttpt) REVERT: F 244 TYR cc_start: 0.7958 (p90) cc_final: 0.7426 (p90) REVERT: F 316 THR cc_start: 0.8522 (m) cc_final: 0.8196 (p) REVERT: F 364 ASP cc_start: 0.7867 (p0) cc_final: 0.7467 (p0) REVERT: F 426 LYS cc_start: 0.9291 (tmtt) cc_final: 0.9072 (tptt) REVERT: F 440 GLU cc_start: 0.8869 (tt0) cc_final: 0.8528 (tp30) REVERT: F 550 MET cc_start: 0.8531 (mtm) cc_final: 0.8220 (mtm) outliers start: 1 outliers final: 0 residues processed: 654 average time/residue: 0.2374 time to fit residues: 244.6949 Evaluate side-chains 503 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 503 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 143 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 238 optimal weight: 8.9990 chunk 290 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 387 optimal weight: 9.9990 chunk 314 optimal weight: 9.9990 chunk 271 optimal weight: 3.9990 chunk 164 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 GLN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 GLN C 764 GLN D 91 ASN D 340 HIS D 398 GLN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.141280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.118184 restraints weight = 82354.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.121042 restraints weight = 48288.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.123005 restraints weight = 32822.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.124298 restraints weight = 24891.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.125170 restraints weight = 20512.791| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 35838 Z= 0.215 Angle : 0.733 8.398 48426 Z= 0.367 Chirality : 0.048 0.197 5418 Planarity : 0.006 0.085 6378 Dihedral : 10.857 175.821 5094 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.13), residues: 4416 helix: 0.07 (0.12), residues: 1932 sheet: -0.83 (0.20), residues: 690 loop : -1.71 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 95 TYR 0.024 0.002 TYR A 244 PHE 0.020 0.002 PHE D 363 TRP 0.009 0.002 TRP B 551 HIS 0.008 0.001 HIS E 406 Details of bonding type rmsd covalent geometry : bond 0.00486 (35820) covalent geometry : angle 0.73250 (48426) hydrogen bonds : bond 0.04220 ( 1386) hydrogen bonds : angle 4.82929 ( 3924) Misc. bond : bond 0.00075 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 604 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8642 (t80) cc_final: 0.8400 (t80) REVERT: A 196 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6652 (mm-30) REVERT: A 221 GLU cc_start: 0.9003 (pt0) cc_final: 0.8612 (pt0) REVERT: A 231 LYS cc_start: 0.9091 (mmmm) cc_final: 0.8599 (ttpt) REVERT: A 316 THR cc_start: 0.8534 (m) cc_final: 0.8115 (p) REVERT: A 364 ASP cc_start: 0.8056 (p0) cc_final: 0.7688 (p0) REVERT: A 438 ASP cc_start: 0.7716 (p0) cc_final: 0.7355 (t70) REVERT: A 611 MET cc_start: 0.6524 (ptm) cc_final: 0.6202 (ptm) REVERT: A 709 ARG cc_start: 0.8563 (ttt180) cc_final: 0.7519 (ttp80) REVERT: A 750 ASN cc_start: 0.8772 (p0) cc_final: 0.8469 (p0) REVERT: B 46 MET cc_start: 0.7816 (ptt) cc_final: 0.7550 (ptt) REVERT: B 162 GLU cc_start: 0.8645 (pm20) cc_final: 0.8286 (pm20) REVERT: B 163 PHE cc_start: 0.8882 (m-80) cc_final: 0.8530 (m-80) REVERT: B 231 LYS cc_start: 0.9118 (mmmm) cc_final: 0.8595 (ttpt) REVERT: B 316 THR cc_start: 0.8730 (m) cc_final: 0.8332 (p) REVERT: B 364 ASP cc_start: 0.8046 (p0) cc_final: 0.7745 (p0) REVERT: B 438 ASP cc_start: 0.7701 (p0) cc_final: 0.7252 (t70) REVERT: B 440 GLU cc_start: 0.8844 (tt0) cc_final: 0.8477 (tp30) REVERT: C 244 TYR cc_start: 0.8135 (p90) cc_final: 0.7573 (p90) REVERT: C 364 ASP cc_start: 0.7994 (p0) cc_final: 0.7606 (p0) REVERT: C 431 ASP cc_start: 0.7895 (t70) cc_final: 0.7659 (t0) REVERT: C 440 GLU cc_start: 0.8853 (tt0) cc_final: 0.8544 (tp30) REVERT: C 517 TYR cc_start: 0.8796 (p90) cc_final: 0.8267 (p90) REVERT: C 550 MET cc_start: 0.8644 (mtm) cc_final: 0.8412 (mtm) REVERT: C 712 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6672 (mt-10) REVERT: C 740 MET cc_start: 0.5575 (ptt) cc_final: 0.5273 (ptt) REVERT: C 744 ARG cc_start: 0.6098 (mmt-90) cc_final: 0.5786 (mmt-90) REVERT: D 131 PHE cc_start: 0.8747 (t80) cc_final: 0.8326 (t80) REVERT: D 147 ARG cc_start: 0.6638 (ptp-110) cc_final: 0.6359 (ptp-170) REVERT: D 196 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6667 (mm-30) REVERT: D 316 THR cc_start: 0.8546 (m) cc_final: 0.8179 (p) REVERT: D 364 ASP cc_start: 0.8060 (p0) cc_final: 0.7682 (p0) REVERT: D 431 ASP cc_start: 0.7753 (t70) cc_final: 0.7539 (t0) REVERT: D 440 GLU cc_start: 0.8620 (tt0) cc_final: 0.8388 (tp30) REVERT: D 449 MET cc_start: 0.7517 (ppp) cc_final: 0.7154 (ppp) REVERT: E 136 LYS cc_start: 0.8991 (mmtt) cc_final: 0.8750 (mmmt) REVERT: E 163 PHE cc_start: 0.8938 (m-80) cc_final: 0.8537 (m-80) REVERT: E 231 LYS cc_start: 0.9088 (mmmm) cc_final: 0.8570 (ttpt) REVERT: E 244 TYR cc_start: 0.8194 (p90) cc_final: 0.7047 (p90) REVERT: E 316 THR cc_start: 0.8707 (m) cc_final: 0.8303 (p) REVERT: E 431 ASP cc_start: 0.7746 (t70) cc_final: 0.7503 (t0) REVERT: E 438 ASP cc_start: 0.7639 (p0) cc_final: 0.7226 (t0) REVERT: E 440 GLU cc_start: 0.8825 (tt0) cc_final: 0.8474 (tp30) REVERT: E 711 ARG cc_start: 0.8523 (ttt-90) cc_final: 0.8198 (mmm-85) REVERT: E 744 ARG cc_start: 0.5817 (mmt-90) cc_final: 0.5370 (mmt-90) REVERT: F 163 PHE cc_start: 0.8822 (m-80) cc_final: 0.8474 (m-80) REVERT: F 203 TYR cc_start: 0.7495 (m-10) cc_final: 0.6900 (m-10) REVERT: F 218 GLU cc_start: 0.8615 (pp20) cc_final: 0.8287 (pp20) REVERT: F 244 TYR cc_start: 0.8005 (p90) cc_final: 0.7337 (p90) REVERT: F 316 THR cc_start: 0.8622 (m) cc_final: 0.8265 (p) REVERT: F 364 ASP cc_start: 0.8044 (p0) cc_final: 0.7659 (p0) REVERT: F 426 LYS cc_start: 0.9385 (tmtt) cc_final: 0.9155 (tptt) REVERT: F 440 GLU cc_start: 0.8857 (tt0) cc_final: 0.8567 (tp30) REVERT: F 550 MET cc_start: 0.8608 (mtm) cc_final: 0.8350 (mtm) REVERT: F 740 MET cc_start: 0.5703 (ptt) cc_final: 0.5384 (ptt) outliers start: 0 outliers final: 0 residues processed: 604 average time/residue: 0.2282 time to fit residues: 220.5966 Evaluate side-chains 482 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 482 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 208 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 89 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 400 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 350 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 432 optimal weight: 0.9990 chunk 343 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 GLN B 327 GLN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 GLN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.142167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.120241 restraints weight = 78185.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.123154 restraints weight = 47320.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.124950 restraints weight = 32597.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.126325 restraints weight = 25200.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.127223 restraints weight = 20740.660| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35838 Z= 0.125 Angle : 0.680 14.513 48426 Z= 0.331 Chirality : 0.046 0.263 5418 Planarity : 0.006 0.081 6378 Dihedral : 10.404 170.618 5094 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.99 (0.13), residues: 4416 helix: 0.24 (0.12), residues: 1944 sheet: -0.70 (0.20), residues: 690 loop : -1.58 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 95 TYR 0.025 0.001 TYR A 138 PHE 0.019 0.001 PHE C 302 TRP 0.009 0.001 TRP C 551 HIS 0.006 0.001 HIS B 735 Details of bonding type rmsd covalent geometry : bond 0.00284 (35820) covalent geometry : angle 0.67964 (48426) hydrogen bonds : bond 0.03478 ( 1386) hydrogen bonds : angle 4.41647 ( 3924) Misc. bond : bond 0.00042 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 621 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8533 (t80) cc_final: 0.8189 (t80) REVERT: A 163 PHE cc_start: 0.8839 (m-80) cc_final: 0.8555 (m-80) REVERT: A 196 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6607 (mm-30) REVERT: A 219 MET cc_start: 0.8377 (ttm) cc_final: 0.7956 (ttt) REVERT: A 221 GLU cc_start: 0.8858 (pt0) cc_final: 0.8445 (pm20) REVERT: A 231 LYS cc_start: 0.9050 (mmmm) cc_final: 0.8589 (ttpt) REVERT: A 316 THR cc_start: 0.8450 (m) cc_final: 0.8132 (p) REVERT: A 321 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7641 (mt-10) REVERT: A 364 ASP cc_start: 0.7960 (p0) cc_final: 0.7559 (p0) REVERT: A 438 ASP cc_start: 0.7527 (p0) cc_final: 0.7237 (t70) REVERT: A 611 MET cc_start: 0.6380 (ptm) cc_final: 0.6019 (ptm) REVERT: A 674 PHE cc_start: 0.5351 (m-10) cc_final: 0.4927 (m-10) REVERT: A 709 ARG cc_start: 0.8470 (ttt180) cc_final: 0.7483 (ttp80) REVERT: A 750 ASN cc_start: 0.8719 (p0) cc_final: 0.8397 (p0) REVERT: B 46 MET cc_start: 0.7763 (ptt) cc_final: 0.7489 (ptt) REVERT: B 162 GLU cc_start: 0.8462 (pm20) cc_final: 0.8216 (pm20) REVERT: B 163 PHE cc_start: 0.8781 (m-80) cc_final: 0.8512 (m-80) REVERT: B 231 LYS cc_start: 0.9068 (mmmm) cc_final: 0.8563 (ttpt) REVERT: B 316 THR cc_start: 0.8601 (m) cc_final: 0.8258 (p) REVERT: B 364 ASP cc_start: 0.7865 (p0) cc_final: 0.7438 (p0) REVERT: B 426 LYS cc_start: 0.9234 (tmtt) cc_final: 0.9018 (tmmt) REVERT: B 438 ASP cc_start: 0.7465 (p0) cc_final: 0.6878 (t70) REVERT: B 440 GLU cc_start: 0.8737 (tt0) cc_final: 0.8421 (tp30) REVERT: B 517 TYR cc_start: 0.8617 (p90) cc_final: 0.8376 (p90) REVERT: C 162 GLU cc_start: 0.8558 (pm20) cc_final: 0.8330 (pm20) REVERT: C 163 PHE cc_start: 0.8661 (m-80) cc_final: 0.8309 (m-80) REVERT: C 244 TYR cc_start: 0.7940 (p90) cc_final: 0.7111 (p90) REVERT: C 364 ASP cc_start: 0.7853 (p0) cc_final: 0.7451 (p0) REVERT: C 431 ASP cc_start: 0.7819 (t70) cc_final: 0.7608 (t0) REVERT: C 440 GLU cc_start: 0.8751 (tt0) cc_final: 0.8470 (tp30) REVERT: C 517 TYR cc_start: 0.8724 (p90) cc_final: 0.8148 (p90) REVERT: C 550 MET cc_start: 0.8495 (mtm) cc_final: 0.8245 (mtm) REVERT: C 712 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6792 (mp0) REVERT: C 740 MET cc_start: 0.5412 (ptt) cc_final: 0.5115 (ptt) REVERT: C 744 ARG cc_start: 0.5967 (mmt-90) cc_final: 0.5640 (mmt-90) REVERT: D 131 PHE cc_start: 0.8567 (t80) cc_final: 0.8254 (t80) REVERT: D 147 ARG cc_start: 0.6643 (ptp-110) cc_final: 0.6372 (ptp-170) REVERT: D 163 PHE cc_start: 0.8820 (m-80) cc_final: 0.8495 (m-80) REVERT: D 196 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6599 (mm-30) REVERT: D 316 THR cc_start: 0.8428 (m) cc_final: 0.8020 (p) REVERT: D 364 ASP cc_start: 0.7979 (p0) cc_final: 0.7601 (p0) REVERT: D 431 ASP cc_start: 0.7832 (t70) cc_final: 0.7574 (t0) REVERT: D 449 MET cc_start: 0.7454 (ppp) cc_final: 0.7243 (ppp) REVERT: D 674 PHE cc_start: 0.5401 (m-10) cc_final: 0.4995 (m-10) REVERT: E 163 PHE cc_start: 0.8821 (m-80) cc_final: 0.8560 (m-80) REVERT: E 231 LYS cc_start: 0.9094 (mmmm) cc_final: 0.8577 (ttpt) REVERT: E 244 TYR cc_start: 0.8187 (p90) cc_final: 0.7382 (p90) REVERT: E 316 THR cc_start: 0.8595 (m) cc_final: 0.8239 (p) REVERT: E 426 LYS cc_start: 0.9212 (tmtt) cc_final: 0.8987 (tmmt) REVERT: E 431 ASP cc_start: 0.7648 (t70) cc_final: 0.7392 (t0) REVERT: E 438 ASP cc_start: 0.7442 (p0) cc_final: 0.6818 (t70) REVERT: E 440 GLU cc_start: 0.8751 (tt0) cc_final: 0.8453 (tp30) REVERT: E 711 ARG cc_start: 0.8369 (ttt-90) cc_final: 0.8093 (mmm-85) REVERT: E 744 ARG cc_start: 0.5876 (mmt-90) cc_final: 0.5466 (mmt-90) REVERT: F 163 PHE cc_start: 0.8788 (m-80) cc_final: 0.8548 (m-80) REVERT: F 218 GLU cc_start: 0.8517 (pp20) cc_final: 0.8164 (pp20) REVERT: F 231 LYS cc_start: 0.9062 (mmmm) cc_final: 0.8816 (mmtm) REVERT: F 244 TYR cc_start: 0.7982 (p90) cc_final: 0.7308 (p90) REVERT: F 316 THR cc_start: 0.8546 (m) cc_final: 0.8278 (p) REVERT: F 364 ASP cc_start: 0.7889 (p0) cc_final: 0.7420 (p0) REVERT: F 426 LYS cc_start: 0.9274 (tmtt) cc_final: 0.9048 (tptt) REVERT: F 440 GLU cc_start: 0.8794 (tt0) cc_final: 0.8523 (tp30) REVERT: F 550 MET cc_start: 0.8456 (mtm) cc_final: 0.8246 (mtm) REVERT: F 740 MET cc_start: 0.5545 (ptt) cc_final: 0.5215 (ptt) outliers start: 0 outliers final: 0 residues processed: 621 average time/residue: 0.2188 time to fit residues: 218.2874 Evaluate side-chains 496 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 496 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 439 optimal weight: 9.9990 chunk 190 optimal weight: 8.9990 chunk 263 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 237 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 382 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 288 optimal weight: 4.9990 chunk 317 optimal weight: 3.9990 chunk 192 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 HIS ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 764 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.140695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.117981 restraints weight = 82745.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.120603 restraints weight = 50200.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.122415 restraints weight = 34846.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.123605 restraints weight = 27017.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.124407 restraints weight = 22638.371| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 35838 Z= 0.243 Angle : 0.772 9.466 48426 Z= 0.389 Chirality : 0.049 0.201 5418 Planarity : 0.006 0.076 6378 Dihedral : 10.963 178.191 5094 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.13), residues: 4416 helix: 0.01 (0.12), residues: 1938 sheet: -0.89 (0.20), residues: 702 loop : -1.78 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 95 TYR 0.027 0.002 TYR A 244 PHE 0.027 0.002 PHE D 563 TRP 0.011 0.002 TRP A 551 HIS 0.008 0.001 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.00549 (35820) covalent geometry : angle 0.77235 (48426) hydrogen bonds : bond 0.04431 ( 1386) hydrogen bonds : angle 4.98583 ( 3924) Misc. bond : bond 0.00146 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 587 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ARG cc_start: 0.6880 (tpt170) cc_final: 0.6589 (mmm-85) REVERT: A 131 PHE cc_start: 0.8744 (t80) cc_final: 0.8489 (t80) REVERT: A 196 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6492 (mm-30) REVERT: A 203 TYR cc_start: 0.7243 (m-10) cc_final: 0.6464 (m-80) REVERT: A 221 GLU cc_start: 0.8957 (pt0) cc_final: 0.8571 (pt0) REVERT: A 231 LYS cc_start: 0.9083 (mmmm) cc_final: 0.8631 (ttpt) REVERT: A 316 THR cc_start: 0.8561 (m) cc_final: 0.8248 (p) REVERT: A 364 ASP cc_start: 0.8057 (p0) cc_final: 0.7795 (p0) REVERT: A 611 MET cc_start: 0.6516 (ptm) cc_final: 0.6205 (ptm) REVERT: A 709 ARG cc_start: 0.8530 (ttt180) cc_final: 0.7515 (ttp80) REVERT: A 750 ASN cc_start: 0.8704 (p0) cc_final: 0.8451 (p0) REVERT: B 162 GLU cc_start: 0.8614 (pm20) cc_final: 0.8303 (pm20) REVERT: B 163 PHE cc_start: 0.8751 (m-80) cc_final: 0.8413 (m-80) REVERT: B 231 LYS cc_start: 0.9103 (mmmm) cc_final: 0.8580 (ttpt) REVERT: B 244 TYR cc_start: 0.8091 (p90) cc_final: 0.7466 (p90) REVERT: B 316 THR cc_start: 0.8755 (m) cc_final: 0.8408 (p) REVERT: B 364 ASP cc_start: 0.7925 (p0) cc_final: 0.7578 (p0) REVERT: B 426 LYS cc_start: 0.9389 (tmtt) cc_final: 0.9155 (tmmt) REVERT: B 438 ASP cc_start: 0.7778 (p0) cc_final: 0.7138 (t70) REVERT: B 440 GLU cc_start: 0.8775 (tt0) cc_final: 0.8444 (tp30) REVERT: B 709 ARG cc_start: 0.8670 (mmp80) cc_final: 0.8355 (mmp80) REVERT: B 712 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6181 (mt-10) REVERT: C 244 TYR cc_start: 0.8148 (p90) cc_final: 0.7485 (p90) REVERT: C 364 ASP cc_start: 0.8023 (p0) cc_final: 0.7567 (p0) REVERT: C 368 ASP cc_start: 0.7617 (t0) cc_final: 0.7397 (t0) REVERT: C 431 ASP cc_start: 0.7975 (t70) cc_final: 0.7755 (t0) REVERT: C 440 GLU cc_start: 0.8824 (tt0) cc_final: 0.8533 (tp30) REVERT: C 449 MET cc_start: 0.7760 (ppp) cc_final: 0.7429 (ppp) REVERT: C 517 TYR cc_start: 0.8794 (p90) cc_final: 0.8259 (p90) REVERT: C 712 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6774 (mt-10) REVERT: C 740 MET cc_start: 0.5620 (ptt) cc_final: 0.5229 (ptt) REVERT: C 744 ARG cc_start: 0.6102 (mmt-90) cc_final: 0.5814 (mmt-90) REVERT: D 113 ARG cc_start: 0.6886 (ttt180) cc_final: 0.6525 (tpt170) REVERT: D 131 PHE cc_start: 0.8759 (t80) cc_final: 0.8545 (t80) REVERT: D 147 ARG cc_start: 0.6566 (ptp-110) cc_final: 0.6344 (ptp-170) REVERT: D 196 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6532 (mm-30) REVERT: D 316 THR cc_start: 0.8565 (m) cc_final: 0.8198 (p) REVERT: D 364 ASP cc_start: 0.8136 (p0) cc_final: 0.7844 (p0) REVERT: D 431 ASP cc_start: 0.7990 (t70) cc_final: 0.7720 (t0) REVERT: D 449 MET cc_start: 0.7504 (ppp) cc_final: 0.7273 (ppp) REVERT: D 611 MET cc_start: 0.6518 (ptm) cc_final: 0.6139 (ptm) REVERT: D 712 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6593 (mp0) REVERT: E 130 LEU cc_start: 0.8567 (mp) cc_final: 0.8330 (tp) REVERT: E 163 PHE cc_start: 0.8917 (m-80) cc_final: 0.8569 (m-80) REVERT: E 231 LYS cc_start: 0.9064 (mmmm) cc_final: 0.8555 (ttpt) REVERT: E 244 TYR cc_start: 0.8220 (p90) cc_final: 0.7358 (p90) REVERT: E 316 THR cc_start: 0.8732 (m) cc_final: 0.8388 (p) REVERT: E 426 LYS cc_start: 0.9338 (tmtt) cc_final: 0.9115 (tmmt) REVERT: E 431 ASP cc_start: 0.7785 (t70) cc_final: 0.7511 (t0) REVERT: E 438 ASP cc_start: 0.7869 (p0) cc_final: 0.7238 (t70) REVERT: E 440 GLU cc_start: 0.8798 (tt0) cc_final: 0.8467 (tp30) REVERT: E 711 ARG cc_start: 0.8543 (ttt-90) cc_final: 0.8062 (mmm-85) REVERT: E 712 GLU cc_start: 0.7093 (tt0) cc_final: 0.6690 (tt0) REVERT: E 744 ARG cc_start: 0.5866 (mmt-90) cc_final: 0.5411 (mmt-90) REVERT: F 163 PHE cc_start: 0.8789 (m-80) cc_final: 0.8452 (m-80) REVERT: F 231 LYS cc_start: 0.9095 (mmmm) cc_final: 0.8645 (ttpt) REVERT: F 244 TYR cc_start: 0.8035 (p90) cc_final: 0.7366 (p90) REVERT: F 316 THR cc_start: 0.8647 (m) cc_final: 0.8270 (p) REVERT: F 364 ASP cc_start: 0.8077 (p0) cc_final: 0.7631 (p0) REVERT: F 426 LYS cc_start: 0.9361 (tmtt) cc_final: 0.9123 (tptt) REVERT: F 440 GLU cc_start: 0.8819 (tt0) cc_final: 0.8561 (tp30) outliers start: 0 outliers final: 0 residues processed: 587 average time/residue: 0.2236 time to fit residues: 210.7377 Evaluate side-chains 485 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 485 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 63 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 9 optimal weight: 0.0770 chunk 419 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 chunk 378 optimal weight: 6.9990 chunk 262 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 325 optimal weight: 4.9990 chunk 74 optimal weight: 0.0870 overall best weight: 1.4320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS B 327 GLN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 340 HIS C 404 HIS ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.142821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.119968 restraints weight = 77796.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.123198 restraints weight = 45037.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.125340 restraints weight = 30029.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.126767 restraints weight = 22427.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.127724 restraints weight = 18268.677| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35838 Z= 0.125 Angle : 0.689 9.790 48426 Z= 0.337 Chirality : 0.046 0.193 5418 Planarity : 0.006 0.075 6378 Dihedral : 10.405 171.922 5094 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.11 % Allowed : 0.40 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.13), residues: 4416 helix: 0.27 (0.12), residues: 1938 sheet: -0.76 (0.20), residues: 690 loop : -1.65 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 147 TYR 0.020 0.002 TYR A 138 PHE 0.018 0.001 PHE E 290 TRP 0.010 0.001 TRP C 551 HIS 0.010 0.001 HIS F 404 Details of bonding type rmsd covalent geometry : bond 0.00281 (35820) covalent geometry : angle 0.68883 (48426) hydrogen bonds : bond 0.03511 ( 1386) hydrogen bonds : angle 4.47046 ( 3924) Misc. bond : bond 0.00044 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6016.34 seconds wall clock time: 104 minutes 43.68 seconds (6283.68 seconds total)