Starting phenix.real_space_refine on Tue Sep 15 04:23:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bpb_30150/09_2026/7bpb_30150.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bpb_30150/09_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_30150/09_2026/7bpb_30150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bpb_30150/09_2026/7bpb_30150.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bpb_30150/09_2026/7bpb_30150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bpb_30150/09_2026/7bpb_30150.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7bpb_30150/09_2026/7bpb_30150.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bpb_30150/09_2026/7bpb_30150.cif" } 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): 0.21s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 7.49, per 1000 atoms: 0.21 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: 2.94 Conformation dependent library (CDL) restraints added in 1.7 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: 1.20 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: 6.99 Time building geometry restraints manager: 3.95 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: 21664 34.85 - 69.71: 494 69.71 - 104.56: 30 104.56 - 139.41: 0 139.41 - 174.27: 6 Dihedral angle restraints: 22194 sinusoidal: 9396 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 22191 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: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 31.090 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 15.657 174.269 13890 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/Z covalent geometry : bond 0.00693 / 0.33 (35820) covalent geometry : angle 1.11832 / 0.58 (48426) hydrogen bonds : bond 0.16144 / 10.98 ( 1386) hydrogen bonds : angle 6.72534 / 4.70 ( 3924) Misc. bond : bond 0.01846 / 1.03 ( 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 : 1.099 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: 0.2723 time to fit residues: 332.1981 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 : 1.151 ------------------------------------------------------------------------------- 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... 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 = 0.143078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.119448 restraints weight = 77501.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.122793 restraints weight = 44085.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.125028 restraints weight = 29180.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.126501 restraints weight = 21739.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.127382 restraints weight = 17690.320| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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= 0.157 Angle : 0.697 7.978 48426 Z= 0.349 Chirality : 0.046 0.178 5418 Planarity : 0.007 0.078 6378 Dihedral : 9.044 168.979 4926 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.89 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 0.023 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/Z covalent geometry : bond 0.00351 / 0.16 (35820) covalent geometry : angle 0.69656 / 0.35 (48426) hydrogen bonds : bond 0.04300 / 2.85 ( 1386) hydrogen bonds : angle 4.99502 / 3.48 ( 3924) Misc. bond : bond 0.00098 / 0.05 ( 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 680 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 680 time to evaluate : 1.373 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: A 46 MET cc_start: 0.8546 (ptt) cc_final: 0.8337 (tpp) REVERT: A 130 LEU cc_start: 0.8794 (mp) cc_final: 0.8527 (tp) REVERT: A 196 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7000 (mm-30) REVERT: A 244 TYR cc_start: 0.7932 (p90) cc_final: 0.7695 (p90) REVERT: A 364 ASP cc_start: 0.7909 (p0) cc_final: 0.7638 (p0) REVERT: A 431 ASP cc_start: 0.7839 (t70) cc_final: 0.7599 (t0) REVERT: A 440 GLU cc_start: 0.8851 (tt0) cc_final: 0.8534 (tp30) REVERT: A 508 MET cc_start: 0.8418 (ptp) cc_final: 0.7748 (ptm) REVERT: A 709 ARG cc_start: 0.8203 (ttt180) cc_final: 0.7280 (ttp80) REVERT: A 740 MET cc_start: 0.5581 (ptt) cc_final: 0.5339 (ptt) REVERT: A 750 ASN cc_start: 0.8767 (p0) cc_final: 0.8551 (p0) REVERT: B 131 PHE cc_start: 0.8664 (t80) cc_final: 0.8461 (t80) REVERT: B 147 ARG cc_start: 0.6794 (ptp-110) cc_final: 0.6410 (ptp-170) REVERT: B 154 VAL cc_start: 0.8430 (m) cc_final: 0.8228 (m) REVERT: B 163 PHE cc_start: 0.8734 (m-80) cc_final: 0.8447 (m-80) REVERT: B 364 ASP cc_start: 0.8096 (p0) cc_final: 0.7838 (p0) REVERT: B 373 ASP cc_start: 0.7364 (p0) cc_final: 0.7131 (p0) REVERT: B 388 MET cc_start: 0.8346 (tpt) cc_final: 0.8133 (tpt) REVERT: B 440 GLU cc_start: 0.9017 (tt0) cc_final: 0.8500 (tp30) REVERT: B 449 MET cc_start: 0.7773 (ppp) cc_final: 0.7214 (ppp) REVERT: B 543 LYS cc_start: 0.8813 (mppt) cc_final: 0.8597 (mtmt) REVERT: B 750 ASN cc_start: 0.8524 (p0) cc_final: 0.8271 (p0) REVERT: C 52 PHE cc_start: 0.8540 (m-10) cc_final: 0.8337 (m-80) REVERT: C 196 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6288 (mm-30) REVERT: C 364 ASP cc_start: 0.7850 (p0) cc_final: 0.7537 (p0) REVERT: C 368 ASP cc_start: 0.7989 (t0) cc_final: 0.7648 (t0) REVERT: C 431 ASP cc_start: 0.7943 (t70) cc_final: 0.7644 (t0) REVERT: C 440 GLU cc_start: 0.8901 (tt0) cc_final: 0.8539 (tp30) REVERT: C 449 MET cc_start: 0.7775 (ppp) cc_final: 0.7112 (ppp) REVERT: C 517 TYR cc_start: 0.8762 (p90) cc_final: 0.8268 (p90) REVERT: C 550 MET cc_start: 0.8594 (mtm) cc_final: 0.8302 (mtm) REVERT: D 46 MET cc_start: 0.8412 (ptt) cc_final: 0.8158 (tpp) REVERT: D 124 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8417 (mp0) REVERT: D 130 LEU cc_start: 0.8756 (mp) cc_final: 0.8515 (tp) REVERT: D 147 ARG cc_start: 0.6729 (ptp-110) cc_final: 0.6471 (ptp-170) REVERT: D 196 GLU cc_start: 0.7458 (mt-10) cc_final: 0.6852 (mm-30) REVERT: D 244 TYR cc_start: 0.8025 (p90) cc_final: 0.7511 (p90) REVERT: D 431 ASP cc_start: 0.7819 (t70) cc_final: 0.7484 (t0) REVERT: D 440 GLU cc_start: 0.8787 (tt0) cc_final: 0.8484 (tp30) REVERT: D 508 MET cc_start: 0.7074 (tmm) cc_final: 0.6730 (ptm) REVERT: E 113 ARG cc_start: 0.6439 (ttt180) cc_final: 0.6182 (mtt-85) REVERT: E 147 ARG cc_start: 0.6833 (ptp-110) cc_final: 0.6632 (ptp-170) REVERT: E 154 VAL cc_start: 0.8427 (m) cc_final: 0.8201 (m) REVERT: E 231 LYS cc_start: 0.9136 (mmmm) cc_final: 0.8602 (ttpt) REVERT: E 364 ASP cc_start: 0.8015 (p0) cc_final: 0.7751 (p0) REVERT: E 368 ASP cc_start: 0.7527 (t0) cc_final: 0.7245 (p0) REVERT: E 440 GLU cc_start: 0.9018 (tt0) cc_final: 0.8474 (tp30) REVERT: E 449 MET cc_start: 0.7747 (ppp) cc_final: 0.7243 (ppp) REVERT: E 517 TYR cc_start: 0.8763 (p90) cc_final: 0.8214 (p90) REVERT: E 712 GLU cc_start: 0.6783 (tt0) cc_final: 0.6199 (tt0) REVERT: E 744 ARG cc_start: 0.5682 (mmt-90) cc_final: 0.5299 (mmt-90) REVERT: F 130 LEU cc_start: 0.8498 (mp) cc_final: 0.8292 (tp) REVERT: F 203 TYR cc_start: 0.7525 (m-10) cc_final: 0.6456 (m-10) REVERT: F 364 ASP cc_start: 0.7892 (p0) cc_final: 0.7616 (p0) REVERT: F 388 MET cc_start: 0.8442 (tpt) cc_final: 0.8202 (tpt) REVERT: F 426 LYS cc_start: 0.9304 (tmtt) cc_final: 0.9071 (tptt) REVERT: F 431 ASP cc_start: 0.7704 (t70) cc_final: 0.7468 (t0) REVERT: F 440 GLU cc_start: 0.8949 (tt0) cc_final: 0.8607 (tp30) REVERT: F 517 TYR cc_start: 0.8809 (p90) cc_final: 0.8219 (p90) REVERT: F 550 MET cc_start: 0.8539 (mtm) cc_final: 0.8302 (mtm) REVERT: F 750 ASN cc_start: 0.8717 (p0) cc_final: 0.8492 (p0) outliers start: 0 outliers final: 0 residues processed: 680 average time/residue: 0.2533 time to fit residues: 265.9103 Evaluate side-chains 520 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 520 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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: 7.9990 chunk 92 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 436 optimal weight: 7.9990 chunk 383 optimal weight: 10.0000 chunk 396 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 374 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 GLN A 226 HIS ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 GLN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3922 r_free = 0.3922 target = 0.140186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.117320 restraints weight = 82847.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.120070 restraints weight = 49893.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.121974 restraints weight = 34612.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.123198 restraints weight = 26507.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.123920 restraints weight = 22108.023| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 35838 Z= 0.268 Angle : 0.793 10.254 48426 Z= 0.403 Chirality : 0.049 0.168 5418 Planarity : 0.007 0.081 6378 Dihedral : 9.489 179.805 4926 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.18 % Allowed : 6.30 % Favored : 93.51 % 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: -1.99 (0.12), residues: 4416 helix: -0.62 (0.11), residues: 1920 sheet: -1.27 (0.19), residues: 690 loop : -2.01 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 635 TYR 0.018 0.002 TYR A 244 PHE 0.024 0.002 PHE F 563 TRP 0.012 0.003 TRP F 454 HIS 0.016 0.002 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.27 (35820) covalent geometry : angle 0.79349 / 0.40 (48426) hydrogen bonds : bond 0.04905 / 3.26 ( 1386) hydrogen bonds : angle 5.28634 / 3.67 ( 3924) Misc. bond : bond 0.00153 / 0.09 ( 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 633 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 626 time to evaluate : 1.444 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: A 130 LEU cc_start: 0.8753 (mp) cc_final: 0.8542 (tp) REVERT: A 131 PHE cc_start: 0.8632 (t80) cc_final: 0.8336 (t80) REVERT: A 196 GLU cc_start: 0.7642 (mt-10) cc_final: 0.6950 (mm-30) REVERT: A 221 GLU cc_start: 0.8929 (pt0) cc_final: 0.8677 (pm20) REVERT: A 364 ASP cc_start: 0.8072 (p0) cc_final: 0.7824 (p0) REVERT: A 431 ASP cc_start: 0.7915 (t70) cc_final: 0.7711 (t0) REVERT: A 440 GLU cc_start: 0.8668 (tt0) cc_final: 0.8462 (tp30) REVERT: A 709 ARG cc_start: 0.8405 (ttt180) cc_final: 0.7326 (ttp80) REVERT: A 750 ASN cc_start: 0.8615 (p0) cc_final: 0.8411 (p0) REVERT: B 46 MET cc_start: 0.7829 (ptt) cc_final: 0.7590 (ptt) REVERT: B 130 LEU cc_start: 0.8536 (mp) cc_final: 0.8331 (tp) REVERT: B 131 PHE cc_start: 0.8685 (t80) cc_final: 0.8389 (t80) REVERT: B 163 PHE cc_start: 0.8804 (m-80) cc_final: 0.8293 (m-80) REVERT: B 231 LYS cc_start: 0.9103 (mmmm) cc_final: 0.8613 (ttpt) REVERT: B 364 ASP cc_start: 0.8201 (p0) cc_final: 0.7935 (p0) REVERT: B 388 MET cc_start: 0.8344 (tpt) cc_final: 0.7893 (tpp) REVERT: B 431 ASP cc_start: 0.7801 (t70) cc_final: 0.7556 (t0) REVERT: B 440 GLU cc_start: 0.8924 (tt0) cc_final: 0.8468 (tp30) REVERT: C 203 TYR cc_start: 0.7138 (m-10) cc_final: 0.5908 (m-10) REVERT: C 364 ASP cc_start: 0.7961 (p0) cc_final: 0.7665 (p0) REVERT: C 431 ASP cc_start: 0.7985 (t70) cc_final: 0.7716 (t0) REVERT: C 440 GLU cc_start: 0.8822 (tt0) cc_final: 0.8506 (tp30) REVERT: C 517 TYR cc_start: 0.8768 (p90) cc_final: 0.8295 (p90) REVERT: C 550 MET cc_start: 0.8648 (mtm) cc_final: 0.8382 (mtm) REVERT: D 130 LEU cc_start: 0.8765 (mp) cc_final: 0.8549 (tp) REVERT: D 131 PHE cc_start: 0.8665 (t80) cc_final: 0.8391 (t80) REVERT: D 147 ARG cc_start: 0.6797 (ptp-110) cc_final: 0.6575 (ptp-170) REVERT: D 196 GLU cc_start: 0.7616 (mt-10) cc_final: 0.6915 (mm-30) REVERT: D 231 LYS cc_start: 0.8896 (mmtm) cc_final: 0.8679 (pttt) REVERT: D 364 ASP cc_start: 0.7968 (p0) cc_final: 0.7692 (p0) REVERT: D 431 ASP cc_start: 0.7816 (t70) cc_final: 0.7572 (t0) REVERT: D 449 MET cc_start: 0.7729 (ppp) cc_final: 0.7506 (ppp) REVERT: D 517 TYR cc_start: 0.8806 (p90) cc_final: 0.8530 (p90) REVERT: E 131 PHE cc_start: 0.8584 (t80) cc_final: 0.8333 (t80) REVERT: E 147 ARG cc_start: 0.6859 (ptp-110) cc_final: 0.6610 (ptp-170) REVERT: E 154 VAL cc_start: 0.8508 (m) cc_final: 0.8297 (m) REVERT: E 244 TYR cc_start: 0.8220 (p90) cc_final: 0.7107 (p90) REVERT: E 440 GLU cc_start: 0.8947 (tt0) cc_final: 0.8494 (tp30) REVERT: E 750 ASN cc_start: 0.8565 (p0) cc_final: 0.8349 (p0) REVERT: F 163 PHE cc_start: 0.8817 (m-80) cc_final: 0.8407 (m-80) REVERT: F 221 GLU cc_start: 0.8948 (pt0) cc_final: 0.8722 (pm20) REVERT: F 231 LYS cc_start: 0.9117 (mmmm) cc_final: 0.8729 (mmtp) REVERT: F 364 ASP cc_start: 0.8009 (p0) cc_final: 0.7661 (p0) REVERT: F 440 GLU cc_start: 0.8913 (tt0) cc_final: 0.8605 (tp30) REVERT: F 517 TYR cc_start: 0.8830 (p90) cc_final: 0.8277 (p90) REVERT: F 550 MET cc_start: 0.8599 (mtm) cc_final: 0.8363 (mtm) outliers start: 7 outliers final: 6 residues processed: 633 average time/residue: 0.2421 time to fit residues: 242.3250 Evaluate side-chains 502 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 496 time to evaluate : 1.544 ------------------------------------------------------------------------------- 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: 4.9990 chunk 15 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 218 optimal weight: 20.0000 chunk 127 optimal weight: 1.9990 chunk 377 optimal weight: 10.0000 chunk 182 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 GLN B 340 HIS B 558 ASN C 340 HIS D 340 HIS ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 ASN F 91 ASN ** 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 = 0.3955 r_free = 0.3955 target = 0.140067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.116884 restraints weight = 78624.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.120048 restraints weight = 45044.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.122182 restraints weight = 30167.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.123611 restraints weight = 22585.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.124547 restraints weight = 18429.929| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35838 Z= 0.166 Angle : 0.681 8.597 48426 Z= 0.339 Chirality : 0.047 0.201 5418 Planarity : 0.006 0.075 6378 Dihedral : 8.964 171.676 4926 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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: -1.54 (0.12), residues: 4416 helix: -0.24 (0.12), residues: 1926 sheet: -0.99 (0.19), residues: 690 loop : -1.81 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 635 TYR 0.018 0.001 TYR A 244 PHE 0.016 0.001 PHE A 139 TRP 0.008 0.002 TRP C 454 HIS 0.004 0.001 HIS C 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (35820) covalent geometry : angle 0.68148 / 0.34 (48426) hydrogen bonds : bond 0.04069 / 2.68 ( 1386) hydrogen bonds : angle 4.77446 / 3.31 ( 3924) Misc. bond : bond 0.00081 / 0.05 ( 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 645 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 645 time to evaluate : 1.411 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: A 46 MET cc_start: 0.8578 (ptm) cc_final: 0.8353 (ptt) REVERT: A 130 LEU cc_start: 0.8756 (mp) cc_final: 0.8548 (tp) REVERT: A 131 PHE cc_start: 0.8620 (t80) cc_final: 0.8350 (t80) REVERT: A 196 GLU cc_start: 0.7516 (mt-10) cc_final: 0.6831 (mm-30) REVERT: A 221 GLU cc_start: 0.9001 (pt0) cc_final: 0.8737 (pt0) REVERT: A 231 LYS cc_start: 0.9069 (mmmm) cc_final: 0.8601 (ttpt) REVERT: A 316 THR cc_start: 0.8605 (m) cc_final: 0.8194 (p) REVERT: A 364 ASP cc_start: 0.8062 (p0) cc_final: 0.7791 (p0) REVERT: A 426 LYS cc_start: 0.9320 (tmtt) cc_final: 0.9080 (tptt) REVERT: A 431 ASP cc_start: 0.7827 (t70) cc_final: 0.7583 (t0) REVERT: A 709 ARG cc_start: 0.8380 (ttt180) cc_final: 0.7573 (ttp80) REVERT: A 750 ASN cc_start: 0.8677 (p0) cc_final: 0.8424 (p0) REVERT: B 130 LEU cc_start: 0.8521 (mp) cc_final: 0.8320 (tp) REVERT: B 163 PHE cc_start: 0.8833 (m-80) cc_final: 0.8411 (m-80) REVERT: B 219 MET cc_start: 0.8224 (ttm) cc_final: 0.7996 (ttm) REVERT: B 231 LYS cc_start: 0.9119 (mmmm) cc_final: 0.8598 (ttpt) REVERT: B 316 THR cc_start: 0.8611 (m) cc_final: 0.8286 (p) REVERT: B 364 ASP cc_start: 0.8173 (p0) cc_final: 0.7808 (p0) REVERT: B 431 ASP cc_start: 0.7704 (t70) cc_final: 0.7454 (t0) REVERT: B 440 GLU cc_start: 0.8924 (tt0) cc_final: 0.8494 (tp30) REVERT: C 218 GLU cc_start: 0.8703 (pp20) cc_final: 0.8253 (pp20) REVERT: C 244 TYR cc_start: 0.8173 (p90) cc_final: 0.7175 (p90) REVERT: C 364 ASP cc_start: 0.7934 (p0) cc_final: 0.7580 (p0) REVERT: C 431 ASP cc_start: 0.7811 (t70) cc_final: 0.7547 (t0) REVERT: C 440 GLU cc_start: 0.8852 (tt0) cc_final: 0.8507 (tp30) REVERT: C 508 MET cc_start: 0.8412 (ptp) cc_final: 0.7970 (ptm) REVERT: C 517 TYR cc_start: 0.8777 (p90) cc_final: 0.8260 (p90) REVERT: C 550 MET cc_start: 0.8608 (mtm) cc_final: 0.8311 (mtm) REVERT: C 740 MET cc_start: 0.5748 (ptt) cc_final: 0.5456 (ptt) REVERT: D 130 LEU cc_start: 0.8769 (mp) cc_final: 0.8558 (tp) REVERT: D 131 PHE cc_start: 0.8615 (t80) cc_final: 0.8397 (t80) REVERT: D 147 ARG cc_start: 0.6643 (ptp-110) cc_final: 0.6300 (ptp-170) REVERT: D 196 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6693 (mm-30) REVERT: D 364 ASP cc_start: 0.7922 (p0) cc_final: 0.7589 (p0) REVERT: D 431 ASP cc_start: 0.7855 (t70) cc_final: 0.7536 (t0) REVERT: E 147 ARG cc_start: 0.6878 (ptp-110) cc_final: 0.6575 (ptp-170) REVERT: E 163 PHE cc_start: 0.8769 (m-80) cc_final: 0.8356 (m-80) REVERT: E 219 MET cc_start: 0.8280 (ttm) cc_final: 0.8023 (ttm) REVERT: E 231 LYS cc_start: 0.9100 (mmmm) cc_final: 0.8591 (ttpt) REVERT: E 316 THR cc_start: 0.8680 (m) cc_final: 0.8295 (p) REVERT: E 344 MET cc_start: 0.8081 (ttm) cc_final: 0.7868 (ttm) REVERT: E 364 ASP cc_start: 0.7931 (p0) cc_final: 0.7690 (p0) REVERT: E 440 GLU cc_start: 0.8918 (tt0) cc_final: 0.8461 (tp30) REVERT: E 711 ARG cc_start: 0.8544 (ttt-90) cc_final: 0.7997 (ttm-80) REVERT: E 744 ARG cc_start: 0.5539 (mmt-90) cc_final: 0.5282 (mmt-90) REVERT: E 750 ASN cc_start: 0.8629 (p0) cc_final: 0.8338 (p0) REVERT: F 163 PHE cc_start: 0.8707 (m-80) cc_final: 0.8366 (m-80) REVERT: F 221 GLU cc_start: 0.8943 (pt0) cc_final: 0.8686 (pt0) REVERT: F 231 LYS cc_start: 0.9154 (mmmm) cc_final: 0.8694 (ttpt) REVERT: F 244 TYR cc_start: 0.8211 (p90) cc_final: 0.7283 (p90) REVERT: F 364 ASP cc_start: 0.7986 (p0) cc_final: 0.7591 (p0) REVERT: F 440 GLU cc_start: 0.8910 (tt0) cc_final: 0.8583 (tp30) REVERT: F 508 MET cc_start: 0.7395 (ptp) cc_final: 0.6975 (tpp) REVERT: F 517 TYR cc_start: 0.8760 (p90) cc_final: 0.8214 (p90) REVERT: F 550 MET cc_start: 0.8572 (mtm) cc_final: 0.8297 (mtm) outliers start: 0 outliers final: 0 residues processed: 645 average time/residue: 0.2304 time to fit residues: 238.2044 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 : 1.358 ------------------------------------------------------------------------------- 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: 7.9990 chunk 340 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 275 optimal weight: 0.0670 chunk 125 optimal weight: 0.7980 chunk 165 optimal weight: 8.9990 chunk 313 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 294 optimal weight: 0.0970 chunk 428 optimal weight: 0.7980 chunk 174 optimal weight: 10.0000 overall best weight: 0.9518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 ASN ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS C 24 ASN C 340 HIS D 24 ASN D 340 HIS E 24 ASN E 327 GLN E 340 HIS E 494 GLN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 494 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.145637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.122702 restraints weight = 77471.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.126032 restraints weight = 44410.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.128245 restraints weight = 29466.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.129710 restraints weight = 21990.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.130682 restraints weight = 17861.120| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 35838 Z= 0.113 Angle : 0.635 9.953 48426 Z= 0.311 Chirality : 0.045 0.147 5418 Planarity : 0.005 0.086 6378 Dihedral : 8.396 165.803 4926 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % 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: -1.09 (0.13), residues: 4416 helix: 0.09 (0.12), residues: 1944 sheet: -0.66 (0.20), residues: 666 loop : -1.58 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG F 95 TYR 0.017 0.001 TYR E 244 PHE 0.016 0.001 PHE A 139 TRP 0.012 0.002 TRP D 476 HIS 0.006 0.001 HIS C 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (35820) covalent geometry : angle 0.63453 / 0.31 (48426) hydrogen bonds : bond 0.03299 / 2.18 ( 1386) hydrogen bonds : angle 4.28719 / 2.97 ( 3924) Misc. bond : bond 0.00058 / 0.03 ( 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 664 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 664 time to evaluate : 1.461 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 131 PHE cc_start: 0.8607 (t80) cc_final: 0.8278 (t80) REVERT: A 196 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6635 (mm-30) REVERT: A 219 MET cc_start: 0.8443 (ttm) cc_final: 0.8201 (ttm) REVERT: A 221 GLU cc_start: 0.8874 (pt0) cc_final: 0.8540 (pm20) REVERT: A 231 LYS cc_start: 0.9042 (mmmm) cc_final: 0.8602 (ttpt) REVERT: A 316 THR cc_start: 0.8354 (m) cc_final: 0.7959 (p) REVERT: A 364 ASP cc_start: 0.8013 (p0) cc_final: 0.7657 (p0) REVERT: A 426 LYS cc_start: 0.9254 (tmtt) cc_final: 0.9016 (tptt) REVERT: A 709 ARG cc_start: 0.8274 (ttt180) cc_final: 0.7324 (ttp80) REVERT: B 163 PHE cc_start: 0.8824 (m-80) cc_final: 0.8538 (m-80) REVERT: B 231 LYS cc_start: 0.9119 (mmmm) cc_final: 0.8613 (ttpt) REVERT: B 316 THR cc_start: 0.8516 (m) cc_final: 0.8168 (p) REVERT: B 364 ASP cc_start: 0.8078 (p0) cc_final: 0.7552 (p0) REVERT: B 427 MET cc_start: 0.6889 (ttt) cc_final: 0.6589 (tpt) REVERT: B 431 ASP cc_start: 0.7646 (t70) cc_final: 0.7379 (t0) REVERT: B 440 GLU cc_start: 0.8860 (tt0) cc_final: 0.8436 (tp30) REVERT: B 517 TYR cc_start: 0.8680 (p90) cc_final: 0.8320 (p90) REVERT: C 121 ASP cc_start: 0.8801 (m-30) cc_final: 0.8462 (m-30) REVERT: C 163 PHE cc_start: 0.8669 (m-80) cc_final: 0.8308 (m-80) REVERT: C 196 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6287 (mm-30) REVERT: C 218 GLU cc_start: 0.8677 (pp20) cc_final: 0.8197 (pp20) REVERT: C 219 MET cc_start: 0.8391 (ttm) cc_final: 0.8170 (ttm) REVERT: C 244 TYR cc_start: 0.8049 (p90) cc_final: 0.7533 (p90) REVERT: C 364 ASP cc_start: 0.7850 (p0) cc_final: 0.7397 (p0) REVERT: C 388 MET cc_start: 0.8099 (tpt) cc_final: 0.7832 (tpp) REVERT: C 431 ASP cc_start: 0.7724 (t70) cc_final: 0.7511 (t0) REVERT: C 440 GLU cc_start: 0.8767 (tt0) cc_final: 0.8489 (tp30) REVERT: C 517 TYR cc_start: 0.8687 (p90) cc_final: 0.8170 (p90) REVERT: C 550 MET cc_start: 0.8476 (mtm) cc_final: 0.8158 (mtm) REVERT: C 744 ARG cc_start: 0.6175 (mmt-90) cc_final: 0.5906 (mmt-90) REVERT: D 147 ARG cc_start: 0.6595 (ptp-110) cc_final: 0.6252 (ptp-170) REVERT: D 196 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6589 (mm-30) REVERT: D 244 TYR cc_start: 0.8034 (p90) cc_final: 0.7227 (p90) REVERT: D 316 THR cc_start: 0.8414 (m) cc_final: 0.8020 (p) REVERT: D 364 ASP cc_start: 0.7953 (p0) cc_final: 0.7533 (p0) REVERT: D 395 ASP cc_start: 0.7519 (t70) cc_final: 0.7236 (t0) REVERT: D 456 LEU cc_start: 0.8816 (tt) cc_final: 0.8511 (tt) REVERT: D 460 ASN cc_start: 0.8164 (p0) cc_final: 0.7881 (m-40) REVERT: D 712 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6100 (mt-10) REVERT: E 163 PHE cc_start: 0.8830 (m-80) cc_final: 0.8514 (m-80) REVERT: E 219 MET cc_start: 0.8309 (ttm) cc_final: 0.8052 (ttm) REVERT: E 231 LYS cc_start: 0.9101 (mmmm) cc_final: 0.8595 (ttpt) REVERT: E 244 TYR cc_start: 0.8044 (p90) cc_final: 0.7134 (p90) REVERT: E 316 THR cc_start: 0.8520 (m) cc_final: 0.8176 (p) REVERT: E 343 VAL cc_start: 0.9045 (p) cc_final: 0.8752 (m) REVERT: E 426 LYS cc_start: 0.9202 (tmtt) cc_final: 0.8940 (tmmt) REVERT: E 427 MET cc_start: 0.6830 (ttt) cc_final: 0.6392 (tpt) REVERT: E 440 GLU cc_start: 0.8897 (tt0) cc_final: 0.8392 (tp30) REVERT: E 711 ARG cc_start: 0.8380 (ttt-90) cc_final: 0.8081 (mmm-85) REVERT: E 712 GLU cc_start: 0.6854 (tt0) cc_final: 0.6560 (tt0) REVERT: E 750 ASN cc_start: 0.8652 (p0) cc_final: 0.8356 (p0) REVERT: F 163 PHE cc_start: 0.8695 (m-80) cc_final: 0.8447 (m-80) REVERT: F 221 GLU cc_start: 0.8801 (pt0) cc_final: 0.8507 (pt0) REVERT: F 231 LYS cc_start: 0.9100 (mmmm) cc_final: 0.8681 (ttpt) REVERT: F 316 THR cc_start: 0.8530 (m) cc_final: 0.8219 (p) REVERT: F 364 ASP cc_start: 0.7941 (p0) cc_final: 0.7450 (p0) REVERT: F 440 GLU cc_start: 0.8848 (tt0) cc_final: 0.8518 (tp30) REVERT: F 550 MET cc_start: 0.8467 (mtm) cc_final: 0.8150 (mtm) REVERT: F 712 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6514 (mt-10) outliers start: 0 outliers final: 0 residues processed: 664 average time/residue: 0.2376 time to fit residues: 251.9102 Evaluate side-chains 516 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 516 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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: 10.0000 chunk 182 optimal weight: 6.9990 chunk 342 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 330 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 397 optimal weight: 8.9990 chunk 181 optimal weight: 0.9980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 GLN ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN B 327 GLN B 340 HIS B 764 GLN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS C 340 HIS C 398 GLN C 494 GLN D 24 ASN D 226 HIS ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 HIS ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.140428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.117392 restraints weight = 78879.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.120640 restraints weight = 44649.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.122831 restraints weight = 29628.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.124232 restraints weight = 22032.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.125179 restraints weight = 17952.527| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 35838 Z= 0.160 Angle : 0.668 8.476 48426 Z= 0.330 Chirality : 0.046 0.200 5418 Planarity : 0.006 0.093 6378 Dihedral : 8.615 169.238 4926 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % 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: -1.06 (0.13), residues: 4416 helix: 0.18 (0.12), residues: 1932 sheet: -0.70 (0.20), residues: 696 loop : -1.63 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG F 95 TYR 0.020 0.001 TYR B 244 PHE 0.017 0.001 PHE C 302 TRP 0.008 0.001 TRP A 454 HIS 0.003 0.001 HIS F 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (35820) covalent geometry : angle 0.66850 / 0.33 (48426) hydrogen bonds : bond 0.03705 / 2.46 ( 1386) hydrogen bonds : angle 4.56559 / 3.19 ( 3924) Misc. bond : bond 0.00081 / 0.06 ( 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 627 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 627 time to evaluate : 1.163 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: 0.8599 (t80) cc_final: 0.8388 (t80) REVERT: A 196 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6646 (mm-30) REVERT: A 221 GLU cc_start: 0.8964 (pt0) cc_final: 0.8558 (pm20) REVERT: A 231 LYS cc_start: 0.9069 (mmmm) cc_final: 0.8600 (ttpt) REVERT: A 316 THR cc_start: 0.8437 (m) cc_final: 0.8054 (p) REVERT: A 364 ASP cc_start: 0.8067 (p0) cc_final: 0.7756 (p0) REVERT: A 426 LYS cc_start: 0.9345 (tmtt) cc_final: 0.9082 (tptt) REVERT: A 709 ARG cc_start: 0.8178 (ttt180) cc_final: 0.7546 (ttp80) REVERT: A 750 ASN cc_start: 0.8553 (p0) cc_final: 0.8283 (p0) REVERT: B 162 GLU cc_start: 0.8628 (pm20) cc_final: 0.8298 (pm20) REVERT: B 163 PHE cc_start: 0.8838 (m-80) cc_final: 0.8473 (m-80) REVERT: B 231 LYS cc_start: 0.9100 (mmmm) cc_final: 0.8585 (ttpt) REVERT: B 316 THR cc_start: 0.8583 (m) cc_final: 0.8244 (p) REVERT: B 364 ASP cc_start: 0.7949 (p0) cc_final: 0.7594 (p0) REVERT: B 388 MET cc_start: 0.8128 (tpt) cc_final: 0.7594 (tpp) REVERT: B 431 ASP cc_start: 0.7731 (t70) cc_final: 0.7466 (t0) REVERT: B 438 ASP cc_start: 0.7370 (p0) cc_final: 0.6840 (t70) REVERT: B 440 GLU cc_start: 0.8820 (tt0) cc_final: 0.8475 (tp30) REVERT: B 517 TYR cc_start: 0.8753 (p90) cc_final: 0.8348 (p90) REVERT: B 712 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6742 (mp0) REVERT: C 196 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6319 (mm-30) REVERT: C 218 GLU cc_start: 0.8755 (pp20) cc_final: 0.8223 (pp20) REVERT: C 219 MET cc_start: 0.8383 (ttm) cc_final: 0.8136 (ttm) REVERT: C 244 TYR cc_start: 0.8037 (p90) cc_final: 0.7228 (p90) REVERT: C 364 ASP cc_start: 0.7974 (p0) cc_final: 0.7570 (p0) REVERT: C 388 MET cc_start: 0.8248 (tpt) cc_final: 0.7991 (tpp) REVERT: C 440 GLU cc_start: 0.8843 (tt0) cc_final: 0.8499 (tp30) REVERT: C 517 TYR cc_start: 0.8747 (p90) cc_final: 0.8191 (p90) REVERT: C 550 MET cc_start: 0.8605 (mtm) cc_final: 0.8327 (mtm) REVERT: C 712 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6718 (mt-10) REVERT: C 740 MET cc_start: 0.5415 (ptt) cc_final: 0.5000 (ptt) REVERT: D 131 PHE cc_start: 0.8646 (t80) cc_final: 0.8298 (t80) REVERT: D 136 LYS cc_start: 0.8899 (mmmt) cc_final: 0.8629 (mmmt) REVERT: D 147 ARG cc_start: 0.6593 (ptp-110) cc_final: 0.6220 (ptp-170) REVERT: D 196 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6596 (mm-30) REVERT: D 244 TYR cc_start: 0.8150 (p90) cc_final: 0.7148 (p90) REVERT: D 316 THR cc_start: 0.8442 (m) cc_final: 0.8040 (p) REVERT: D 364 ASP cc_start: 0.8012 (p0) cc_final: 0.7615 (p0) REVERT: D 438 ASP cc_start: 0.7471 (p0) cc_final: 0.7217 (t70) REVERT: D 709 ARG cc_start: 0.8539 (mmp80) cc_final: 0.8294 (mmp80) REVERT: D 712 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6213 (mt-10) REVERT: E 130 LEU cc_start: 0.8555 (mp) cc_final: 0.8346 (tp) REVERT: E 163 PHE cc_start: 0.8865 (m-80) cc_final: 0.8497 (m-80) REVERT: E 196 GLU cc_start: 0.7559 (mt-10) cc_final: 0.6950 (mm-30) REVERT: E 219 MET cc_start: 0.8323 (ttm) cc_final: 0.8050 (ttm) REVERT: E 231 LYS cc_start: 0.9102 (mmmm) cc_final: 0.8596 (ttpt) REVERT: E 244 TYR cc_start: 0.8010 (p90) cc_final: 0.7412 (p90) REVERT: E 316 THR cc_start: 0.8578 (m) cc_final: 0.8217 (p) REVERT: E 388 MET cc_start: 0.7856 (tpt) cc_final: 0.7428 (tpp) REVERT: E 440 GLU cc_start: 0.8915 (tt0) cc_final: 0.8483 (tp30) REVERT: E 711 ARG cc_start: 0.8521 (ttt-90) cc_final: 0.8161 (mmm-85) REVERT: E 712 GLU cc_start: 0.6972 (tt0) cc_final: 0.6675 (tt0) REVERT: E 750 ASN cc_start: 0.8670 (p0) cc_final: 0.8410 (p0) REVERT: F 91 ASN cc_start: 0.8108 (t0) cc_final: 0.7847 (t0) REVERT: F 163 PHE cc_start: 0.8753 (m-80) cc_final: 0.8463 (m-80) REVERT: F 221 GLU cc_start: 0.8882 (pt0) cc_final: 0.8480 (pm20) REVERT: F 231 LYS cc_start: 0.9097 (mmmm) cc_final: 0.8709 (ttpt) REVERT: F 316 THR cc_start: 0.8505 (m) cc_final: 0.8139 (p) REVERT: F 364 ASP cc_start: 0.7964 (p0) cc_final: 0.7620 (p0) REVERT: F 440 GLU cc_start: 0.8923 (tt0) cc_final: 0.8576 (tp30) REVERT: F 517 TYR cc_start: 0.8759 (p90) cc_final: 0.8220 (p90) REVERT: F 550 MET cc_start: 0.8574 (mtm) cc_final: 0.8292 (mtm) REVERT: F 560 ARG cc_start: 0.7823 (mtt180) cc_final: 0.7536 (ttm170) REVERT: F 712 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6615 (mt-10) outliers start: 0 outliers final: 0 residues processed: 627 average time/residue: 0.2205 time to fit residues: 220.8733 Evaluate side-chains 498 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 498 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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: 6.9990 chunk 418 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 316 optimal weight: 6.9990 chunk 227 optimal weight: 20.0000 chunk 310 optimal weight: 0.9990 chunk 398 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 170 optimal weight: 0.4980 chunk 75 optimal weight: 7.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN A 406 HIS B 340 HIS B 406 HIS C 340 HIS C 398 GLN C 406 HIS C 494 GLN D 398 GLN D 406 HIS E 340 HIS E 398 GLN E 406 HIS ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.146751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.124154 restraints weight = 80891.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.127156 restraints weight = 47525.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.129246 restraints weight = 32260.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.130595 restraints weight = 24212.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.131431 restraints weight = 19833.190| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35838 Z= 0.122 Angle : 0.643 8.190 48426 Z= 0.315 Chirality : 0.045 0.158 5418 Planarity : 0.005 0.075 6378 Dihedral : 8.355 166.482 4926 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: -0.89 (0.13), residues: 4416 helix: 0.30 (0.12), residues: 1932 sheet: -0.61 (0.20), residues: 684 loop : -1.51 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 766 TYR 0.018 0.001 TYR E 244 PHE 0.011 0.001 PHE A 290 TRP 0.007 0.001 TRP A 454 HIS 0.015 0.001 HIS C 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (35820) covalent geometry : angle 0.64279 / 0.31 (48426) hydrogen bonds : bond 0.03336 / 2.18 ( 1386) hydrogen bonds : angle 4.33197 / 3.01 ( 3924) Misc. bond : bond 0.00269 / 0.18 ( 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 643 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 643 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: A 113 ARG cc_start: 0.6893 (ttt180) cc_final: 0.6635 (tpt170) REVERT: A 144 ARG cc_start: 0.7956 (mtt-85) cc_final: 0.7532 (mmm-85) REVERT: A 163 PHE cc_start: 0.8794 (m-80) cc_final: 0.8482 (m-80) REVERT: A 196 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6629 (mm-30) REVERT: A 219 MET cc_start: 0.8411 (ttm) cc_final: 0.8195 (ttm) REVERT: A 221 GLU cc_start: 0.8862 (pt0) cc_final: 0.8513 (pm20) REVERT: A 231 LYS cc_start: 0.9054 (mmmm) cc_final: 0.8604 (ttpt) REVERT: A 316 THR cc_start: 0.8423 (m) cc_final: 0.7967 (p) REVERT: A 364 ASP cc_start: 0.7925 (p0) cc_final: 0.7610 (p0) REVERT: A 426 LYS cc_start: 0.9355 (tmtt) cc_final: 0.9113 (tptt) REVERT: A 438 ASP cc_start: 0.7250 (p0) cc_final: 0.7041 (t70) REVERT: A 709 ARG cc_start: 0.8016 (ttt180) cc_final: 0.7379 (ttp80) REVERT: A 750 ASN cc_start: 0.8555 (p0) cc_final: 0.8232 (p0) REVERT: B 162 GLU cc_start: 0.8542 (pm20) cc_final: 0.8257 (pm20) REVERT: B 163 PHE cc_start: 0.8766 (m-80) cc_final: 0.8480 (m-80) REVERT: B 231 LYS cc_start: 0.9069 (mmmm) cc_final: 0.8557 (ttpt) REVERT: B 316 THR cc_start: 0.8523 (m) cc_final: 0.8176 (p) REVERT: B 364 ASP cc_start: 0.7854 (p0) cc_final: 0.7424 (p0) REVERT: B 388 MET cc_start: 0.8053 (tpt) cc_final: 0.7529 (tpp) REVERT: B 426 LYS cc_start: 0.9239 (tmtt) cc_final: 0.9015 (tmmt) REVERT: B 431 ASP cc_start: 0.7679 (t70) cc_final: 0.7376 (t0) REVERT: B 438 ASP cc_start: 0.7279 (p0) cc_final: 0.7027 (t70) REVERT: B 440 GLU cc_start: 0.8794 (tt0) cc_final: 0.8422 (tp30) REVERT: B 712 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6817 (mt-10) REVERT: C 163 PHE cc_start: 0.8658 (m-80) cc_final: 0.8332 (m-80) REVERT: C 196 GLU cc_start: 0.6798 (mt-10) cc_final: 0.6261 (mm-30) REVERT: C 219 MET cc_start: 0.8328 (ttm) cc_final: 0.8039 (ttm) REVERT: C 244 TYR cc_start: 0.8037 (p90) cc_final: 0.6853 (p90) REVERT: C 364 ASP cc_start: 0.7851 (p0) cc_final: 0.7365 (p0) REVERT: C 431 ASP cc_start: 0.7755 (t70) cc_final: 0.7550 (t0) REVERT: C 440 GLU cc_start: 0.8810 (tt0) cc_final: 0.8496 (tp30) REVERT: C 517 TYR cc_start: 0.8713 (p90) cc_final: 0.8174 (p90) REVERT: C 550 MET cc_start: 0.8496 (mtm) cc_final: 0.8199 (mtm) REVERT: C 712 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6635 (mt-10) REVERT: D 113 ARG cc_start: 0.6753 (ttt180) cc_final: 0.6485 (tpt170) REVERT: D 131 PHE cc_start: 0.8591 (t80) cc_final: 0.8274 (t80) REVERT: D 136 LYS cc_start: 0.8905 (mmmt) cc_final: 0.8623 (mmmt) REVERT: D 147 ARG cc_start: 0.6541 (ptp-110) cc_final: 0.6218 (ptp-170) REVERT: D 163 PHE cc_start: 0.8824 (m-80) cc_final: 0.8526 (m-80) REVERT: D 196 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6543 (mm-30) REVERT: D 244 TYR cc_start: 0.8121 (p90) cc_final: 0.7328 (p90) REVERT: D 316 THR cc_start: 0.8422 (m) cc_final: 0.8017 (p) REVERT: D 364 ASP cc_start: 0.7911 (p0) cc_final: 0.7495 (p0) REVERT: D 438 ASP cc_start: 0.7405 (p0) cc_final: 0.7157 (t70) REVERT: D 709 ARG cc_start: 0.8566 (mmp80) cc_final: 0.8333 (mmp80) REVERT: D 712 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6056 (mt-10) REVERT: E 130 LEU cc_start: 0.8531 (mp) cc_final: 0.8304 (tp) REVERT: E 163 PHE cc_start: 0.8876 (m-80) cc_final: 0.8549 (m-80) REVERT: E 219 MET cc_start: 0.8279 (ttm) cc_final: 0.8013 (ttm) REVERT: E 231 LYS cc_start: 0.9089 (mmmm) cc_final: 0.8597 (ttpt) REVERT: E 316 THR cc_start: 0.8550 (m) cc_final: 0.8207 (p) REVERT: E 388 MET cc_start: 0.7746 (tpt) cc_final: 0.7313 (tpp) REVERT: E 426 LYS cc_start: 0.9257 (tmtt) cc_final: 0.9028 (tmmt) REVERT: E 438 ASP cc_start: 0.7375 (p0) cc_final: 0.6780 (t70) REVERT: E 440 GLU cc_start: 0.8795 (tt0) cc_final: 0.8466 (tp30) REVERT: E 711 ARG cc_start: 0.8459 (ttt-90) cc_final: 0.8153 (mmm-85) REVERT: E 712 GLU cc_start: 0.6974 (tt0) cc_final: 0.6700 (tt0) REVERT: E 750 ASN cc_start: 0.8569 (p0) cc_final: 0.8234 (p0) REVERT: F 121 ASP cc_start: 0.8775 (m-30) cc_final: 0.8449 (m-30) REVERT: F 163 PHE cc_start: 0.8679 (m-80) cc_final: 0.8428 (m-80) REVERT: F 221 GLU cc_start: 0.8772 (pt0) cc_final: 0.8378 (pm20) REVERT: F 231 LYS cc_start: 0.9059 (mmmm) cc_final: 0.8688 (ttpt) REVERT: F 316 THR cc_start: 0.8471 (m) cc_final: 0.8155 (p) REVERT: F 364 ASP cc_start: 0.7881 (p0) cc_final: 0.7427 (p0) REVERT: F 440 GLU cc_start: 0.8846 (tt0) cc_final: 0.8541 (tp30) REVERT: F 508 MET cc_start: 0.8109 (ttp) cc_final: 0.7712 (ttp) REVERT: F 550 MET cc_start: 0.8524 (mtm) cc_final: 0.8228 (mtm) REVERT: F 560 ARG cc_start: 0.7753 (mtt180) cc_final: 0.7398 (ttm170) outliers start: 0 outliers final: 0 residues processed: 643 average time/residue: 0.2354 time to fit residues: 242.0809 Evaluate side-chains 505 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 505 time to evaluate : 1.423 ------------------------------------------------------------------------------- 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: 7.9990 chunk 4 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 238 optimal weight: 1.9990 chunk 290 optimal weight: 0.9980 chunk 139 optimal weight: 0.0970 chunk 387 optimal weight: 0.5980 chunk 314 optimal weight: 10.0000 chunk 271 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 HIS A 398 GLN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS C 340 HIS C 398 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 GLN E 398 GLN F 91 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.148896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.126339 restraints weight = 80079.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.129443 restraints weight = 46791.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.131561 restraints weight = 31637.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.132955 restraints weight = 23758.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.133809 restraints weight = 19364.015| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 35838 Z= 0.110 Angle : 0.653 14.221 48426 Z= 0.314 Chirality : 0.046 0.284 5418 Planarity : 0.005 0.092 6378 Dihedral : 8.076 163.214 4926 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.03 % Allowed : 1.19 % Favored : 98.79 % 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: -0.83 (0.13), residues: 4416 helix: 0.36 (0.12), residues: 1932 sheet: -0.50 (0.20), residues: 678 loop : -1.51 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 709 TYR 0.032 0.001 TYR E 244 PHE 0.011 0.001 PHE D 290 TRP 0.014 0.002 TRP C 551 HIS 0.002 0.001 HIS C 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (35820) covalent geometry : angle 0.65319 / 0.31 (48426) hydrogen bonds : bond 0.03098 / 2.05 ( 1386) hydrogen bonds : angle 4.15262 / 2.88 ( 3924) Misc. bond : bond 0.00048 / 0.03 ( 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 652 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 651 time to evaluate : 1.532 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: A 43 GLN cc_start: 0.7522 (mm-40) cc_final: 0.7299 (tm-30) REVERT: A 46 MET cc_start: 0.8390 (ptt) cc_final: 0.8127 (ptt) REVERT: A 113 ARG cc_start: 0.6707 (ttt180) cc_final: 0.6420 (tpt170) REVERT: A 163 PHE cc_start: 0.8762 (m-80) cc_final: 0.8531 (m-80) REVERT: A 196 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6693 (mm-30) REVERT: A 221 GLU cc_start: 0.8856 (pt0) cc_final: 0.8462 (pm20) REVERT: A 231 LYS cc_start: 0.9027 (mmmm) cc_final: 0.8630 (ttpt) REVERT: A 316 THR cc_start: 0.8341 (m) cc_final: 0.8081 (p) REVERT: A 426 LYS cc_start: 0.9313 (tmtt) cc_final: 0.8840 (ttmm) REVERT: A 438 ASP cc_start: 0.7083 (p0) cc_final: 0.6786 (t70) REVERT: A 704 GLU cc_start: 0.7818 (tp30) cc_final: 0.7560 (tp30) REVERT: A 709 ARG cc_start: 0.8030 (ttt180) cc_final: 0.7428 (ttp80) REVERT: B 163 PHE cc_start: 0.8772 (m-80) cc_final: 0.8523 (m-80) REVERT: B 231 LYS cc_start: 0.9120 (mmmm) cc_final: 0.8614 (ttpt) REVERT: B 316 THR cc_start: 0.8448 (m) cc_final: 0.8101 (p) REVERT: B 364 ASP cc_start: 0.7782 (p0) cc_final: 0.7290 (p0) REVERT: B 388 MET cc_start: 0.8051 (tpt) cc_final: 0.7530 (tpp) REVERT: B 431 ASP cc_start: 0.7621 (t70) cc_final: 0.7369 (t0) REVERT: B 438 ASP cc_start: 0.7244 (p0) cc_final: 0.6890 (t70) REVERT: B 440 GLU cc_start: 0.8783 (tt0) cc_final: 0.8397 (tp30) REVERT: B 517 TYR cc_start: 0.8601 (p90) cc_final: 0.8310 (p90) REVERT: B 712 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6909 (mt-10) REVERT: C 121 ASP cc_start: 0.8809 (m-30) cc_final: 0.8491 (m-30) REVERT: C 163 PHE cc_start: 0.8622 (m-80) cc_final: 0.8317 (m-80) REVERT: C 196 GLU cc_start: 0.6798 (mt-10) cc_final: 0.6258 (mm-30) REVERT: C 219 MET cc_start: 0.8356 (ttm) cc_final: 0.8004 (ttm) REVERT: C 244 TYR cc_start: 0.7982 (p90) cc_final: 0.6861 (p90) REVERT: C 364 ASP cc_start: 0.7917 (p0) cc_final: 0.7402 (p0) REVERT: C 431 ASP cc_start: 0.7789 (t70) cc_final: 0.7565 (t0) REVERT: C 440 GLU cc_start: 0.8781 (tt0) cc_final: 0.8456 (tp30) REVERT: C 454 TRP cc_start: 0.8806 (t60) cc_final: 0.8172 (t60) REVERT: C 517 TYR cc_start: 0.8678 (p90) cc_final: 0.8147 (p90) REVERT: C 550 MET cc_start: 0.8493 (mtm) cc_final: 0.8146 (mtm) REVERT: C 712 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6671 (mt-10) REVERT: C 744 ARG cc_start: 0.6381 (mmt-90) cc_final: 0.5930 (mmt-90) REVERT: D 113 ARG cc_start: 0.6630 (ttt180) cc_final: 0.6351 (tpt170) REVERT: D 131 PHE cc_start: 0.8494 (t80) cc_final: 0.8230 (t80) REVERT: D 136 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8581 (mmmt) REVERT: D 147 ARG cc_start: 0.6614 (ptp-110) cc_final: 0.6317 (ptp-170) REVERT: D 163 PHE cc_start: 0.8807 (m-80) cc_final: 0.8526 (m-80) REVERT: D 196 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6679 (mm-30) REVERT: D 244 TYR cc_start: 0.8088 (p90) cc_final: 0.7466 (p90) REVERT: D 316 THR cc_start: 0.8337 (m) cc_final: 0.7932 (p) REVERT: D 364 ASP cc_start: 0.7919 (p0) cc_final: 0.7430 (p0) REVERT: D 449 MET cc_start: 0.7289 (ppp) cc_final: 0.7088 (ppp) REVERT: D 712 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6349 (mt-10) REVERT: E 163 PHE cc_start: 0.8863 (m-80) cc_final: 0.8605 (m-80) REVERT: E 219 MET cc_start: 0.8318 (ttm) cc_final: 0.8075 (ttm) REVERT: E 231 LYS cc_start: 0.9042 (mmmm) cc_final: 0.8587 (ttpt) REVERT: E 316 THR cc_start: 0.8501 (m) cc_final: 0.8133 (p) REVERT: E 388 MET cc_start: 0.7714 (tpt) cc_final: 0.7272 (tpp) REVERT: E 426 LYS cc_start: 0.9207 (tmtt) cc_final: 0.8969 (tmmt) REVERT: E 438 ASP cc_start: 0.7401 (p0) cc_final: 0.6890 (t70) REVERT: E 440 GLU cc_start: 0.8748 (tt0) cc_final: 0.8379 (tp30) REVERT: E 454 TRP cc_start: 0.8834 (t60) cc_final: 0.8561 (t60) REVERT: E 712 GLU cc_start: 0.6898 (tt0) cc_final: 0.6609 (tt0) REVERT: E 750 ASN cc_start: 0.8572 (p0) cc_final: 0.8227 (p0) REVERT: F 163 PHE cc_start: 0.8682 (m-80) cc_final: 0.8464 (m-80) REVERT: F 219 MET cc_start: 0.8159 (ttt) cc_final: 0.7717 (ttm) REVERT: F 221 GLU cc_start: 0.8699 (pt0) cc_final: 0.8357 (pm20) REVERT: F 231 LYS cc_start: 0.9040 (mmmm) cc_final: 0.8702 (ttpt) REVERT: F 296 ASN cc_start: 0.8876 (t0) cc_final: 0.8427 (t0) REVERT: F 316 THR cc_start: 0.8353 (m) cc_final: 0.8076 (p) REVERT: F 364 ASP cc_start: 0.7856 (p0) cc_final: 0.7420 (p0) REVERT: F 440 GLU cc_start: 0.8812 (tt0) cc_final: 0.8553 (tp30) REVERT: F 508 MET cc_start: 0.8226 (ttp) cc_final: 0.7947 (ttp) REVERT: F 550 MET cc_start: 0.8481 (mtm) cc_final: 0.8162 (mtm) REVERT: F 560 ARG cc_start: 0.7759 (mtt180) cc_final: 0.7346 (ttm170) outliers start: 1 outliers final: 1 residues processed: 652 average time/residue: 0.2355 time to fit residues: 245.5944 Evaluate side-chains 522 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 521 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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: 4.9990 chunk 116 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 400 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 350 optimal weight: 0.9980 chunk 156 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 432 optimal weight: 9.9990 chunk 343 optimal weight: 0.4980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 GLN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN C 340 HIS C 764 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 GLN D 458 GLN E 398 GLN E 494 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.144341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.121901 restraints weight = 77478.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.125031 restraints weight = 45896.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.127104 restraints weight = 31037.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.128500 restraints weight = 23323.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.129441 restraints weight = 19062.232| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35838 Z= 0.131 Angle : 0.654 9.290 48426 Z= 0.319 Chirality : 0.046 0.219 5418 Planarity : 0.005 0.075 6378 Dihedral : 8.170 165.204 4926 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.03 % Allowed : 1.13 % Favored : 98.84 % 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: -0.81 (0.13), residues: 4416 helix: 0.38 (0.12), residues: 1932 sheet: -0.52 (0.20), residues: 684 loop : -1.50 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 256 TYR 0.018 0.001 TYR E 244 PHE 0.013 0.001 PHE C 290 TRP 0.033 0.002 TRP D 454 HIS 0.004 0.001 HIS D 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (35820) covalent geometry : angle 0.65409 / 0.32 (48426) hydrogen bonds : bond 0.03302 / 2.16 ( 1386) hydrogen bonds : angle 4.26195 / 2.98 ( 3924) Misc. bond : bond 0.00045 / 0.03 ( 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 638 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 637 time to evaluate : 1.337 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 113 ARG cc_start: 0.6713 (ttt180) cc_final: 0.6422 (tpt170) REVERT: A 163 PHE cc_start: 0.8800 (m-80) cc_final: 0.8495 (m-80) REVERT: A 196 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6710 (mm-30) REVERT: A 221 GLU cc_start: 0.8881 (pt0) cc_final: 0.8478 (pm20) REVERT: A 231 LYS cc_start: 0.9022 (mmmm) cc_final: 0.8820 (mmtm) REVERT: A 316 THR cc_start: 0.8437 (m) cc_final: 0.8056 (p) REVERT: A 340 HIS cc_start: 0.6845 (m90) cc_final: 0.5981 (m90) REVERT: A 426 LYS cc_start: 0.9351 (tmtt) cc_final: 0.8879 (ttmm) REVERT: A 438 ASP cc_start: 0.7041 (p0) cc_final: 0.6794 (t70) REVERT: A 611 MET cc_start: 0.6550 (ptm) cc_final: 0.6168 (ptm) REVERT: A 709 ARG cc_start: 0.7976 (ttt180) cc_final: 0.7518 (ttp80) REVERT: B 163 PHE cc_start: 0.8851 (m-80) cc_final: 0.8522 (m-80) REVERT: B 231 LYS cc_start: 0.9032 (mmmm) cc_final: 0.8570 (ttpt) REVERT: B 316 THR cc_start: 0.8497 (m) cc_final: 0.8141 (p) REVERT: B 364 ASP cc_start: 0.7836 (p0) cc_final: 0.7352 (p0) REVERT: B 388 MET cc_start: 0.8029 (tpt) cc_final: 0.7496 (tpp) REVERT: B 426 LYS cc_start: 0.9214 (tmtt) cc_final: 0.9009 (tmmt) REVERT: B 431 ASP cc_start: 0.7628 (t70) cc_final: 0.7403 (t0) REVERT: B 438 ASP cc_start: 0.7270 (p0) cc_final: 0.7034 (t70) REVERT: B 440 GLU cc_start: 0.8756 (tt0) cc_final: 0.8400 (tp30) REVERT: C 163 PHE cc_start: 0.8629 (m-80) cc_final: 0.8322 (m-80) REVERT: C 196 GLU cc_start: 0.6807 (mt-10) cc_final: 0.6297 (mm-30) REVERT: C 244 TYR cc_start: 0.8045 (p90) cc_final: 0.6810 (p90) REVERT: C 364 ASP cc_start: 0.7896 (p0) cc_final: 0.7433 (p0) REVERT: C 440 GLU cc_start: 0.8764 (tt0) cc_final: 0.8461 (tp30) REVERT: C 517 TYR cc_start: 0.8690 (p90) cc_final: 0.8160 (p90) REVERT: C 550 MET cc_start: 0.8521 (mtm) cc_final: 0.8210 (mtm) REVERT: C 712 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6642 (mt-10) REVERT: C 744 ARG cc_start: 0.6419 (mmt-90) cc_final: 0.5984 (mmt-90) REVERT: D 131 PHE cc_start: 0.8501 (t80) cc_final: 0.8237 (t80) REVERT: D 147 ARG cc_start: 0.6509 (ptp-110) cc_final: 0.6177 (ptp-170) REVERT: D 163 PHE cc_start: 0.8816 (m-80) cc_final: 0.8522 (m-80) REVERT: D 196 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6653 (mm-30) REVERT: D 316 THR cc_start: 0.8376 (m) cc_final: 0.7987 (p) REVERT: D 364 ASP cc_start: 0.7996 (p0) cc_final: 0.7476 (p0) REVERT: D 709 ARG cc_start: 0.8526 (mmp80) cc_final: 0.8320 (mmp80) REVERT: D 712 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6416 (mt-10) REVERT: E 163 PHE cc_start: 0.8864 (m-80) cc_final: 0.8544 (m-80) REVERT: E 219 MET cc_start: 0.8292 (ttm) cc_final: 0.8021 (ttm) REVERT: E 231 LYS cc_start: 0.9054 (mmmm) cc_final: 0.8594 (ttpt) REVERT: E 244 TYR cc_start: 0.8041 (p90) cc_final: 0.7508 (p90) REVERT: E 316 THR cc_start: 0.8544 (m) cc_final: 0.8155 (p) REVERT: E 388 MET cc_start: 0.7733 (tpt) cc_final: 0.7312 (tpp) REVERT: E 426 LYS cc_start: 0.9256 (tmtt) cc_final: 0.9014 (tmmt) REVERT: E 438 ASP cc_start: 0.7463 (p0) cc_final: 0.6948 (t70) REVERT: E 440 GLU cc_start: 0.8732 (tt0) cc_final: 0.8376 (tp30) REVERT: E 712 GLU cc_start: 0.6873 (tt0) cc_final: 0.6657 (tt0) REVERT: E 750 ASN cc_start: 0.8569 (p0) cc_final: 0.8233 (p0) REVERT: F 121 ASP cc_start: 0.8743 (m-30) cc_final: 0.8426 (m-30) REVERT: F 163 PHE cc_start: 0.8658 (m-80) cc_final: 0.8421 (m-80) REVERT: F 196 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6501 (mm-30) REVERT: F 219 MET cc_start: 0.8222 (ttt) cc_final: 0.7947 (ttm) REVERT: F 221 GLU cc_start: 0.8763 (pt0) cc_final: 0.8358 (pt0) REVERT: F 231 LYS cc_start: 0.9019 (mmmm) cc_final: 0.8773 (mmtm) REVERT: F 316 THR cc_start: 0.8391 (m) cc_final: 0.8061 (p) REVERT: F 364 ASP cc_start: 0.7843 (p0) cc_final: 0.7424 (p0) REVERT: F 440 GLU cc_start: 0.8774 (tt0) cc_final: 0.8568 (tp30) REVERT: F 508 MET cc_start: 0.8265 (ttp) cc_final: 0.8020 (ttp) REVERT: F 550 MET cc_start: 0.8546 (mtm) cc_final: 0.8214 (mtm) REVERT: F 560 ARG cc_start: 0.7710 (mtt180) cc_final: 0.7311 (ttm170) outliers start: 1 outliers final: 0 residues processed: 638 average time/residue: 0.2346 time to fit residues: 239.1442 Evaluate side-chains 501 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 501 time to evaluate : 1.290 ------------------------------------------------------------------------------- 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: 7.9990 chunk 190 optimal weight: 5.9990 chunk 263 optimal weight: 0.6980 chunk 40 optimal weight: 8.9990 chunk 237 optimal weight: 0.0050 chunk 15 optimal weight: 5.9990 chunk 382 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 288 optimal weight: 9.9990 chunk 317 optimal weight: 5.9990 chunk 192 optimal weight: 0.8980 overall best weight: 2.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 GLN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.143007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.120769 restraints weight = 78252.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.123734 restraints weight = 46847.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.125723 restraints weight = 32066.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.127036 restraints weight = 24337.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.127826 restraints weight = 20068.445| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35838 Z= 0.143 Angle : 0.672 9.500 48426 Z= 0.330 Chirality : 0.046 0.215 5418 Planarity : 0.005 0.074 6378 Dihedral : 8.332 167.319 4926 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: -0.87 (0.13), residues: 4416 helix: 0.33 (0.12), residues: 1932 sheet: -0.50 (0.20), residues: 684 loop : -1.56 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 147 TYR 0.025 0.002 TYR A 244 PHE 0.019 0.001 PHE B 563 TRP 0.038 0.002 TRP D 454 HIS 0.005 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (35820) covalent geometry : angle 0.67189 / 0.33 (48426) hydrogen bonds : bond 0.03468 / 2.29 ( 1386) hydrogen bonds : angle 4.37544 / 3.05 ( 3924) Misc. bond : bond 0.00047 / 0.03 ( 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 621 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 621 time to evaluate : 1.553 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: A 163 PHE cc_start: 0.8832 (m-80) cc_final: 0.8522 (m-80) REVERT: A 196 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6745 (mm-30) REVERT: A 219 MET cc_start: 0.8496 (ttm) cc_final: 0.8234 (ttt) REVERT: A 221 GLU cc_start: 0.8918 (pt0) cc_final: 0.8496 (pm20) REVERT: A 316 THR cc_start: 0.8455 (m) cc_final: 0.8110 (p) REVERT: A 364 ASP cc_start: 0.8007 (p0) cc_final: 0.7582 (p0) REVERT: A 426 LYS cc_start: 0.9334 (tmtt) cc_final: 0.8940 (ttmt) REVERT: A 438 ASP cc_start: 0.7160 (p0) cc_final: 0.6909 (t70) REVERT: A 611 MET cc_start: 0.6500 (ptm) cc_final: 0.6138 (ptm) REVERT: A 709 ARG cc_start: 0.8363 (ttt180) cc_final: 0.7451 (ttp80) REVERT: B 163 PHE cc_start: 0.8897 (m-80) cc_final: 0.8556 (m-80) REVERT: B 196 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6713 (mm-30) REVERT: B 231 LYS cc_start: 0.9035 (mmmm) cc_final: 0.8577 (ttpt) REVERT: B 316 THR cc_start: 0.8539 (m) cc_final: 0.8199 (p) REVERT: B 364 ASP cc_start: 0.7860 (p0) cc_final: 0.7342 (p0) REVERT: B 388 MET cc_start: 0.8033 (tpt) cc_final: 0.7519 (tpp) REVERT: B 426 LYS cc_start: 0.9274 (tmtt) cc_final: 0.9039 (tmmt) REVERT: B 431 ASP cc_start: 0.7673 (t70) cc_final: 0.7389 (t0) REVERT: B 438 ASP cc_start: 0.7461 (p0) cc_final: 0.7034 (t70) REVERT: B 440 GLU cc_start: 0.8759 (tt0) cc_final: 0.8435 (tp30) REVERT: C 163 PHE cc_start: 0.8665 (m-80) cc_final: 0.8339 (m-80) REVERT: C 196 GLU cc_start: 0.6758 (mt-10) cc_final: 0.6241 (mm-30) REVERT: C 244 TYR cc_start: 0.8147 (p90) cc_final: 0.7460 (p90) REVERT: C 256 ARG cc_start: 0.8922 (tpp80) cc_final: 0.8690 (tpp80) REVERT: C 364 ASP cc_start: 0.7887 (p0) cc_final: 0.7446 (p0) REVERT: C 440 GLU cc_start: 0.8811 (tt0) cc_final: 0.8484 (tp30) REVERT: C 517 TYR cc_start: 0.8723 (p90) cc_final: 0.8185 (p90) REVERT: C 550 MET cc_start: 0.8520 (mtm) cc_final: 0.8232 (mtm) REVERT: C 712 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6545 (mt-10) REVERT: C 740 MET cc_start: 0.5480 (ptt) cc_final: 0.5098 (ptt) REVERT: C 744 ARG cc_start: 0.6235 (mmt-90) cc_final: 0.6015 (mmt-90) REVERT: D 131 PHE cc_start: 0.8552 (t80) cc_final: 0.8261 (t80) REVERT: D 147 ARG cc_start: 0.6631 (ptp-110) cc_final: 0.6317 (ptp-170) REVERT: D 163 PHE cc_start: 0.8818 (m-80) cc_final: 0.8482 (m-80) REVERT: D 196 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6710 (mm-30) REVERT: D 316 THR cc_start: 0.8414 (m) cc_final: 0.8043 (p) REVERT: D 364 ASP cc_start: 0.8016 (p0) cc_final: 0.7655 (p0) REVERT: D 449 MET cc_start: 0.7629 (ppp) cc_final: 0.7425 (ppp) REVERT: D 712 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6398 (mt-10) REVERT: E 130 LEU cc_start: 0.8498 (mp) cc_final: 0.8255 (tp) REVERT: E 162 GLU cc_start: 0.8570 (pm20) cc_final: 0.8263 (pm20) REVERT: E 163 PHE cc_start: 0.8825 (m-80) cc_final: 0.8533 (m-80) REVERT: E 219 MET cc_start: 0.8306 (ttm) cc_final: 0.8054 (ttm) REVERT: E 231 LYS cc_start: 0.9081 (mmmm) cc_final: 0.8610 (ttpt) REVERT: E 316 THR cc_start: 0.8557 (m) cc_final: 0.8234 (p) REVERT: E 388 MET cc_start: 0.7728 (tpt) cc_final: 0.7310 (tpp) REVERT: E 426 LYS cc_start: 0.9264 (tmtt) cc_final: 0.9024 (tmmt) REVERT: E 438 ASP cc_start: 0.7613 (p0) cc_final: 0.7120 (t70) REVERT: E 440 GLU cc_start: 0.8753 (tt0) cc_final: 0.8416 (tp30) REVERT: E 712 GLU cc_start: 0.7012 (tt0) cc_final: 0.6770 (tt0) REVERT: E 750 ASN cc_start: 0.8603 (p0) cc_final: 0.8263 (p0) REVERT: F 95 ARG cc_start: 0.6647 (mtm-85) cc_final: 0.6397 (mtm180) REVERT: F 163 PHE cc_start: 0.8693 (m-80) cc_final: 0.8434 (m-80) REVERT: F 196 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6583 (mm-30) REVERT: F 219 MET cc_start: 0.8314 (ttt) cc_final: 0.8062 (ttm) REVERT: F 221 GLU cc_start: 0.8798 (pt0) cc_final: 0.8397 (pt0) REVERT: F 231 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8795 (mmtm) REVERT: F 316 THR cc_start: 0.8414 (m) cc_final: 0.8090 (p) REVERT: F 364 ASP cc_start: 0.7870 (p0) cc_final: 0.7483 (p0) REVERT: F 440 GLU cc_start: 0.8822 (tt0) cc_final: 0.8594 (tp30) REVERT: F 550 MET cc_start: 0.8489 (mtm) cc_final: 0.8193 (mtm) REVERT: F 560 ARG cc_start: 0.7741 (mtt180) cc_final: 0.7349 (ttm170) outliers start: 0 outliers final: 0 residues processed: 621 average time/residue: 0.2329 time to fit residues: 230.5257 Evaluate side-chains 499 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 499 time to evaluate : 1.382 ------------------------------------------------------------------------------- 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: 5.9990 chunk 9 optimal weight: 9.9990 chunk 419 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 182 optimal weight: 5.9990 chunk 378 optimal weight: 6.9990 chunk 262 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 chunk 325 optimal weight: 0.0970 chunk 74 optimal weight: 4.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 ASN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN C 398 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** F 91 ASN ** 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 = 0.3968 r_free = 0.3968 target = 0.143540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.120723 restraints weight = 81452.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.123546 restraints weight = 48439.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.125507 restraints weight = 33153.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.126783 restraints weight = 25340.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.127574 restraints weight = 20952.593| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3713 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 : 0.705 9.113 48426 Z= 0.351 Chirality : 0.047 0.218 5418 Planarity : 0.006 0.116 6378 Dihedral : 8.606 171.470 4926 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: -1.01 (0.13), residues: 4416 helix: 0.24 (0.12), residues: 1938 sheet: -0.60 (0.20), residues: 696 loop : -1.67 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 95 TYR 0.024 0.002 TYR A 138 PHE 0.029 0.002 PHE F 563 TRP 0.035 0.002 TRP D 454 HIS 0.006 0.001 HIS E 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (35820) covalent geometry : angle 0.70503 / 0.35 (48426) hydrogen bonds : bond 0.03860 / 2.53 ( 1386) hydrogen bonds : angle 4.55878 / 3.18 ( 3924) Misc. bond : bond 0.00051 / 0.03 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6259.62 seconds wall clock time: 108 minutes 53.63 seconds (6533.63 seconds total)