Starting phenix.real_space_refine on Fri Mar 6 21:11:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bp8_30147/03_2026/7bp8_30147.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bp8_30147/03_2026/7bp8_30147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bp8_30147/03_2026/7bp8_30147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bp8_30147/03_2026/7bp8_30147.map" model { file = "/net/cci-nas-00/data/ceres_data/7bp8_30147/03_2026/7bp8_30147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bp8_30147/03_2026/7bp8_30147.cif" } resolution = 3.9 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= 0.049 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 24 5.49 5 S 180 5.16 5 C 21996 2.51 5 N 6246 2.21 5 O 6744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35190 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5811 Classifications: {'peptide': 740} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 699} Chain breaks: 1 Chain: "B" Number of atoms: 5811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5811 Classifications: {'peptide': 740} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 699} Chain breaks: 1 Chain: "C" Number of atoms: 5811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5811 Classifications: {'peptide': 740} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 699} Chain breaks: 1 Chain: "D" Number of atoms: 5811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5811 Classifications: {'peptide': 740} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 699} Chain breaks: 1 Chain: "E" Number of atoms: 5811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5811 Classifications: {'peptide': 740} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 699} Chain breaks: 1 Chain: "F" Number of atoms: 5811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5811 Classifications: {'peptide': 740} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 699} Chain breaks: 1 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.18, per 1000 atoms: 0.20 Number of scatterers: 35190 At special positions: 0 Unit cell: (167.99, 178.69, 101.65, 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 24 15.00 O 6744 8.00 N 6246 7.00 C 21996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.5 seconds 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8304 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 30 sheets defined 47.6% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 130 through 139 removed outlier: 4.271A 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 202 through 206 removed outlier: 3.723A pdb=" N ILE A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.610A pdb=" N LEU A 224 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.905A pdb=" N ILE A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 278 through 296 removed outlier: 3.706A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.632A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 334 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.148A 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 395 through 403 removed outlier: 3.568A pdb=" N VAL A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 438 through 444 Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 482 through 499 removed outlier: 3.943A pdb=" N GLU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) Proline residue: A 496 - end of helix removed outlier: 3.681A pdb=" N HIS A 499 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 523 through 536 Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.803A 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 Processing helix chain 'A' and resid 591 through 595 removed outlier: 4.312A pdb=" N GLY A 595 " --> pdb=" O ASP A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.783A pdb=" N LEU A 634 " --> pdb=" O PRO A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 662 removed outlier: 4.036A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 711 Processing helix chain 'A' and resid 732 through 740 removed outlier: 4.107A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 748 through 761 removed outlier: 4.101A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 130 through 139 removed outlier: 4.272A 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 202 through 206 removed outlier: 3.724A pdb=" N ILE B 206 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 220 Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.610A pdb=" N LEU B 224 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 250 through 263 removed outlier: 3.905A pdb=" N ILE B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 278 through 296 removed outlier: 3.708A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.633A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 334 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.148A 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 395 through 403 removed outlier: 3.568A pdb=" N VAL B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 438 through 444 Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 482 through 499 removed outlier: 3.941A pdb=" N GLU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) Proline residue: B 496 - end of helix removed outlier: 3.661A pdb=" N HIS B 499 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 523 through 536 Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.803A 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 Processing helix chain 'B' and resid 591 through 595 removed outlier: 4.313A pdb=" N GLY B 595 " --> pdb=" O ASP B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 610 Processing helix chain 'B' and resid 630 through 634 removed outlier: 3.781A pdb=" N LEU B 634 " --> pdb=" O PRO B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 662 removed outlier: 4.037A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 711 Processing helix chain 'B' and resid 732 through 740 removed outlier: 4.108A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 743 No H-bonds generated for 'chain 'B' and resid 741 through 743' Processing helix chain 'B' and resid 748 through 761 removed outlier: 4.101A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 130 through 139 removed outlier: 4.272A 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 202 through 206 removed outlier: 3.725A pdb=" N ILE C 206 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 220 Processing helix chain 'C' and resid 220 through 226 removed outlier: 3.610A pdb=" N LEU C 224 " --> pdb=" O VAL C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 250 through 263 removed outlier: 3.906A pdb=" N ILE C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 278 through 296 removed outlier: 3.705A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.632A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 334 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.148A 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 395 through 403 removed outlier: 3.566A pdb=" N VAL C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 425 Processing helix chain 'C' and resid 438 through 444 Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 482 through 499 removed outlier: 3.941A pdb=" N GLU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) Proline residue: C 496 - end of helix removed outlier: 3.678A pdb=" N HIS C 499 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 507 Processing helix chain 'C' and resid 523 through 536 Processing helix chain 'C' and resid 543 through 553 removed outlier: 3.802A 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 Processing helix chain 'C' and resid 591 through 595 removed outlier: 4.312A pdb=" N GLY C 595 " --> pdb=" O ASP C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 610 Processing helix chain 'C' and resid 630 through 634 removed outlier: 3.781A pdb=" N LEU C 634 " --> pdb=" O PRO C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 662 removed outlier: 4.036A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 711 Processing helix chain 'C' and resid 732 through 740 removed outlier: 4.108A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 743 No H-bonds generated for 'chain 'C' and resid 741 through 743' Processing helix chain 'C' and resid 748 through 761 removed outlier: 4.101A pdb=" N ILE C 752 " --> pdb=" O SER C 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 49 Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 130 through 139 removed outlier: 4.281A 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 202 through 206 removed outlier: 3.723A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 220 Processing helix chain 'D' and resid 220 through 226 removed outlier: 3.611A pdb=" N LEU D 224 " --> pdb=" O VAL D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 250 through 263 removed outlier: 3.905A pdb=" N ILE D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 278 through 296 removed outlier: 3.707A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.632A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 334 Processing helix chain 'D' and resid 349 through 353 removed outlier: 4.147A 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 395 through 403 removed outlier: 3.567A pdb=" N VAL D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 425 Processing helix chain 'D' and resid 438 through 444 Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 482 through 499 removed outlier: 3.942A pdb=" N GLU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) Proline residue: D 496 - end of helix removed outlier: 3.758A pdb=" N HIS D 499 " --> pdb=" O TYR D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 507 Processing helix chain 'D' and resid 523 through 536 Processing helix chain 'D' and resid 543 through 553 removed outlier: 3.803A 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 Processing helix chain 'D' and resid 591 through 595 removed outlier: 4.313A pdb=" N GLY D 595 " --> pdb=" O ASP D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 610 Processing helix chain 'D' and resid 630 through 634 removed outlier: 3.783A pdb=" N LEU D 634 " --> pdb=" O PRO D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 662 removed outlier: 4.036A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 711 Processing helix chain 'D' and resid 732 through 740 removed outlier: 4.106A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 743 No H-bonds generated for 'chain 'D' and resid 741 through 743' Processing helix chain 'D' and resid 748 through 761 removed outlier: 4.100A pdb=" N ILE D 752 " --> pdb=" O SER D 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 49 Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 130 through 139 removed outlier: 4.281A 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 202 through 206 removed outlier: 3.724A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 220 Processing helix chain 'E' and resid 220 through 226 removed outlier: 3.610A pdb=" N LEU E 224 " --> pdb=" O VAL E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 232 Processing helix chain 'E' and resid 250 through 263 removed outlier: 3.905A pdb=" N ILE E 254 " --> pdb=" O GLY E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 278 through 296 removed outlier: 3.708A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.634A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 334 Processing helix chain 'E' and resid 349 through 353 removed outlier: 4.148A 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 395 through 403 removed outlier: 3.568A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 425 Processing helix chain 'E' and resid 438 through 444 Processing helix chain 'E' and resid 448 through 458 Processing helix chain 'E' and resid 482 through 499 removed outlier: 3.941A pdb=" N GLU E 491 " --> pdb=" O ARG E 487 " (cutoff:3.500A) Proline residue: E 496 - end of helix removed outlier: 3.657A pdb=" N HIS E 499 " --> pdb=" O TYR E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 507 Processing helix chain 'E' and resid 523 through 536 Processing helix chain 'E' and resid 543 through 553 removed outlier: 3.803A 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 Processing helix chain 'E' and resid 591 through 595 removed outlier: 4.312A pdb=" N GLY E 595 " --> pdb=" O ASP E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 610 Processing helix chain 'E' and resid 630 through 634 removed outlier: 3.781A pdb=" N LEU E 634 " --> pdb=" O PRO E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 662 removed outlier: 4.038A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 Processing helix chain 'E' and resid 683 through 711 Processing helix chain 'E' and resid 732 through 740 removed outlier: 4.108A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 743 No H-bonds generated for 'chain 'E' and resid 741 through 743' Processing helix chain 'E' and resid 748 through 761 removed outlier: 4.103A pdb=" N ILE E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 49 Processing helix chain 'F' and resid 85 through 92 Processing helix chain 'F' and resid 130 through 139 removed outlier: 4.277A 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 202 through 206 removed outlier: 3.725A pdb=" N ILE F 206 " --> pdb=" O TYR F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 220 Processing helix chain 'F' and resid 220 through 226 removed outlier: 3.610A pdb=" N LEU F 224 " --> pdb=" O VAL F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 Processing helix chain 'F' and resid 250 through 263 removed outlier: 3.905A pdb=" N ILE F 254 " --> pdb=" O GLY F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 278 through 296 removed outlier: 3.706A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.633A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 334 Processing helix chain 'F' and resid 349 through 353 removed outlier: 4.148A 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 395 through 403 removed outlier: 3.566A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 425 Processing helix chain 'F' and resid 438 through 444 Processing helix chain 'F' and resid 448 through 458 Processing helix chain 'F' and resid 482 through 499 removed outlier: 3.942A pdb=" N GLU F 491 " --> pdb=" O ARG F 487 " (cutoff:3.500A) Proline residue: F 496 - end of helix removed outlier: 3.663A pdb=" N HIS F 499 " --> pdb=" O TYR F 495 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 507 Processing helix chain 'F' and resid 523 through 536 Processing helix chain 'F' and resid 543 through 553 removed outlier: 3.803A 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 Processing helix chain 'F' and resid 591 through 595 removed outlier: 4.312A pdb=" N GLY F 595 " --> pdb=" O ASP F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 610 Processing helix chain 'F' and resid 630 through 634 removed outlier: 3.781A pdb=" N LEU F 634 " --> pdb=" O PRO F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 662 removed outlier: 4.037A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 711 Processing helix chain 'F' and resid 732 through 740 removed outlier: 4.108A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 743 No H-bonds generated for 'chain 'F' and resid 741 through 743' Processing helix chain 'F' and resid 748 through 761 removed outlier: 4.102A pdb=" N ILE F 752 " --> pdb=" O SER F 748 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 29 removed outlier: 6.229A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N VAL A 39 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 26 " --> pdb=" O ILE A 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 118 removed outlier: 6.950A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.531A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 540 through 542 removed outlier: 6.453A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A 514 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR A 623 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N PHE A 516 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 26 through 29 removed outlier: 6.228A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL B 39 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B 26 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 115 through 118 removed outlier: 6.952A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AA9, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.532A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 540 through 542 removed outlier: 6.454A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL B 514 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR B 623 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N PHE B 516 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 26 through 29 removed outlier: 6.228A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N MET C 84 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASP C 29 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL C 39 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 26 " --> pdb=" O ILE C 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 115 through 118 removed outlier: 6.952A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 146 through 147 Processing sheet with id=AB5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.532A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 540 through 542 removed outlier: 6.454A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL C 514 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N THR C 623 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N PHE C 516 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 26 through 29 removed outlier: 6.229A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N VAL D 39 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU D 26 " --> pdb=" O ILE D 100 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 115 through 118 removed outlier: 6.950A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 146 through 147 Processing sheet with id=AC1, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.532A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 540 through 542 removed outlier: 6.453A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL D 514 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR D 623 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N PHE D 516 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 26 through 29 removed outlier: 6.228A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL E 39 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU E 26 " --> pdb=" O ILE E 100 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 115 through 118 removed outlier: 6.952A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 146 through 147 Processing sheet with id=AC6, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.533A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 540 through 542 removed outlier: 6.455A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL E 514 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N THR E 623 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N PHE E 516 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 26 through 29 removed outlier: 6.228A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N MET F 84 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASP F 29 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL F 39 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU F 26 " --> pdb=" O ILE F 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 115 through 118 removed outlier: 6.952A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 146 through 147 Processing sheet with id=AD2, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.532A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY F 240 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 540 through 542 removed outlier: 6.454A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N THR F 623 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE F 516 " --> pdb=" O THR F 623 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) 1446 hydrogen bonds defined for protein. 4140 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: 6.71 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10544 1.34 - 1.46: 5809 1.46 - 1.58: 19077 1.58 - 1.70: 54 1.70 - 1.82: 288 Bond restraints: 35772 Sorted by residual: bond pdb=" C LYS E 136 " pdb=" N PRO E 137 " ideal model delta sigma weight residual 1.337 1.396 -0.059 1.11e-02 8.12e+03 2.83e+01 bond pdb=" C LYS F 136 " pdb=" N PRO F 137 " ideal model delta sigma weight residual 1.337 1.396 -0.059 1.11e-02 8.12e+03 2.83e+01 bond pdb=" C LYS B 136 " pdb=" N PRO B 137 " ideal model delta sigma weight residual 1.337 1.395 -0.059 1.11e-02 8.12e+03 2.82e+01 bond pdb=" C LYS C 136 " pdb=" N PRO C 137 " ideal model delta sigma weight residual 1.337 1.395 -0.058 1.11e-02 8.12e+03 2.74e+01 bond pdb=" C LYS D 136 " pdb=" N PRO D 137 " ideal model delta sigma weight residual 1.337 1.393 -0.057 1.11e-02 8.12e+03 2.63e+01 ... (remaining 35767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 44392 2.38 - 4.76: 3393 4.76 - 7.13: 487 7.13 - 9.51: 46 9.51 - 11.89: 36 Bond angle restraints: 48354 Sorted by residual: angle pdb=" C LYS B 136 " pdb=" N PRO B 137 " pdb=" CA PRO B 137 " ideal model delta sigma weight residual 119.87 126.51 -6.64 1.04e+00 9.25e-01 4.08e+01 angle pdb=" C LYS A 136 " pdb=" N PRO A 137 " pdb=" CA PRO A 137 " ideal model delta sigma weight residual 119.87 126.35 -6.48 1.04e+00 9.25e-01 3.89e+01 angle pdb=" C LYS F 136 " pdb=" N PRO F 137 " pdb=" CA PRO F 137 " ideal model delta sigma weight residual 119.87 126.14 -6.27 1.04e+00 9.25e-01 3.64e+01 angle pdb=" C LYS D 136 " pdb=" N PRO D 137 " pdb=" CA PRO D 137 " ideal model delta sigma weight residual 119.87 126.11 -6.24 1.04e+00 9.25e-01 3.60e+01 angle pdb=" C LYS C 136 " pdb=" N PRO C 137 " pdb=" CA PRO C 137 " ideal model delta sigma weight residual 119.87 125.87 -6.00 1.04e+00 9.25e-01 3.33e+01 ... (remaining 48349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.40: 21771 33.40 - 66.80: 357 66.80 - 100.21: 66 100.21 - 133.61: 12 133.61 - 167.01: 12 Dihedral angle restraints: 22218 sinusoidal: 9420 harmonic: 12798 Sorted by residual: dihedral pdb=" O1B ADP F 901 " pdb=" O3A ADP F 901 " pdb=" PB ADP F 901 " pdb=" PA ADP F 901 " ideal model delta sinusoidal sigma weight residual 300.00 132.99 167.01 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O1B ADP C 901 " pdb=" O3A ADP C 901 " pdb=" PB ADP C 901 " pdb=" PA ADP C 901 " ideal model delta sinusoidal sigma weight residual 300.00 133.01 166.99 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O1B ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PB ADP B 901 " pdb=" PA ADP B 901 " ideal model delta sinusoidal sigma weight residual 300.00 133.03 166.97 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 22215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4466 0.098 - 0.196: 794 0.196 - 0.293: 122 0.293 - 0.391: 24 0.391 - 0.489: 12 Chirality restraints: 5418 Sorted by residual: chirality pdb=" CB ILE F 102 " pdb=" CA ILE F 102 " pdb=" CG1 ILE F 102 " pdb=" CG2 ILE F 102 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" CB ILE C 102 " pdb=" CA ILE C 102 " pdb=" CG1 ILE C 102 " pdb=" CG2 ILE C 102 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" CB ILE E 102 " pdb=" CA ILE E 102 " pdb=" CG1 ILE E 102 " pdb=" CG2 ILE E 102 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.88e+00 ... (remaining 5415 not shown) Planarity restraints: 6372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 189 " -0.017 2.00e-02 2.50e+03 3.53e-02 1.24e+01 pdb=" C ILE C 189 " 0.061 2.00e-02 2.50e+03 pdb=" O ILE C 189 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS C 190 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 189 " -0.017 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C ILE E 189 " 0.061 2.00e-02 2.50e+03 pdb=" O ILE E 189 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS E 190 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 189 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C ILE F 189 " -0.060 2.00e-02 2.50e+03 pdb=" O ILE F 189 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS F 190 " 0.020 2.00e-02 2.50e+03 ... (remaining 6369 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 9647 2.83 - 3.35: 32926 3.35 - 3.87: 55858 3.87 - 4.38: 62821 4.38 - 4.90: 107426 Nonbonded interactions: 268678 Sorted by model distance: nonbonded pdb=" O SER B 555 " pdb=" OG SER B 555 " model vdw 2.313 3.040 nonbonded pdb=" O SER E 555 " pdb=" OG SER E 555 " model vdw 2.313 3.040 nonbonded pdb=" O SER D 555 " pdb=" OG SER D 555 " model vdw 2.314 3.040 nonbonded pdb=" O SER A 555 " pdb=" OG SER A 555 " model vdw 2.314 3.040 nonbonded pdb=" O SER C 555 " pdb=" OG SER C 555 " model vdw 2.314 3.040 ... (remaining 268673 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 30.340 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 : 0.008 0.068 35772 Z= 0.414 Angle : 1.380 11.890 48354 Z= 0.782 Chirality : 0.082 0.489 5418 Planarity : 0.008 0.068 6372 Dihedral : 15.249 167.011 13914 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.18 % Allowed : 3.01 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -3.18 (0.11), residues: 4416 helix: -1.66 (0.10), residues: 1806 sheet: -1.69 (0.17), residues: 642 loop : -2.64 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 599 TYR 0.028 0.004 TYR B 644 PHE 0.035 0.004 PHE B 131 TRP 0.019 0.003 TRP E 454 HIS 0.008 0.002 HIS E 183 Details of bonding type rmsd covalent geometry : bond 0.00809 (35772) covalent geometry : angle 1.38025 (48354) hydrogen bonds : bond 0.18533 ( 1446) hydrogen bonds : angle 7.14186 ( 4140) *********************** 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 634 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 627 time to evaluate : 1.371 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: A 231 LYS cc_start: 0.7607 (mmmt) cc_final: 0.7285 (mmtt) REVERT: A 275 MET cc_start: 0.7733 (mmm) cc_final: 0.7447 (mtp) REVERT: A 351 ASN cc_start: 0.7113 (p0) cc_final: 0.6656 (p0) REVERT: B 231 LYS cc_start: 0.7670 (mmmt) cc_final: 0.7336 (mmtt) REVERT: B 239 ARG cc_start: 0.6867 (ptp-110) cc_final: 0.6510 (mtm180) REVERT: B 275 MET cc_start: 0.7914 (mmm) cc_final: 0.7695 (mtp) REVERT: B 327 GLN cc_start: 0.8487 (tp-100) cc_final: 0.8174 (tp-100) REVERT: B 351 ASN cc_start: 0.7242 (p0) cc_final: 0.6776 (p0) REVERT: B 420 LEU cc_start: 0.8920 (mt) cc_final: 0.8696 (mt) REVERT: C 239 ARG cc_start: 0.7130 (ptp-110) cc_final: 0.6723 (mtm180) REVERT: C 351 ASN cc_start: 0.7265 (p0) cc_final: 0.7047 (p0) REVERT: D 231 LYS cc_start: 0.7615 (mmmt) cc_final: 0.7254 (mmtt) REVERT: D 239 ARG cc_start: 0.6964 (ptp-110) cc_final: 0.6494 (mtt90) REVERT: D 275 MET cc_start: 0.7720 (mmm) cc_final: 0.7430 (mtp) REVERT: D 351 ASN cc_start: 0.7158 (p0) cc_final: 0.6726 (p0) REVERT: D 508 MET cc_start: 0.7970 (ttp) cc_final: 0.7666 (ttp) REVERT: E 80 GLU cc_start: 0.6165 (pm20) cc_final: 0.5478 (mp0) REVERT: E 231 LYS cc_start: 0.7672 (mmmt) cc_final: 0.7347 (mmtt) REVERT: E 239 ARG cc_start: 0.6839 (ptp-110) cc_final: 0.6507 (mtm180) REVERT: E 327 GLN cc_start: 0.8438 (tp-100) cc_final: 0.8111 (tp-100) REVERT: E 351 ASN cc_start: 0.7242 (p0) cc_final: 0.6898 (p0) REVERT: E 508 MET cc_start: 0.7761 (ttp) cc_final: 0.7539 (ttp) REVERT: F 239 ARG cc_start: 0.7144 (ptp-110) cc_final: 0.6731 (mtm180) REVERT: F 351 ASN cc_start: 0.7273 (p0) cc_final: 0.7025 (p0) outliers start: 7 outliers final: 0 residues processed: 633 average time/residue: 0.2670 time to fit residues: 255.8677 Evaluate side-chains 353 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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: 0.4980 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 0.9980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 GLN B 460 ASN C 348 ASN C 421 GLN C 460 ASN C 735 HIS D 421 GLN D 460 ASN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 ASN ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN F 421 GLN F 460 ASN F 735 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.138663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.110508 restraints weight = 64500.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109058 restraints weight = 81342.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.110470 restraints weight = 79557.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.110678 restraints weight = 51416.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.111429 restraints weight = 48107.839| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35772 Z= 0.147 Angle : 0.692 10.850 48354 Z= 0.340 Chirality : 0.047 0.179 5418 Planarity : 0.005 0.053 6372 Dihedral : 11.458 159.471 4968 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.37 % Allowed : 9.46 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.95 (0.12), residues: 4416 helix: -0.45 (0.12), residues: 1854 sheet: -1.57 (0.18), residues: 678 loop : -1.97 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 465 TYR 0.031 0.002 TYR D 203 PHE 0.011 0.001 PHE E 131 TRP 0.008 0.001 TRP B 454 HIS 0.003 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00324 (35772) covalent geometry : angle 0.69174 (48354) hydrogen bonds : bond 0.04326 ( 1446) hydrogen bonds : angle 5.09479 ( 4140) *********************** 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 455 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 403 time to evaluate : 1.430 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: A 58 LEU cc_start: 0.7228 (tp) cc_final: 0.6910 (tt) REVERT: A 115 HIS cc_start: 0.5645 (OUTLIER) cc_final: 0.5262 (t70) REVERT: B 58 LEU cc_start: 0.7342 (tp) cc_final: 0.7132 (tt) REVERT: B 327 GLN cc_start: 0.8587 (tp-100) cc_final: 0.8234 (tp-100) REVERT: B 332 MET cc_start: 0.8738 (mmm) cc_final: 0.8308 (mmm) REVERT: B 351 ASN cc_start: 0.7428 (p0) cc_final: 0.7167 (p0) REVERT: C 239 ARG cc_start: 0.7012 (ptp-110) cc_final: 0.6652 (mtm110) REVERT: C 327 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8051 (tp-100) REVERT: C 332 MET cc_start: 0.8840 (mmm) cc_final: 0.8334 (mmm) REVERT: C 473 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7556 (mm-40) REVERT: D 58 LEU cc_start: 0.7212 (tp) cc_final: 0.6886 (tt) REVERT: D 115 HIS cc_start: 0.5712 (OUTLIER) cc_final: 0.5338 (t70) REVERT: E 58 LEU cc_start: 0.7330 (tp) cc_final: 0.7086 (tt) REVERT: E 239 ARG cc_start: 0.6994 (ptp-110) cc_final: 0.6773 (mtt90) REVERT: E 327 GLN cc_start: 0.8579 (tp-100) cc_final: 0.8215 (tp-100) REVERT: F 239 ARG cc_start: 0.7107 (ptp-110) cc_final: 0.6697 (mtm180) REVERT: F 327 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8064 (tp-100) REVERT: F 473 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7645 (mm-40) outliers start: 52 outliers final: 37 residues processed: 444 average time/residue: 0.2282 time to fit residues: 163.2642 Evaluate side-chains 385 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 346 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 732 ARG Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 732 ARG Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 732 ARG Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain D residue 732 ARG Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 732 ARG Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 732 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 28 optimal weight: 8.9990 chunk 250 optimal weight: 4.9990 chunk 263 optimal weight: 8.9990 chunk 256 optimal weight: 10.0000 chunk 297 optimal weight: 40.0000 chunk 362 optimal weight: 20.0000 chunk 382 optimal weight: 50.0000 chunk 66 optimal weight: 20.0000 chunk 314 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 ASN A 460 ASN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN B 348 ASN B 443 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 HIS C 443 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN E 443 ASN E 460 ASN ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN E 735 HIS F 443 ASN ** F 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.133191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.105581 restraints weight = 65899.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.104845 restraints weight = 81778.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.105645 restraints weight = 89965.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.105969 restraints weight = 59750.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.107350 restraints weight = 52304.540| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 35772 Z= 0.286 Angle : 0.760 11.885 48354 Z= 0.373 Chirality : 0.050 0.196 5418 Planarity : 0.005 0.059 6372 Dihedral : 11.008 137.454 4968 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.95 % Allowed : 13.34 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.84 (0.12), residues: 4416 helix: -0.39 (0.12), residues: 1854 sheet: -1.29 (0.19), residues: 678 loop : -1.98 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 662 TYR 0.029 0.002 TYR A 203 PHE 0.011 0.002 PHE D 360 TRP 0.017 0.003 TRP E 454 HIS 0.005 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00671 (35772) covalent geometry : angle 0.76018 (48354) hydrogen bonds : bond 0.04792 ( 1446) hydrogen bonds : angle 5.07569 ( 4140) *********************** 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 416 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 342 time to evaluate : 1.415 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: A 115 HIS cc_start: 0.5648 (OUTLIER) cc_final: 0.5390 (t70) REVERT: A 239 ARG cc_start: 0.6979 (ptp-110) cc_final: 0.6642 (mtt90) REVERT: B 115 HIS cc_start: 0.5915 (OUTLIER) cc_final: 0.5527 (t70) REVERT: C 115 HIS cc_start: 0.5673 (OUTLIER) cc_final: 0.5163 (t70) REVERT: C 239 ARG cc_start: 0.7132 (ptp-110) cc_final: 0.6743 (mtt90) REVERT: C 473 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7632 (mm-40) REVERT: D 72 LEU cc_start: 0.8002 (tp) cc_final: 0.7800 (tp) REVERT: D 239 ARG cc_start: 0.6976 (ptp-110) cc_final: 0.6679 (mtt90) REVERT: E 115 HIS cc_start: 0.6080 (OUTLIER) cc_final: 0.5772 (t70) REVERT: E 239 ARG cc_start: 0.7071 (ptp-110) cc_final: 0.6850 (mtt90) REVERT: F 115 HIS cc_start: 0.5863 (OUTLIER) cc_final: 0.5436 (t70) REVERT: F 239 ARG cc_start: 0.7107 (ptp-110) cc_final: 0.6721 (mtt90) REVERT: F 473 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7598 (mm-40) outliers start: 74 outliers final: 51 residues processed: 392 average time/residue: 0.2355 time to fit residues: 148.6675 Evaluate side-chains 364 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 308 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain D residue 749 ASP Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain F residue 115 HIS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 404 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 185 optimal weight: 0.0870 chunk 441 optimal weight: 9.9990 chunk 420 optimal weight: 3.9990 chunk 443 optimal weight: 8.9990 chunk 264 optimal weight: 30.0000 chunk 334 optimal weight: 9.9990 chunk 442 optimal weight: 4.9990 chunk 341 optimal weight: 6.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 HIS ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 HIS E 460 ASN ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.135000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.106881 restraints weight = 64792.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.105654 restraints weight = 74811.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.106804 restraints weight = 83115.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.107060 restraints weight = 53644.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.107473 restraints weight = 47595.020| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 35772 Z= 0.166 Angle : 0.647 11.925 48354 Z= 0.314 Chirality : 0.046 0.191 5418 Planarity : 0.004 0.061 6372 Dihedral : 10.180 130.006 4968 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.19 % Allowed : 15.29 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.37 (0.12), residues: 4416 helix: 0.12 (0.12), residues: 1842 sheet: -1.09 (0.19), residues: 678 loop : -1.83 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 359 TYR 0.020 0.002 TYR A 203 PHE 0.015 0.001 PHE F 363 TRP 0.012 0.001 TRP E 454 HIS 0.004 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00382 (35772) covalent geometry : angle 0.64707 (48354) hydrogen bonds : bond 0.03904 ( 1446) hydrogen bonds : angle 4.71515 ( 4140) *********************** 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 443 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 360 time to evaluate : 1.378 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: A 115 HIS cc_start: 0.5940 (OUTLIER) cc_final: 0.5689 (t70) REVERT: A 239 ARG cc_start: 0.6932 (ptp-110) cc_final: 0.6505 (mtm-85) REVERT: A 332 MET cc_start: 0.8814 (tpp) cc_final: 0.8323 (tpp) REVERT: B 115 HIS cc_start: 0.6058 (OUTLIER) cc_final: 0.5766 (t70) REVERT: B 611 MET cc_start: 0.6990 (OUTLIER) cc_final: 0.6769 (ttm) REVERT: C 115 HIS cc_start: 0.5574 (OUTLIER) cc_final: 0.5239 (t70) REVERT: C 239 ARG cc_start: 0.7022 (ptp-110) cc_final: 0.6633 (mtm-85) REVERT: C 473 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7495 (mm-40) REVERT: D 115 HIS cc_start: 0.5884 (OUTLIER) cc_final: 0.5628 (t70) REVERT: D 239 ARG cc_start: 0.6974 (ptp-110) cc_final: 0.6577 (mtm-85) REVERT: E 115 HIS cc_start: 0.5894 (OUTLIER) cc_final: 0.5613 (t70) REVERT: E 351 ASN cc_start: 0.7690 (p0) cc_final: 0.7458 (p0) REVERT: F 115 HIS cc_start: 0.5709 (OUTLIER) cc_final: 0.5423 (t70) REVERT: F 239 ARG cc_start: 0.7061 (ptp-110) cc_final: 0.6628 (mtm-85) REVERT: F 473 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7499 (mm-40) outliers start: 83 outliers final: 59 residues processed: 417 average time/residue: 0.2239 time to fit residues: 152.5247 Evaluate side-chains 397 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 331 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 732 ARG Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 115 HIS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 732 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 115 optimal weight: 10.0000 chunk 404 optimal weight: 0.9990 chunk 260 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 chunk 61 optimal weight: 0.0980 chunk 336 optimal weight: 9.9990 chunk 392 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN C 602 ASN D 406 HIS D 460 ASN D 494 GLN E 460 ASN ** E 494 GLN ** 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 = 0.3835 r_free = 0.3835 target = 0.136657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.108162 restraints weight = 64738.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.106481 restraints weight = 74581.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.107914 restraints weight = 76793.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.108153 restraints weight = 50221.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.108782 restraints weight = 46549.298| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35772 Z= 0.122 Angle : 0.625 10.734 48354 Z= 0.300 Chirality : 0.045 0.175 5418 Planarity : 0.004 0.060 6372 Dihedral : 9.538 135.565 4968 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.93 % Allowed : 16.30 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.12), residues: 4416 helix: 0.37 (0.12), residues: 1854 sheet: -0.87 (0.19), residues: 678 loop : -1.75 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 662 TYR 0.018 0.002 TYR D 203 PHE 0.011 0.001 PHE F 363 TRP 0.013 0.001 TRP E 454 HIS 0.002 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00280 (35772) covalent geometry : angle 0.62500 (48354) hydrogen bonds : bond 0.03541 ( 1446) hydrogen bonds : angle 4.48535 ( 4140) *********************** 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 451 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 378 time to evaluate : 1.309 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: A 115 HIS cc_start: 0.5888 (OUTLIER) cc_final: 0.5681 (t70) REVERT: A 239 ARG cc_start: 0.6892 (ptp-110) cc_final: 0.6448 (mtm-85) REVERT: A 332 MET cc_start: 0.8827 (tpp) cc_final: 0.8330 (tpp) REVERT: B 115 HIS cc_start: 0.5970 (OUTLIER) cc_final: 0.5577 (t70) REVERT: B 458 GLN cc_start: 0.7605 (pm20) cc_final: 0.7310 (pm20) REVERT: C 115 HIS cc_start: 0.5622 (OUTLIER) cc_final: 0.5384 (t70) REVERT: C 239 ARG cc_start: 0.7009 (ptp-110) cc_final: 0.6615 (mtm-85) REVERT: D 239 ARG cc_start: 0.6918 (ptp-110) cc_final: 0.6521 (mtm-85) REVERT: D 494 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7319 (mp10) REVERT: E 351 ASN cc_start: 0.7730 (p0) cc_final: 0.7508 (p0) REVERT: E 458 GLN cc_start: 0.7642 (pm20) cc_final: 0.7337 (pm20) REVERT: F 115 HIS cc_start: 0.5691 (OUTLIER) cc_final: 0.5461 (t70) REVERT: F 239 ARG cc_start: 0.6983 (ptp-110) cc_final: 0.6559 (mtm110) outliers start: 73 outliers final: 53 residues processed: 427 average time/residue: 0.2125 time to fit residues: 149.4181 Evaluate side-chains 395 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 337 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 732 ARG Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 115 HIS Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 732 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 260 optimal weight: 0.3980 chunk 364 optimal weight: 6.9990 chunk 304 optimal weight: 40.0000 chunk 52 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 308 optimal weight: 30.0000 chunk 274 optimal weight: 10.0000 chunk 349 optimal weight: 8.9990 chunk 177 optimal weight: 8.9990 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 GLN D 750 ASN E 33 ASN ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.133888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.106005 restraints weight = 65318.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.104598 restraints weight = 77392.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.105784 restraints weight = 84731.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.106004 restraints weight = 58004.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.107020 restraints weight = 51242.487| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 35772 Z= 0.204 Angle : 0.682 13.661 48354 Z= 0.328 Chirality : 0.047 0.173 5418 Planarity : 0.004 0.060 6372 Dihedral : 9.515 142.919 4968 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.25 % Allowed : 17.22 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.15 (0.12), residues: 4416 helix: 0.33 (0.12), residues: 1860 sheet: -0.87 (0.19), residues: 678 loop : -1.82 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 753 TYR 0.031 0.002 TYR C 203 PHE 0.014 0.001 PHE F 363 TRP 0.017 0.002 TRP B 454 HIS 0.003 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00477 (35772) covalent geometry : angle 0.68201 (48354) hydrogen bonds : bond 0.03973 ( 1446) hydrogen bonds : angle 4.60085 ( 4140) *********************** 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 429 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 344 time to evaluate : 1.303 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: A 115 HIS cc_start: 0.5931 (OUTLIER) cc_final: 0.5694 (t70) REVERT: A 239 ARG cc_start: 0.7029 (ptp-110) cc_final: 0.6466 (mtm-85) REVERT: A 332 MET cc_start: 0.8825 (tpp) cc_final: 0.8313 (tpp) REVERT: B 115 HIS cc_start: 0.6073 (OUTLIER) cc_final: 0.5664 (t70) REVERT: B 504 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8682 (tp) REVERT: C 115 HIS cc_start: 0.5792 (OUTLIER) cc_final: 0.5556 (t70) REVERT: C 239 ARG cc_start: 0.7111 (ptp-110) cc_final: 0.6639 (mtm110) REVERT: C 332 MET cc_start: 0.8796 (mmm) cc_final: 0.8592 (mmm) REVERT: D 84 MET cc_start: 0.5203 (tmm) cc_final: 0.4927 (tmm) REVERT: D 239 ARG cc_start: 0.7025 (ptp-110) cc_final: 0.6553 (mtm-85) REVERT: E 504 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8678 (tp) REVERT: F 115 HIS cc_start: 0.5780 (OUTLIER) cc_final: 0.5542 (t70) REVERT: F 239 ARG cc_start: 0.7133 (ptp-110) cc_final: 0.6652 (mtm110) outliers start: 85 outliers final: 68 residues processed: 407 average time/residue: 0.2138 time to fit residues: 142.0707 Evaluate side-chains 403 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 329 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 732 ARG Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 115 HIS Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 732 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 302 optimal weight: 20.0000 chunk 371 optimal weight: 30.0000 chunk 55 optimal weight: 5.9990 chunk 309 optimal weight: 20.0000 chunk 417 optimal weight: 4.9990 chunk 1 optimal weight: 30.0000 chunk 254 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 404 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 265 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 750 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 494 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.134545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106266 restraints weight = 65371.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.105129 restraints weight = 71398.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.106284 restraints weight = 76382.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.106528 restraints weight = 49117.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.106900 restraints weight = 45128.434| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 35772 Z= 0.169 Angle : 0.656 12.489 48354 Z= 0.314 Chirality : 0.046 0.170 5418 Planarity : 0.004 0.061 6372 Dihedral : 9.227 147.957 4968 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.56 % Allowed : 17.88 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.12), residues: 4416 helix: 0.47 (0.12), residues: 1860 sheet: -0.70 (0.20), residues: 642 loop : -1.75 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 635 TYR 0.020 0.002 TYR B 244 PHE 0.014 0.001 PHE F 363 TRP 0.013 0.002 TRP A 454 HIS 0.002 0.001 HIS D 406 Details of bonding type rmsd covalent geometry : bond 0.00393 (35772) covalent geometry : angle 0.65609 (48354) hydrogen bonds : bond 0.03737 ( 1446) hydrogen bonds : angle 4.51759 ( 4140) *********************** 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 443 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 346 time to evaluate : 1.382 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: A 239 ARG cc_start: 0.7136 (ptp-110) cc_final: 0.6649 (mtm-85) REVERT: A 332 MET cc_start: 0.8848 (tpp) cc_final: 0.8419 (tpp) REVERT: A 473 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7332 (mm-40) REVERT: B 84 MET cc_start: 0.5427 (tmm) cc_final: 0.5194 (tmm) REVERT: B 504 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8656 (tp) REVERT: C 115 HIS cc_start: 0.5707 (OUTLIER) cc_final: 0.5481 (t70) REVERT: C 239 ARG cc_start: 0.7219 (ptp-110) cc_final: 0.6714 (mtm110) REVERT: C 332 MET cc_start: 0.8824 (mmm) cc_final: 0.8582 (mmm) REVERT: D 239 ARG cc_start: 0.7207 (ptp-110) cc_final: 0.6756 (mtm-85) REVERT: D 473 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7389 (mm-40) REVERT: E 494 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7407 (mt0) REVERT: E 504 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8677 (tp) REVERT: F 115 HIS cc_start: 0.5765 (OUTLIER) cc_final: 0.5551 (t70) REVERT: F 239 ARG cc_start: 0.7115 (ptp-110) cc_final: 0.6664 (mtm110) outliers start: 97 outliers final: 72 residues processed: 419 average time/residue: 0.2156 time to fit residues: 149.5520 Evaluate side-chains 408 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 331 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 732 ARG Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 115 HIS Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 732 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 328 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 235 optimal weight: 20.0000 chunk 371 optimal weight: 40.0000 chunk 338 optimal weight: 20.0000 chunk 144 optimal weight: 7.9990 chunk 333 optimal weight: 6.9990 chunk 224 optimal weight: 0.6980 chunk 231 optimal weight: 6.9990 chunk 379 optimal weight: 6.9990 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN E 33 ASN E 538 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.133260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.105111 restraints weight = 65555.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.103720 restraints weight = 74331.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.105006 restraints weight = 82620.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.105217 restraints weight = 52959.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.105773 restraints weight = 48984.611| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 35772 Z= 0.213 Angle : 0.698 11.949 48354 Z= 0.336 Chirality : 0.047 0.172 5418 Planarity : 0.005 0.061 6372 Dihedral : 9.114 150.269 4968 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.43 % Allowed : 18.12 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.05 (0.12), residues: 4416 helix: 0.40 (0.12), residues: 1860 sheet: -0.75 (0.20), residues: 642 loop : -1.76 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 25 TYR 0.022 0.002 TYR C 244 PHE 0.016 0.001 PHE F 363 TRP 0.013 0.002 TRP F 454 HIS 0.004 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00497 (35772) covalent geometry : angle 0.69791 (48354) hydrogen bonds : bond 0.04021 ( 1446) hydrogen bonds : angle 4.63334 ( 4140) *********************** 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 428 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 336 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: A 239 ARG cc_start: 0.7215 (ptp-110) cc_final: 0.6700 (mtm-85) REVERT: A 332 MET cc_start: 0.8807 (tpp) cc_final: 0.8480 (tpp) REVERT: A 473 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7374 (mm-40) REVERT: B 84 MET cc_start: 0.5642 (tmm) cc_final: 0.5418 (tmm) REVERT: B 504 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8673 (tp) REVERT: C 115 HIS cc_start: 0.5809 (OUTLIER) cc_final: 0.5583 (t70) REVERT: C 239 ARG cc_start: 0.7196 (ptp-110) cc_final: 0.6756 (mtm110) REVERT: C 489 LEU cc_start: 0.9388 (mm) cc_final: 0.9139 (mm) REVERT: D 239 ARG cc_start: 0.7332 (ptp-110) cc_final: 0.6881 (mtm-85) REVERT: D 473 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7428 (mm-40) REVERT: E 504 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8716 (tp) REVERT: F 239 ARG cc_start: 0.7151 (ptp-110) cc_final: 0.6740 (mtm110) REVERT: F 489 LEU cc_start: 0.9423 (mm) cc_final: 0.9169 (mm) outliers start: 92 outliers final: 78 residues processed: 406 average time/residue: 0.2230 time to fit residues: 148.4628 Evaluate side-chains 407 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 326 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 732 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 260 optimal weight: 2.9990 chunk 224 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 258 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 335 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.136056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.107893 restraints weight = 65006.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.106514 restraints weight = 73883.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.107856 restraints weight = 78432.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.108068 restraints weight = 51118.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.108493 restraints weight = 46829.850| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35772 Z= 0.117 Angle : 0.656 13.942 48354 Z= 0.312 Chirality : 0.045 0.169 5418 Planarity : 0.004 0.059 6372 Dihedral : 8.799 148.019 4968 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.72 % Allowed : 19.15 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.72 (0.13), residues: 4416 helix: 0.71 (0.12), residues: 1860 sheet: -0.56 (0.21), residues: 642 loop : -1.64 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 732 TYR 0.019 0.002 TYR F 138 PHE 0.010 0.001 PHE F 363 TRP 0.009 0.001 TRP B 454 HIS 0.007 0.001 HIS C 735 Details of bonding type rmsd covalent geometry : bond 0.00268 (35772) covalent geometry : angle 0.65561 (48354) hydrogen bonds : bond 0.03359 ( 1446) hydrogen bonds : angle 4.37309 ( 4140) *********************** 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 419 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 354 time to evaluate : 1.433 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: A 239 ARG cc_start: 0.7294 (ptp-110) cc_final: 0.6741 (mtm-85) REVERT: A 332 MET cc_start: 0.8812 (tpp) cc_final: 0.8252 (tpp) REVERT: A 473 GLN cc_start: 0.7598 (mm-40) cc_final: 0.7342 (mm-40) REVERT: A 635 ARG cc_start: 0.7927 (ttp-110) cc_final: 0.7621 (mtp-110) REVERT: C 239 ARG cc_start: 0.7247 (ptp-110) cc_final: 0.6743 (mtm110) REVERT: D 239 ARG cc_start: 0.7253 (ptp-110) cc_final: 0.6743 (mtm-85) REVERT: D 473 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7367 (mm-40) REVERT: F 239 ARG cc_start: 0.7070 (ptp-110) cc_final: 0.6652 (mtm110) outliers start: 65 outliers final: 53 residues processed: 399 average time/residue: 0.2173 time to fit residues: 142.0800 Evaluate side-chains 387 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 334 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 732 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 194 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 158 optimal weight: 0.0570 chunk 250 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 134 optimal weight: 0.0980 chunk 323 optimal weight: 2.9990 chunk 317 optimal weight: 0.0010 chunk 220 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.6308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 406 HIS E 460 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.137528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.109594 restraints weight = 65007.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.108311 restraints weight = 80454.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.109805 restraints weight = 79943.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.110031 restraints weight = 50498.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.111036 restraints weight = 46795.217| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35772 Z= 0.111 Angle : 0.664 10.579 48354 Z= 0.313 Chirality : 0.045 0.198 5418 Planarity : 0.004 0.059 6372 Dihedral : 8.633 146.215 4968 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.56 % Allowed : 19.70 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.55 (0.13), residues: 4416 helix: 0.83 (0.12), residues: 1866 sheet: -0.46 (0.21), residues: 642 loop : -1.53 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 25 TYR 0.022 0.002 TYR C 138 PHE 0.009 0.001 PHE F 363 TRP 0.008 0.001 TRP F 454 HIS 0.003 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00249 (35772) covalent geometry : angle 0.66382 (48354) hydrogen bonds : bond 0.03171 ( 1446) hydrogen bonds : angle 4.23437 ( 4140) ********************** 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 432 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 373 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.7137 (ptp-110) cc_final: 0.6630 (mtm-85) REVERT: A 332 MET cc_start: 0.8812 (tpp) cc_final: 0.8267 (tpp) REVERT: A 473 GLN cc_start: 0.7516 (mm-40) cc_final: 0.7299 (mm-40) REVERT: A 635 ARG cc_start: 0.7917 (ttp-110) cc_final: 0.7613 (mtp-110) REVERT: C 239 ARG cc_start: 0.7232 (ptp-110) cc_final: 0.6793 (mtm110) REVERT: C 332 MET cc_start: 0.8671 (mmm) cc_final: 0.8471 (mmm) REVERT: D 239 ARG cc_start: 0.7133 (ptp-110) cc_final: 0.6665 (mtm-85) REVERT: D 473 GLN cc_start: 0.7519 (mm-40) cc_final: 0.7317 (mm-40) REVERT: D 635 ARG cc_start: 0.7935 (ttp-110) cc_final: 0.7619 (mtp-110) REVERT: F 239 ARG cc_start: 0.7222 (ptp-110) cc_final: 0.6711 (mtm110) outliers start: 59 outliers final: 52 residues processed: 418 average time/residue: 0.2101 time to fit residues: 144.4405 Evaluate side-chains 398 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 346 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 732 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 94 optimal weight: 3.9990 chunk 237 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 428 optimal weight: 5.9990 chunk 389 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 177 optimal weight: 0.1980 chunk 199 optimal weight: 0.1980 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 HIS ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 616 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 = 0.3821 r_free = 0.3821 target = 0.135696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.107450 restraints weight = 64968.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.105929 restraints weight = 77675.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.107376 restraints weight = 77682.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.107554 restraints weight = 51608.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.108230 restraints weight = 47591.395| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35772 Z= 0.147 Angle : 0.683 13.258 48354 Z= 0.322 Chirality : 0.046 0.235 5418 Planarity : 0.004 0.059 6372 Dihedral : 8.650 146.152 4968 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.64 % Allowed : 19.81 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.54 (0.13), residues: 4416 helix: 0.86 (0.12), residues: 1854 sheet: -0.50 (0.21), residues: 642 loop : -1.52 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 753 TYR 0.017 0.002 TYR F 138 PHE 0.010 0.001 PHE F 363 TRP 0.015 0.001 TRP B 454 HIS 0.003 0.001 HIS E 183 Details of bonding type rmsd covalent geometry : bond 0.00342 (35772) covalent geometry : angle 0.68288 (48354) hydrogen bonds : bond 0.03391 ( 1446) hydrogen bonds : angle 4.31276 ( 4140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4677.57 seconds wall clock time: 82 minutes 9.66 seconds (4929.66 seconds total)