Starting phenix.real_space_refine on Fri Mar 22 21:12:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftj_3295/03_2024/5ftj_3295_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftj_3295/03_2024/5ftj_3295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftj_3295/03_2024/5ftj_3295.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftj_3295/03_2024/5ftj_3295.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftj_3295/03_2024/5ftj_3295_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftj_3295/03_2024/5ftj_3295_updated.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 24 5.49 5 S 180 5.16 5 C 21654 2.51 5 N 6066 2.21 5 O 6672 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34602 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5659 Classifications: {'peptide': 723} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 36, 'TRANS': 682} Chain breaks: 1 Chain: "B" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5659 Classifications: {'peptide': 723} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 36, 'TRANS': 682} Chain breaks: 1 Chain: "C" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5659 Classifications: {'peptide': 723} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 36, 'TRANS': 682} Chain breaks: 1 Chain: "D" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5659 Classifications: {'peptide': 723} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 36, 'TRANS': 682} Chain breaks: 1 Chain: "E" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5659 Classifications: {'peptide': 723} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 36, 'TRANS': 682} Chain breaks: 1 Chain: "F" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5659 Classifications: {'peptide': 723} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 36, 'TRANS': 682} Chain breaks: 1 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 88 Unusual residues: {'ADP': 2, 'OJA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 88 Unusual residues: {'ADP': 2, 'OJA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 88 Unusual residues: {'ADP': 2, 'OJA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 88 Unusual residues: {'ADP': 2, 'OJA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 88 Unusual residues: {'ADP': 2, 'OJA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 88 Unusual residues: {'ADP': 2, 'OJA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "F" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Time building chain proxies: 17.14, per 1000 atoms: 0.50 Number of scatterers: 34602 At special positions: 0 Unit cell: (168.805, 180.271, 98.735, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 180 16.00 P 24 15.00 F 6 9.00 O 6672 8.00 N 6066 7.00 C 21654 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 - 3.50 Amino acid : False - 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: 13.33 Conformation dependent library (CDL) restraints added in 6.2 seconds 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8100 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 174 helices and 30 sheets defined 37.3% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.81 Creating SS restraints... Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 135 through 138 No H-bonds generated for 'chain 'A' and resid 135 through 138' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 213 through 225 removed outlier: 3.508A pdb=" N MET A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 232 removed outlier: 4.225A pdb=" N LYS A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 232' Processing helix chain 'A' and resid 251 through 262 removed outlier: 3.629A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 276 No H-bonds generated for 'chain 'A' and resid 273 through 276' Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.534A pdb=" N ALA A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 320 through 333 Processing helix chain 'A' and resid 355 through 358 removed outlier: 3.533A pdb=" N ARG A 358 " --> pdb=" O PRO A 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 355 through 358' Processing helix chain 'A' and resid 374 through 384 removed outlier: 4.589A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 Processing helix chain 'A' and resid 408 through 425 removed outlier: 3.812A pdb=" N ALA A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 483 through 498 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 500 through 505 removed outlier: 3.559A pdb=" N LYS A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 534 removed outlier: 3.516A pdb=" N ILE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'A' and resid 557 through 568 removed outlier: 3.544A pdb=" N ARG A 560 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A 561 " --> pdb=" O ASN A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 599 through 609 removed outlier: 3.542A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 634 Processing helix chain 'A' and resid 650 through 660 Processing helix chain 'A' and resid 672 through 678 removed outlier: 3.981A pdb=" N ALA A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 706 removed outlier: 3.550A pdb=" N ILE A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 742 removed outlier: 3.958A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 762 removed outlier: 3.918A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS A 754 " --> pdb=" O ASN A 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 92 Processing helix chain 'B' and resid 135 through 138 No H-bonds generated for 'chain 'B' and resid 135 through 138' Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 213 through 225 removed outlier: 3.508A pdb=" N MET B 219 " --> pdb=" O GLN B 215 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 232 removed outlier: 4.224A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 232' Processing helix chain 'B' and resid 251 through 262 removed outlier: 3.629A pdb=" N ALA B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 276 No H-bonds generated for 'chain 'B' and resid 273 through 276' Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.534A pdb=" N ALA B 289 " --> pdb=" O ASN B 285 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 320 through 333 Processing helix chain 'B' and resid 355 through 358 removed outlier: 3.533A pdb=" N ARG B 358 " --> pdb=" O PRO B 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 355 through 358' Processing helix chain 'B' and resid 374 through 384 removed outlier: 4.589A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 380 " --> pdb=" O GLY B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 401 Processing helix chain 'B' and resid 408 through 425 removed outlier: 3.812A pdb=" N ALA B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 429 No H-bonds generated for 'chain 'B' and resid 427 through 429' Processing helix chain 'B' and resid 449 through 458 Processing helix chain 'B' and resid 483 through 498 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 505 removed outlier: 3.559A pdb=" N LYS B 505 " --> pdb=" O ASP B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 534 removed outlier: 3.516A pdb=" N ILE B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 552 Processing helix chain 'B' and resid 557 through 568 removed outlier: 3.543A pdb=" N ARG B 560 " --> pdb=" O ALA B 557 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B 561 " --> pdb=" O ASN B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 585 Processing helix chain 'B' and resid 599 through 609 removed outlier: 3.542A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 634 Processing helix chain 'B' and resid 650 through 660 Processing helix chain 'B' and resid 672 through 678 removed outlier: 3.980A pdb=" N ALA B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 706 removed outlier: 3.550A pdb=" N ILE B 690 " --> pdb=" O ASP B 686 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 742 removed outlier: 3.959A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 762 removed outlier: 3.919A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 135 through 138 No H-bonds generated for 'chain 'C' and resid 135 through 138' Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 213 through 225 removed outlier: 3.508A pdb=" N MET C 219 " --> pdb=" O GLN C 215 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 232 removed outlier: 4.224A pdb=" N LYS C 231 " --> pdb=" O PRO C 227 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 227 through 232' Processing helix chain 'C' and resid 251 through 262 removed outlier: 3.629A pdb=" N ALA C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 276 No H-bonds generated for 'chain 'C' and resid 273 through 276' Processing helix chain 'C' and resid 281 through 295 removed outlier: 3.534A pdb=" N ALA C 289 " --> pdb=" O ASN C 285 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 320 through 333 Processing helix chain 'C' and resid 355 through 358 removed outlier: 3.533A pdb=" N ARG C 358 " --> pdb=" O PRO C 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 355 through 358' Processing helix chain 'C' and resid 374 through 384 removed outlier: 4.589A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 380 " --> pdb=" O GLY C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 401 Processing helix chain 'C' and resid 408 through 425 removed outlier: 3.812A pdb=" N ALA C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 423 " --> pdb=" O ALA C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 429 No H-bonds generated for 'chain 'C' and resid 427 through 429' Processing helix chain 'C' and resid 449 through 458 Processing helix chain 'C' and resid 483 through 498 Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 500 through 505 removed outlier: 3.558A pdb=" N LYS C 505 " --> pdb=" O ASP C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 534 removed outlier: 3.517A pdb=" N ILE C 531 " --> pdb=" O LEU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.544A pdb=" N ARG C 560 " --> pdb=" O ALA C 557 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU C 561 " --> pdb=" O ASN C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 599 through 609 removed outlier: 3.542A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 634 Processing helix chain 'C' and resid 650 through 660 Processing helix chain 'C' and resid 672 through 678 removed outlier: 3.981A pdb=" N ALA C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS C 677 " --> pdb=" O GLU C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 706 removed outlier: 3.549A pdb=" N ILE C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 742 removed outlier: 3.958A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 762 removed outlier: 3.917A pdb=" N ARG C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 92 Processing helix chain 'D' and resid 135 through 138 No H-bonds generated for 'chain 'D' and resid 135 through 138' Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 213 through 225 removed outlier: 3.508A pdb=" N MET D 219 " --> pdb=" O GLN D 215 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 232 removed outlier: 4.224A pdb=" N LYS D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 227 through 232' Processing helix chain 'D' and resid 251 through 262 removed outlier: 3.629A pdb=" N ALA D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 276 No H-bonds generated for 'chain 'D' and resid 273 through 276' Processing helix chain 'D' and resid 281 through 295 removed outlier: 3.534A pdb=" N ALA D 289 " --> pdb=" O ASN D 285 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 320 through 333 Processing helix chain 'D' and resid 355 through 358 removed outlier: 3.533A pdb=" N ARG D 358 " --> pdb=" O PRO D 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 355 through 358' Processing helix chain 'D' and resid 374 through 384 removed outlier: 4.588A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE D 380 " --> pdb=" O GLY D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 401 Processing helix chain 'D' and resid 408 through 425 removed outlier: 3.812A pdb=" N ALA D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 429 No H-bonds generated for 'chain 'D' and resid 427 through 429' Processing helix chain 'D' and resid 449 through 458 Processing helix chain 'D' and resid 483 through 498 Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 500 through 505 removed outlier: 3.559A pdb=" N LYS D 505 " --> pdb=" O ASP D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 534 removed outlier: 3.516A pdb=" N ILE D 531 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 552 Processing helix chain 'D' and resid 557 through 568 removed outlier: 3.544A pdb=" N ARG D 560 " --> pdb=" O ALA D 557 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 561 " --> pdb=" O ASN D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 585 Processing helix chain 'D' and resid 599 through 609 removed outlier: 3.542A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 634 Processing helix chain 'D' and resid 650 through 660 Processing helix chain 'D' and resid 672 through 678 removed outlier: 3.982A pdb=" N ALA D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 706 removed outlier: 3.549A pdb=" N ILE D 690 " --> pdb=" O ASP D 686 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 735 through 742 removed outlier: 3.959A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 762 removed outlier: 3.918A pdb=" N ARG D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 92 Processing helix chain 'E' and resid 135 through 138 No H-bonds generated for 'chain 'E' and resid 135 through 138' Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 213 through 225 removed outlier: 3.508A pdb=" N MET E 219 " --> pdb=" O GLN E 215 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 232 removed outlier: 4.224A pdb=" N LYS E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 227 through 232' Processing helix chain 'E' and resid 251 through 262 removed outlier: 3.629A pdb=" N ALA E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 276 No H-bonds generated for 'chain 'E' and resid 273 through 276' Processing helix chain 'E' and resid 281 through 295 removed outlier: 3.534A pdb=" N ALA E 289 " --> pdb=" O ASN E 285 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 320 through 333 Processing helix chain 'E' and resid 355 through 358 removed outlier: 3.533A pdb=" N ARG E 358 " --> pdb=" O PRO E 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 355 through 358' Processing helix chain 'E' and resid 374 through 384 removed outlier: 4.588A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE E 380 " --> pdb=" O GLY E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 401 Processing helix chain 'E' and resid 408 through 425 removed outlier: 3.813A pdb=" N ALA E 422 " --> pdb=" O ALA E 418 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE E 423 " --> pdb=" O ALA E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 429 No H-bonds generated for 'chain 'E' and resid 427 through 429' Processing helix chain 'E' and resid 449 through 458 Processing helix chain 'E' and resid 483 through 498 Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 500 through 505 removed outlier: 3.559A pdb=" N LYS E 505 " --> pdb=" O ASP E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 534 removed outlier: 3.516A pdb=" N ILE E 531 " --> pdb=" O LEU E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 552 Processing helix chain 'E' and resid 557 through 568 removed outlier: 3.544A pdb=" N ARG E 560 " --> pdb=" O ALA E 557 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU E 561 " --> pdb=" O ASN E 558 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 585 Processing helix chain 'E' and resid 599 through 609 removed outlier: 3.541A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 634 Processing helix chain 'E' and resid 650 through 660 Processing helix chain 'E' and resid 672 through 678 removed outlier: 3.981A pdb=" N ALA E 676 " --> pdb=" O LEU E 672 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 706 removed outlier: 3.549A pdb=" N ILE E 690 " --> pdb=" O ASP E 686 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 735 through 742 removed outlier: 3.958A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 762 removed outlier: 3.918A pdb=" N ARG E 753 " --> pdb=" O ASP E 749 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 92 Processing helix chain 'F' and resid 135 through 138 No H-bonds generated for 'chain 'F' and resid 135 through 138' Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 213 through 225 removed outlier: 3.509A pdb=" N MET F 219 " --> pdb=" O GLN F 215 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 232 removed outlier: 4.225A pdb=" N LYS F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 227 through 232' Processing helix chain 'F' and resid 251 through 262 removed outlier: 3.629A pdb=" N ALA F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU F 261 " --> pdb=" O ALA F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 276 No H-bonds generated for 'chain 'F' and resid 273 through 276' Processing helix chain 'F' and resid 281 through 295 removed outlier: 3.534A pdb=" N ALA F 289 " --> pdb=" O ASN F 285 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 320 through 333 Processing helix chain 'F' and resid 355 through 358 removed outlier: 3.533A pdb=" N ARG F 358 " --> pdb=" O PRO F 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 355 through 358' Processing helix chain 'F' and resid 374 through 384 removed outlier: 4.589A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE F 380 " --> pdb=" O GLY F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 401 Processing helix chain 'F' and resid 408 through 425 removed outlier: 3.813A pdb=" N ALA F 422 " --> pdb=" O ALA F 418 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE F 423 " --> pdb=" O ALA F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 429 No H-bonds generated for 'chain 'F' and resid 427 through 429' Processing helix chain 'F' and resid 449 through 458 Processing helix chain 'F' and resid 483 through 498 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 505 removed outlier: 3.559A pdb=" N LYS F 505 " --> pdb=" O ASP F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 534 removed outlier: 3.517A pdb=" N ILE F 531 " --> pdb=" O LEU F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 552 Processing helix chain 'F' and resid 557 through 568 removed outlier: 3.544A pdb=" N ARG F 560 " --> pdb=" O ALA F 557 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU F 561 " --> pdb=" O ASN F 558 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 585 Processing helix chain 'F' and resid 599 through 609 removed outlier: 3.542A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 634 Processing helix chain 'F' and resid 650 through 660 Processing helix chain 'F' and resid 672 through 678 removed outlier: 3.982A pdb=" N ALA F 676 " --> pdb=" O LEU F 672 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS F 677 " --> pdb=" O GLU F 673 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 706 removed outlier: 3.549A pdb=" N ILE F 690 " --> pdb=" O ASP F 686 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU F 706 " --> pdb=" O SER F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 735 through 742 removed outlier: 3.958A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 762 removed outlier: 3.918A pdb=" N ARG F 753 " --> pdb=" O ASP F 749 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS F 754 " --> pdb=" O ASN F 750 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.320A pdb=" N ILE A 70 " --> pdb=" O VAL A 39 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 57 through 60 removed outlier: 3.745A pdb=" N VAL A 57 " --> pdb=" O CYS A 69 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS A 69 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 153 through 156 removed outlier: 3.675A pdb=" N VAL A 161 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 365 through 368 removed outlier: 3.853A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 641 through 644 removed outlier: 3.662A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.321A pdb=" N ILE B 70 " --> pdb=" O VAL B 39 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 57 through 60 removed outlier: 3.744A pdb=" N VAL B 57 " --> pdb=" O CYS B 69 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS B 69 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 153 through 156 removed outlier: 3.675A pdb=" N VAL B 161 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 365 through 368 removed outlier: 3.853A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 641 through 644 removed outlier: 3.662A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 38 through 40 removed outlier: 6.320A pdb=" N ILE C 70 " --> pdb=" O VAL C 39 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 57 through 60 removed outlier: 3.745A pdb=" N VAL C 57 " --> pdb=" O CYS C 69 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS C 69 " --> pdb=" O VAL C 57 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 153 through 156 removed outlier: 3.675A pdb=" N VAL C 161 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 365 through 368 removed outlier: 3.853A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 641 through 644 removed outlier: 3.662A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 38 through 40 removed outlier: 6.320A pdb=" N ILE D 70 " --> pdb=" O VAL D 39 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'D' and resid 57 through 60 removed outlier: 3.746A pdb=" N VAL D 57 " --> pdb=" O CYS D 69 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS D 69 " --> pdb=" O VAL D 57 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 153 through 156 removed outlier: 3.675A pdb=" N VAL D 161 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 365 through 368 removed outlier: 3.853A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 641 through 644 removed outlier: 3.661A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 38 through 40 removed outlier: 6.321A pdb=" N ILE E 70 " --> pdb=" O VAL E 39 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'E' and resid 57 through 60 removed outlier: 3.745A pdb=" N VAL E 57 " --> pdb=" O CYS E 69 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS E 69 " --> pdb=" O VAL E 57 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 153 through 156 removed outlier: 3.675A pdb=" N VAL E 161 " --> pdb=" O VAL E 154 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 365 through 368 removed outlier: 3.853A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 641 through 644 removed outlier: 3.662A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 38 through 40 removed outlier: 6.321A pdb=" N ILE F 70 " --> pdb=" O VAL F 39 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'F' and resid 57 through 60 removed outlier: 3.745A pdb=" N VAL F 57 " --> pdb=" O CYS F 69 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS F 69 " --> pdb=" O VAL F 57 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 153 through 156 removed outlier: 3.674A pdb=" N VAL F 161 " --> pdb=" O VAL F 154 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 365 through 368 removed outlier: 3.853A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 641 through 644 removed outlier: 3.662A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) 864 hydrogen bonds defined for protein. 2412 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: 11.45 Time building geometry restraints manager: 14.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11253 1.34 - 1.46: 5447 1.46 - 1.58: 18058 1.58 - 1.70: 36 1.70 - 1.82: 288 Bond restraints: 35082 Sorted by residual: bond pdb=" C GLY D 271 " pdb=" N PRO D 272 " ideal model delta sigma weight residual 1.332 1.388 -0.056 8.20e-03 1.49e+04 4.71e+01 bond pdb=" C GLY A 271 " pdb=" N PRO A 272 " ideal model delta sigma weight residual 1.332 1.388 -0.056 8.20e-03 1.49e+04 4.70e+01 bond pdb=" C GLY F 271 " pdb=" N PRO F 272 " ideal model delta sigma weight residual 1.332 1.388 -0.056 8.20e-03 1.49e+04 4.69e+01 bond pdb=" C GLY B 271 " pdb=" N PRO B 272 " ideal model delta sigma weight residual 1.332 1.388 -0.056 8.20e-03 1.49e+04 4.66e+01 bond pdb=" C GLY E 271 " pdb=" N PRO E 272 " ideal model delta sigma weight residual 1.332 1.388 -0.056 8.20e-03 1.49e+04 4.66e+01 ... (remaining 35077 not shown) Histogram of bond angle deviations from ideal: 97.92 - 106.19: 1210 106.19 - 114.45: 20613 114.45 - 122.72: 21595 122.72 - 130.99: 3906 130.99 - 139.25: 136 Bond angle restraints: 47460 Sorted by residual: angle pdb=" N ARG C 599 " pdb=" CA ARG C 599 " pdb=" C ARG C 599 " ideal model delta sigma weight residual 111.28 120.40 -9.12 1.09e+00 8.42e-01 7.01e+01 angle pdb=" N ARG E 599 " pdb=" CA ARG E 599 " pdb=" C ARG E 599 " ideal model delta sigma weight residual 111.28 120.36 -9.08 1.09e+00 8.42e-01 6.94e+01 angle pdb=" N SER D 459 " pdb=" CA SER D 459 " pdb=" C SER D 459 " ideal model delta sigma weight residual 111.28 120.16 -8.88 1.09e+00 8.42e-01 6.64e+01 angle pdb=" N SER A 459 " pdb=" CA SER A 459 " pdb=" C SER A 459 " ideal model delta sigma weight residual 111.28 120.14 -8.86 1.09e+00 8.42e-01 6.61e+01 angle pdb=" N SER C 459 " pdb=" CA SER C 459 " pdb=" C SER C 459 " ideal model delta sigma weight residual 111.28 120.14 -8.86 1.09e+00 8.42e-01 6.61e+01 ... (remaining 47455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.49: 21258 34.49 - 68.99: 366 68.99 - 103.48: 60 103.48 - 137.97: 42 137.97 - 172.47: 6 Dihedral angle restraints: 21732 sinusoidal: 9240 harmonic: 12492 Sorted by residual: dihedral pdb=" O2A ADP E 807 " pdb=" O3A ADP E 807 " pdb=" PA ADP E 807 " pdb=" PB ADP E 807 " ideal model delta sinusoidal sigma weight residual -60.00 112.47 -172.47 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP B 807 " pdb=" O3A ADP B 807 " pdb=" PA ADP B 807 " pdb=" PB ADP B 807 " ideal model delta sinusoidal sigma weight residual -60.00 112.45 -172.45 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP A 807 " pdb=" O3A ADP A 807 " pdb=" PA ADP A 807 " pdb=" PB ADP A 807 " ideal model delta sinusoidal sigma weight residual -60.00 112.44 -172.44 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 21729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3962 0.077 - 0.154: 1173 0.154 - 0.231: 133 0.231 - 0.308: 48 0.308 - 0.385: 6 Chirality restraints: 5322 Sorted by residual: chirality pdb=" CA ARG B 599 " pdb=" N ARG B 599 " pdb=" C ARG B 599 " pdb=" CB ARG B 599 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA ARG C 599 " pdb=" N ARG C 599 " pdb=" C ARG C 599 " pdb=" CB ARG C 599 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA ARG E 599 " pdb=" N ARG E 599 " pdb=" C ARG E 599 " pdb=" CB ARG E 599 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.69e+00 ... (remaining 5319 not shown) Planarity restraints: 6198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 728 " -0.050 5.00e-02 4.00e+02 7.61e-02 9.26e+00 pdb=" N PRO A 729 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 729 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 729 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 728 " -0.050 5.00e-02 4.00e+02 7.60e-02 9.24e+00 pdb=" N PRO C 729 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 729 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 729 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 728 " 0.050 5.00e-02 4.00e+02 7.60e-02 9.24e+00 pdb=" N PRO D 729 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO D 729 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 729 " 0.042 5.00e-02 4.00e+02 ... (remaining 6195 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 306 2.47 - 3.08: 25665 3.08 - 3.68: 53269 3.68 - 4.29: 78974 4.29 - 4.90: 123286 Nonbonded interactions: 281500 Sorted by model distance: nonbonded pdb=" CD2 LEU D 26 " pdb=" O ILE D 100 " model vdw 1.862 3.460 nonbonded pdb=" CD2 LEU E 26 " pdb=" O ILE E 100 " model vdw 1.862 3.460 nonbonded pdb=" CD2 LEU A 26 " pdb=" O ILE A 100 " model vdw 1.863 3.460 nonbonded pdb=" CD2 LEU F 26 " pdb=" O ILE F 100 " model vdw 1.863 3.460 nonbonded pdb=" CD2 LEU C 26 " pdb=" O ILE C 100 " model vdw 1.863 3.460 ... (remaining 281495 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 8.730 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 86.710 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 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 : 0.010 0.099 35082 Z= 0.639 Angle : 1.303 14.252 47460 Z= 0.736 Chirality : 0.072 0.385 5322 Planarity : 0.008 0.076 6198 Dihedral : 15.430 172.467 13632 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 40.83 Ramachandran Plot: Outliers : 0.97 % Allowed : 5.70 % Favored : 93.32 % Rotamer: Outliers : 0.81 % Allowed : 2.93 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.10), residues: 4314 helix: -2.64 (0.10), residues: 1596 sheet: -1.66 (0.18), residues: 546 loop : -1.91 (0.11), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP F 551 HIS 0.020 0.005 HIS F 340 PHE 0.047 0.005 PHE C 360 TYR 0.036 0.005 TYR C 644 ARG 0.020 0.002 ARG F 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 782 time to evaluate : 3.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 GLN cc_start: 0.7359 (tt0) cc_final: 0.7124 (tt0) REVERT: A 222 LEU cc_start: 0.7723 (mt) cc_final: 0.7415 (mm) REVERT: A 236 LYS cc_start: 0.5599 (tptp) cc_final: 0.5292 (tptt) REVERT: A 239 ARG cc_start: 0.5620 (mtt180) cc_final: 0.5145 (mmp-170) REVERT: A 288 LYS cc_start: 0.7113 (ttmt) cc_final: 0.6699 (pttp) REVERT: A 291 GLU cc_start: 0.5898 (tm-30) cc_final: 0.5597 (tm-30) REVERT: A 304 ASP cc_start: 0.7896 (p0) cc_final: 0.7164 (t0) REVERT: A 349 ARG cc_start: 0.6483 (mtt180) cc_final: 0.6163 (mtm-85) REVERT: A 360 PHE cc_start: 0.6345 (t80) cc_final: 0.5989 (t80) REVERT: A 389 LYS cc_start: 0.5271 (tptm) cc_final: 0.4853 (tptt) REVERT: A 397 GLU cc_start: 0.6494 (tt0) cc_final: 0.5974 (tm-30) REVERT: A 470 GLU cc_start: 0.7372 (tt0) cc_final: 0.7130 (pm20) REVERT: A 505 LYS cc_start: 0.6131 (tttm) cc_final: 0.5665 (mmpt) REVERT: A 546 GLU cc_start: 0.8306 (tt0) cc_final: 0.7729 (tp30) REVERT: A 636 PRO cc_start: 0.7356 (Cg_exo) cc_final: 0.7050 (Cg_endo) REVERT: A 638 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6692 (mmt-90) REVERT: A 738 GLU cc_start: 0.6619 (tp30) cc_final: 0.6306 (tt0) REVERT: A 741 ARG cc_start: 0.6288 (mtp-110) cc_final: 0.4841 (tpp-160) REVERT: A 754 LYS cc_start: 0.5869 (mmtt) cc_final: 0.5348 (ptmt) REVERT: B 215 GLN cc_start: 0.7309 (tt0) cc_final: 0.7006 (tt0) REVERT: B 239 ARG cc_start: 0.5667 (mtt180) cc_final: 0.5301 (mmp-170) REVERT: B 288 LYS cc_start: 0.6963 (ttmt) cc_final: 0.6679 (pttp) REVERT: B 291 GLU cc_start: 0.5977 (tm-30) cc_final: 0.5673 (tm-30) REVERT: B 349 ARG cc_start: 0.6494 (mtt180) cc_final: 0.6161 (mtm-85) REVERT: B 397 GLU cc_start: 0.6536 (tt0) cc_final: 0.5942 (tm-30) REVERT: B 465 ARG cc_start: 0.5937 (mmt180) cc_final: 0.5332 (mtt-85) REVERT: B 470 GLU cc_start: 0.7282 (tt0) cc_final: 0.7082 (pm20) REVERT: B 546 GLU cc_start: 0.8313 (tt0) cc_final: 0.7763 (tp30) REVERT: B 636 PRO cc_start: 0.7422 (Cg_exo) cc_final: 0.7120 (Cg_endo) REVERT: B 638 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6797 (mmt-90) REVERT: B 674 PHE cc_start: 0.6233 (t80) cc_final: 0.5957 (t80) REVERT: B 689 GLU cc_start: 0.6955 (tm-30) cc_final: 0.6690 (tm-30) REVERT: B 738 GLU cc_start: 0.6586 (tp30) cc_final: 0.6310 (tt0) REVERT: B 741 ARG cc_start: 0.6253 (mtp-110) cc_final: 0.5665 (mmt-90) REVERT: B 754 LYS cc_start: 0.5778 (mmtt) cc_final: 0.5270 (ptmt) REVERT: C 215 GLN cc_start: 0.7372 (tt0) cc_final: 0.7061 (tt0) REVERT: C 236 LYS cc_start: 0.5821 (tptp) cc_final: 0.5547 (tptt) REVERT: C 239 ARG cc_start: 0.5586 (mtt180) cc_final: 0.5198 (mmp-170) REVERT: C 349 ARG cc_start: 0.6483 (mtt180) cc_final: 0.6078 (mtm-85) REVERT: C 397 GLU cc_start: 0.6537 (tt0) cc_final: 0.5943 (tm-30) REVERT: C 470 GLU cc_start: 0.7348 (tt0) cc_final: 0.7093 (pm20) REVERT: C 495 TYR cc_start: 0.8093 (m-10) cc_final: 0.7832 (m-10) REVERT: C 546 GLU cc_start: 0.8301 (tt0) cc_final: 0.7739 (tp30) REVERT: C 636 PRO cc_start: 0.7515 (Cg_exo) cc_final: 0.7187 (Cg_endo) REVERT: C 638 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.6744 (mmt-90) REVERT: C 650 GLU cc_start: 0.5829 (pm20) cc_final: 0.5611 (pm20) REVERT: C 701 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6599 (tp30) REVERT: C 738 GLU cc_start: 0.6621 (tp30) cc_final: 0.6301 (tt0) REVERT: C 741 ARG cc_start: 0.6334 (mtp-110) cc_final: 0.5727 (mmt-90) REVERT: C 754 LYS cc_start: 0.5888 (mmtt) cc_final: 0.5336 (ptmt) REVERT: D 222 LEU cc_start: 0.7803 (mt) cc_final: 0.7477 (mm) REVERT: D 236 LYS cc_start: 0.5627 (tptp) cc_final: 0.5314 (tptt) REVERT: D 239 ARG cc_start: 0.5593 (mtt180) cc_final: 0.5145 (mmp-170) REVERT: D 288 LYS cc_start: 0.7107 (ttmt) cc_final: 0.6708 (pttp) REVERT: D 291 GLU cc_start: 0.5839 (tm-30) cc_final: 0.5525 (tm-30) REVERT: D 304 ASP cc_start: 0.7864 (p0) cc_final: 0.7180 (t0) REVERT: D 321 GLU cc_start: 0.6732 (tp30) cc_final: 0.6088 (pm20) REVERT: D 349 ARG cc_start: 0.6477 (mtt180) cc_final: 0.6138 (mtm-85) REVERT: D 360 PHE cc_start: 0.6412 (t80) cc_final: 0.6044 (t80) REVERT: D 397 GLU cc_start: 0.6575 (tt0) cc_final: 0.6040 (tm-30) REVERT: D 465 ARG cc_start: 0.5956 (mmt180) cc_final: 0.5483 (mtt-85) REVERT: D 470 GLU cc_start: 0.7401 (tt0) cc_final: 0.7166 (pm20) REVERT: D 546 GLU cc_start: 0.8289 (tt0) cc_final: 0.7723 (tp30) REVERT: D 636 PRO cc_start: 0.7338 (Cg_exo) cc_final: 0.7016 (Cg_endo) REVERT: D 638 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.6751 (mmt-90) REVERT: D 738 GLU cc_start: 0.6608 (tp30) cc_final: 0.6326 (tt0) REVERT: D 741 ARG cc_start: 0.6255 (mtp-110) cc_final: 0.4841 (tpp-160) REVERT: D 754 LYS cc_start: 0.5859 (mmtt) cc_final: 0.5341 (ptmt) REVERT: E 215 GLN cc_start: 0.7308 (tt0) cc_final: 0.7001 (tt0) REVERT: E 239 ARG cc_start: 0.5660 (mtt180) cc_final: 0.5293 (mmp-170) REVERT: E 288 LYS cc_start: 0.6981 (ttmt) cc_final: 0.6697 (pttp) REVERT: E 291 GLU cc_start: 0.5952 (tm-30) cc_final: 0.5645 (tm-30) REVERT: E 349 ARG cc_start: 0.6505 (mtt180) cc_final: 0.6172 (mtm-85) REVERT: E 397 GLU cc_start: 0.6537 (tt0) cc_final: 0.5937 (tm-30) REVERT: E 465 ARG cc_start: 0.5929 (mmt180) cc_final: 0.5323 (mtt-85) REVERT: E 546 GLU cc_start: 0.8314 (tt0) cc_final: 0.7760 (tp30) REVERT: E 636 PRO cc_start: 0.7416 (Cg_exo) cc_final: 0.7111 (Cg_endo) REVERT: E 638 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.6795 (mmt-90) REVERT: E 650 GLU cc_start: 0.5877 (pm20) cc_final: 0.5672 (pm20) REVERT: E 674 PHE cc_start: 0.6240 (t80) cc_final: 0.5968 (t80) REVERT: E 689 GLU cc_start: 0.6958 (tm-30) cc_final: 0.6696 (tm-30) REVERT: E 738 GLU cc_start: 0.6562 (tp30) cc_final: 0.6333 (tt0) REVERT: E 741 ARG cc_start: 0.6242 (mtp-110) cc_final: 0.5660 (mmt-90) REVERT: E 754 LYS cc_start: 0.5788 (mmtt) cc_final: 0.5536 (ttpt) REVERT: F 215 GLN cc_start: 0.7374 (tt0) cc_final: 0.7064 (tt0) REVERT: F 236 LYS cc_start: 0.5822 (tptp) cc_final: 0.5546 (tptt) REVERT: F 239 ARG cc_start: 0.5599 (mtt180) cc_final: 0.5208 (mmp-170) REVERT: F 288 LYS cc_start: 0.7054 (ttmt) cc_final: 0.6833 (pttt) REVERT: F 291 GLU cc_start: 0.5962 (tm-30) cc_final: 0.5691 (tm-30) REVERT: F 321 GLU cc_start: 0.6487 (tp30) cc_final: 0.5947 (pm20) REVERT: F 349 ARG cc_start: 0.6480 (mtt180) cc_final: 0.6073 (mtm-85) REVERT: F 397 GLU cc_start: 0.6540 (tt0) cc_final: 0.5941 (tm-30) REVERT: F 470 GLU cc_start: 0.7367 (tt0) cc_final: 0.7100 (pm20) REVERT: F 495 TYR cc_start: 0.8095 (m-10) cc_final: 0.7860 (m-10) REVERT: F 546 GLU cc_start: 0.8303 (tt0) cc_final: 0.7737 (tp30) REVERT: F 636 PRO cc_start: 0.7500 (Cg_exo) cc_final: 0.7178 (Cg_endo) REVERT: F 638 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.6755 (mmt-90) REVERT: F 650 GLU cc_start: 0.5815 (pm20) cc_final: 0.5576 (pm20) REVERT: F 701 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6630 (tp30) REVERT: F 738 GLU cc_start: 0.6630 (tp30) cc_final: 0.6303 (tt0) REVERT: F 741 ARG cc_start: 0.6331 (mtp-110) cc_final: 0.5729 (mmt-90) REVERT: F 754 LYS cc_start: 0.5917 (mmtt) cc_final: 0.5366 (ptmt) outliers start: 30 outliers final: 15 residues processed: 806 average time/residue: 1.7867 time to fit residues: 1659.7510 Evaluate side-chains 534 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 513 time to evaluate : 3.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 669 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 638 ARG Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 638 ARG Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 638 ARG Chi-restraints excluded: chain E residue 669 ASP Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 638 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 20.0000 chunk 327 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 220 optimal weight: 20.0000 chunk 174 optimal weight: 2.9990 chunk 338 optimal weight: 0.0170 chunk 131 optimal weight: 6.9990 chunk 205 optimal weight: 9.9990 chunk 252 optimal weight: 5.9990 chunk 392 optimal weight: 6.9990 overall best weight: 4.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN A 226 HIS A 533 ASN A 536 GLN A 568 GLN A 603 GLN A 616 ASN A 692 GLN A 763 GLN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN B 226 HIS B 533 ASN B 536 GLN B 568 GLN B 603 GLN B 616 ASN B 692 GLN B 763 GLN ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 GLN C 226 HIS C 533 ASN C 536 GLN C 568 GLN C 603 GLN C 616 ASN C 692 GLN C 763 GLN ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 GLN D 226 HIS D 533 ASN D 536 GLN D 568 GLN D 603 GLN D 616 ASN D 692 GLN D 763 GLN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 GLN E 226 HIS E 533 ASN E 536 GLN E 568 GLN E 603 GLN E 616 ASN E 692 GLN E 763 GLN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 GLN F 226 HIS F 533 ASN F 536 GLN F 568 GLN F 603 GLN F 616 ASN F 692 GLN F 763 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 35082 Z= 0.288 Angle : 0.860 10.595 47460 Z= 0.427 Chirality : 0.051 0.230 5322 Planarity : 0.006 0.067 6198 Dihedral : 14.427 147.613 5033 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.19 % Favored : 94.39 % Rotamer: Outliers : 3.90 % Allowed : 11.44 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.11), residues: 4314 helix: -1.58 (0.11), residues: 1596 sheet: -1.04 (0.20), residues: 588 loop : -1.65 (0.12), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 551 HIS 0.011 0.002 HIS B 340 PHE 0.027 0.002 PHE B 360 TYR 0.014 0.002 TYR E 495 ARG 0.006 0.001 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 634 time to evaluate : 3.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 GLN cc_start: 0.7155 (tt0) cc_final: 0.6862 (tt0) REVERT: A 224 LEU cc_start: 0.7191 (mt) cc_final: 0.6880 (pp) REVERT: A 239 ARG cc_start: 0.5651 (mtt180) cc_final: 0.5269 (mmp-170) REVERT: A 270 ASN cc_start: 0.7266 (t0) cc_final: 0.6903 (t0) REVERT: A 288 LYS cc_start: 0.7212 (ttmt) cc_final: 0.6829 (tmmt) REVERT: A 304 ASP cc_start: 0.7935 (p0) cc_final: 0.7215 (t70) REVERT: A 349 ARG cc_start: 0.6491 (mtt180) cc_final: 0.6158 (mtp-110) REVERT: A 360 PHE cc_start: 0.6131 (t80) cc_final: 0.5742 (t80) REVERT: A 397 GLU cc_start: 0.6154 (tt0) cc_final: 0.5693 (tm-30) REVERT: A 427 MET cc_start: 0.4034 (mmm) cc_final: 0.3827 (mmt) REVERT: A 440 GLU cc_start: 0.4683 (tm-30) cc_final: 0.4397 (mt-10) REVERT: A 456 LEU cc_start: 0.7075 (tp) cc_final: 0.6825 (mt) REVERT: A 458 GLN cc_start: 0.6953 (mm110) cc_final: 0.6751 (mm-40) REVERT: A 470 GLU cc_start: 0.7395 (tt0) cc_final: 0.7135 (pm20) REVERT: A 546 GLU cc_start: 0.8179 (tt0) cc_final: 0.7613 (tp30) REVERT: A 567 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6993 (ttm-80) REVERT: A 633 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7811 (mm) REVERT: A 693 ARG cc_start: 0.7170 (tpp80) cc_final: 0.6783 (mmt180) REVERT: A 741 ARG cc_start: 0.6232 (mtp-110) cc_final: 0.5569 (mmt-90) REVERT: A 753 ARG cc_start: 0.5500 (mtp180) cc_final: 0.5152 (mtp-110) REVERT: A 754 LYS cc_start: 0.5987 (mmtt) cc_final: 0.5488 (ttpt) REVERT: A 757 MET cc_start: 0.6683 (ttm) cc_final: 0.6247 (ptm) REVERT: B 215 GLN cc_start: 0.7188 (tt0) cc_final: 0.6845 (tt0) REVERT: B 224 LEU cc_start: 0.7213 (mt) cc_final: 0.6854 (pp) REVERT: B 239 ARG cc_start: 0.5622 (mtt180) cc_final: 0.5230 (mmp-170) REVERT: B 270 ASN cc_start: 0.7319 (t0) cc_final: 0.6993 (t0) REVERT: B 288 LYS cc_start: 0.7177 (ttmt) cc_final: 0.6797 (tmmt) REVERT: B 349 ARG cc_start: 0.6585 (mtt180) cc_final: 0.6213 (mtm-85) REVERT: B 397 GLU cc_start: 0.6145 (tt0) cc_final: 0.5624 (tm-30) REVERT: B 434 ASP cc_start: 0.2840 (OUTLIER) cc_final: 0.2158 (t0) REVERT: B 456 LEU cc_start: 0.7090 (tp) cc_final: 0.6756 (mt) REVERT: B 465 ARG cc_start: 0.6008 (mmt180) cc_final: 0.5171 (mtt-85) REVERT: B 470 GLU cc_start: 0.7335 (tt0) cc_final: 0.7062 (pm20) REVERT: B 491 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6390 (mm-30) REVERT: B 546 GLU cc_start: 0.8195 (tt0) cc_final: 0.7609 (tp30) REVERT: B 567 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.6996 (ttm-80) REVERT: B 578 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6923 (mt-10) REVERT: B 638 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6437 (mmt-90) REVERT: B 693 ARG cc_start: 0.7229 (tpp80) cc_final: 0.6803 (ttm-80) REVERT: B 741 ARG cc_start: 0.6348 (mtp-110) cc_final: 0.5643 (mmt-90) REVERT: B 754 LYS cc_start: 0.6032 (mmtt) cc_final: 0.5675 (ttpt) REVERT: B 758 PHE cc_start: 0.6542 (t80) cc_final: 0.6216 (t80) REVERT: C 215 GLN cc_start: 0.7117 (tt0) cc_final: 0.6881 (tt0) REVERT: C 221 GLU cc_start: 0.6640 (mm-30) cc_final: 0.6335 (mm-30) REVERT: C 224 LEU cc_start: 0.7215 (mt) cc_final: 0.6901 (pp) REVERT: C 236 LYS cc_start: 0.5745 (tptp) cc_final: 0.5403 (tptt) REVERT: C 239 ARG cc_start: 0.5589 (mtt180) cc_final: 0.5206 (mmp-170) REVERT: C 270 ASN cc_start: 0.7297 (t0) cc_final: 0.6972 (t0) REVERT: C 340 HIS cc_start: 0.5764 (OUTLIER) cc_final: 0.5532 (m-70) REVERT: C 349 ARG cc_start: 0.6426 (mtt180) cc_final: 0.6128 (mtp-110) REVERT: C 397 GLU cc_start: 0.6120 (tt0) cc_final: 0.5642 (tm-30) REVERT: C 456 LEU cc_start: 0.7032 (tp) cc_final: 0.6777 (mt) REVERT: C 458 GLN cc_start: 0.6981 (mm110) cc_final: 0.6701 (mm-40) REVERT: C 465 ARG cc_start: 0.6077 (mmt90) cc_final: 0.5253 (mtt-85) REVERT: C 470 GLU cc_start: 0.7347 (tt0) cc_final: 0.7024 (pm20) REVERT: C 546 GLU cc_start: 0.8200 (tt0) cc_final: 0.7644 (tp30) REVERT: C 567 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7028 (ttm-80) REVERT: C 638 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6168 (mmt-90) REVERT: C 689 GLU cc_start: 0.6961 (tm-30) cc_final: 0.6685 (tm-30) REVERT: C 693 ARG cc_start: 0.7197 (tpp80) cc_final: 0.6806 (mmt180) REVERT: C 738 GLU cc_start: 0.6353 (tp30) cc_final: 0.6064 (tt0) REVERT: C 741 ARG cc_start: 0.6217 (mtp-110) cc_final: 0.5555 (mmt-90) REVERT: C 754 LYS cc_start: 0.5887 (mmtt) cc_final: 0.5412 (ttpt) REVERT: C 757 MET cc_start: 0.6712 (ttm) cc_final: 0.6268 (ptm) REVERT: D 224 LEU cc_start: 0.7179 (mt) cc_final: 0.6824 (pp) REVERT: D 239 ARG cc_start: 0.5640 (mtt180) cc_final: 0.5233 (mmp-170) REVERT: D 288 LYS cc_start: 0.7241 (ttmt) cc_final: 0.6841 (tmmt) REVERT: D 304 ASP cc_start: 0.7915 (p0) cc_final: 0.7224 (t70) REVERT: D 349 ARG cc_start: 0.6489 (mtt180) cc_final: 0.6157 (mtp-110) REVERT: D 360 PHE cc_start: 0.6132 (t80) cc_final: 0.5737 (t80) REVERT: D 397 GLU cc_start: 0.6183 (tt0) cc_final: 0.5742 (tm-30) REVERT: D 451 ASP cc_start: 0.7033 (m-30) cc_final: 0.6657 (m-30) REVERT: D 456 LEU cc_start: 0.7070 (tp) cc_final: 0.6815 (mt) REVERT: D 465 ARG cc_start: 0.6017 (mmt180) cc_final: 0.5536 (mtt-85) REVERT: D 470 GLU cc_start: 0.7396 (tt0) cc_final: 0.7149 (pm20) REVERT: D 546 GLU cc_start: 0.8188 (tt0) cc_final: 0.7620 (tp30) REVERT: D 567 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7015 (ttm-80) REVERT: D 633 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7880 (mm) REVERT: D 741 ARG cc_start: 0.6213 (mtp-110) cc_final: 0.5542 (mmt-90) REVERT: D 753 ARG cc_start: 0.5461 (mtp180) cc_final: 0.5118 (mtp-110) REVERT: D 754 LYS cc_start: 0.5963 (mmtt) cc_final: 0.5495 (ttpt) REVERT: D 757 MET cc_start: 0.6660 (OUTLIER) cc_final: 0.6244 (ptm) REVERT: E 215 GLN cc_start: 0.7188 (tt0) cc_final: 0.6845 (tt0) REVERT: E 224 LEU cc_start: 0.7168 (mt) cc_final: 0.6836 (pp) REVERT: E 239 ARG cc_start: 0.5619 (mtt180) cc_final: 0.5226 (mmp-170) REVERT: E 270 ASN cc_start: 0.7317 (t0) cc_final: 0.6991 (t0) REVERT: E 288 LYS cc_start: 0.7182 (ttmt) cc_final: 0.6798 (tmmt) REVERT: E 349 ARG cc_start: 0.6555 (mtt180) cc_final: 0.6206 (mtm-85) REVERT: E 397 GLU cc_start: 0.6144 (tt0) cc_final: 0.5622 (tm-30) REVERT: E 456 LEU cc_start: 0.7088 (tp) cc_final: 0.6754 (mt) REVERT: E 465 ARG cc_start: 0.5980 (mmt180) cc_final: 0.5471 (mtt-85) REVERT: E 491 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6374 (mm-30) REVERT: E 546 GLU cc_start: 0.8198 (tt0) cc_final: 0.7607 (tp30) REVERT: E 567 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6992 (ttm-80) REVERT: E 578 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6920 (mt-10) REVERT: E 638 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6434 (mmt-90) REVERT: E 693 ARG cc_start: 0.7222 (tpp80) cc_final: 0.6793 (ttm-80) REVERT: E 741 ARG cc_start: 0.6326 (mtp-110) cc_final: 0.5626 (mmt-90) REVERT: E 754 LYS cc_start: 0.6052 (mmtt) cc_final: 0.5690 (ttpt) REVERT: E 758 PHE cc_start: 0.6565 (t80) cc_final: 0.6237 (t80) REVERT: F 215 GLN cc_start: 0.7117 (tt0) cc_final: 0.6880 (tt0) REVERT: F 221 GLU cc_start: 0.6668 (mm-30) cc_final: 0.6322 (mm-30) REVERT: F 224 LEU cc_start: 0.7222 (mt) cc_final: 0.6909 (pp) REVERT: F 236 LYS cc_start: 0.5749 (tptp) cc_final: 0.5399 (tptt) REVERT: F 239 ARG cc_start: 0.5596 (mtt180) cc_final: 0.5197 (mmp-170) REVERT: F 270 ASN cc_start: 0.7297 (t0) cc_final: 0.6998 (t0) REVERT: F 288 LYS cc_start: 0.7148 (ttmt) cc_final: 0.6794 (tmmt) REVERT: F 340 HIS cc_start: 0.5769 (OUTLIER) cc_final: 0.5537 (m-70) REVERT: F 349 ARG cc_start: 0.6456 (mtt180) cc_final: 0.6084 (mtm-85) REVERT: F 360 PHE cc_start: 0.5936 (t80) cc_final: 0.5460 (t80) REVERT: F 397 GLU cc_start: 0.6114 (tt0) cc_final: 0.5643 (tm-30) REVERT: F 451 ASP cc_start: 0.6953 (m-30) cc_final: 0.6701 (m-30) REVERT: F 456 LEU cc_start: 0.7033 (tp) cc_final: 0.6777 (mt) REVERT: F 458 GLN cc_start: 0.6982 (mm110) cc_final: 0.6704 (mm-40) REVERT: F 465 ARG cc_start: 0.6083 (mmt90) cc_final: 0.5254 (mtt-85) REVERT: F 470 GLU cc_start: 0.7346 (tt0) cc_final: 0.7024 (pm20) REVERT: F 491 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6446 (mm-30) REVERT: F 546 GLU cc_start: 0.8201 (tt0) cc_final: 0.7647 (tp30) REVERT: F 567 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7027 (ttm-80) REVERT: F 607 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7877 (mm-30) REVERT: F 636 PRO cc_start: 0.7105 (Cg_exo) cc_final: 0.6740 (Cg_endo) REVERT: F 638 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.6188 (mmt-90) REVERT: F 689 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6708 (tm-30) REVERT: F 693 ARG cc_start: 0.7190 (tpp80) cc_final: 0.6814 (mmt180) REVERT: F 738 GLU cc_start: 0.6367 (tp30) cc_final: 0.6077 (tt0) REVERT: F 741 ARG cc_start: 0.6220 (mtp-110) cc_final: 0.5560 (mmt-90) REVERT: F 754 LYS cc_start: 0.5866 (mmtt) cc_final: 0.5405 (ttpt) REVERT: F 757 MET cc_start: 0.6669 (ttm) cc_final: 0.6241 (ptm) outliers start: 144 outliers final: 52 residues processed: 735 average time/residue: 1.6030 time to fit residues: 1379.1667 Evaluate side-chains 591 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 519 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 638 ARG Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 567 ARG Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 638 ARG Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 502 LYS Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 638 ARG Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain F residue 502 LYS Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 607 GLU Chi-restraints excluded: chain F residue 638 ARG Chi-restraints excluded: chain F residue 678 MET Chi-restraints excluded: chain F residue 688 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 0.0980 chunk 121 optimal weight: 4.9990 chunk 326 optimal weight: 9.9990 chunk 267 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 393 optimal weight: 0.0050 chunk 424 optimal weight: 0.0270 chunk 350 optimal weight: 10.0000 chunk 389 optimal weight: 0.0970 chunk 133 optimal weight: 0.0570 chunk 315 optimal weight: 10.0000 overall best weight: 0.0568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 401 ASN A 460 ASN A 533 ASN ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN B 533 ASN C 533 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 GLN D 351 ASN D 401 ASN D 460 ASN D 533 ASN ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 ASN E 533 ASN F 533 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 35082 Z= 0.178 Angle : 0.706 8.392 47460 Z= 0.343 Chirality : 0.047 0.211 5322 Planarity : 0.004 0.052 6198 Dihedral : 12.741 117.548 5016 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.59 % Favored : 95.27 % Rotamer: Outliers : 3.33 % Allowed : 15.37 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.12), residues: 4314 helix: -0.59 (0.12), residues: 1578 sheet: -0.80 (0.21), residues: 582 loop : -1.31 (0.12), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 551 HIS 0.008 0.001 HIS A 340 PHE 0.019 0.002 PHE B 360 TYR 0.013 0.001 TYR A 495 ARG 0.008 0.000 ARG B 465 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 612 time to evaluate : 3.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.4623 (OUTLIER) cc_final: 0.4277 (m) REVERT: A 215 GLN cc_start: 0.7111 (tt0) cc_final: 0.6760 (tt0) REVERT: A 221 GLU cc_start: 0.6647 (mm-30) cc_final: 0.6241 (mm-30) REVERT: A 239 ARG cc_start: 0.5672 (mtt180) cc_final: 0.5231 (mmp-170) REVERT: A 270 ASN cc_start: 0.7343 (t0) cc_final: 0.6850 (t0) REVERT: A 288 LYS cc_start: 0.7270 (ttmt) cc_final: 0.6576 (ptmm) REVERT: A 291 GLU cc_start: 0.5702 (tm-30) cc_final: 0.5424 (tm-30) REVERT: A 304 ASP cc_start: 0.7868 (p0) cc_final: 0.7299 (t70) REVERT: A 322 ARG cc_start: 0.6578 (ttp-110) cc_final: 0.5726 (mmt180) REVERT: A 349 ARG cc_start: 0.6457 (mtt180) cc_final: 0.6129 (mtp-110) REVERT: A 360 PHE cc_start: 0.5848 (t80) cc_final: 0.5633 (t80) REVERT: A 397 GLU cc_start: 0.5994 (tt0) cc_final: 0.5592 (tm-30) REVERT: A 427 MET cc_start: 0.3892 (mmm) cc_final: 0.3691 (mmt) REVERT: A 449 MET cc_start: 0.5332 (tpt) cc_final: 0.4912 (tpt) REVERT: A 451 ASP cc_start: 0.6812 (m-30) cc_final: 0.6531 (m-30) REVERT: A 465 ARG cc_start: 0.5993 (mmt90) cc_final: 0.5312 (mtt-85) REVERT: A 491 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6470 (mm-30) REVERT: A 546 GLU cc_start: 0.8171 (tt0) cc_final: 0.7648 (tp30) REVERT: A 567 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6886 (ttm-80) REVERT: A 578 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6471 (mp0) REVERT: A 627 ASP cc_start: 0.7032 (OUTLIER) cc_final: 0.6498 (m-30) REVERT: A 633 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7830 (mm) REVERT: A 638 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6330 (mmt-90) REVERT: A 693 ARG cc_start: 0.7024 (tpp80) cc_final: 0.6756 (mtt180) REVERT: A 741 ARG cc_start: 0.6027 (mtp-110) cc_final: 0.5371 (mmt-90) REVERT: A 753 ARG cc_start: 0.5546 (mtp180) cc_final: 0.5162 (mtp-110) REVERT: A 754 LYS cc_start: 0.5812 (mmtt) cc_final: 0.5234 (ptmt) REVERT: A 757 MET cc_start: 0.6494 (ttm) cc_final: 0.6125 (ptm) REVERT: A 758 PHE cc_start: 0.6259 (t80) cc_final: 0.6000 (t80) REVERT: B 215 GLN cc_start: 0.7065 (tt0) cc_final: 0.6638 (tt0) REVERT: B 239 ARG cc_start: 0.5481 (mtt180) cc_final: 0.5063 (mmp-170) REVERT: B 270 ASN cc_start: 0.7371 (t0) cc_final: 0.6950 (t0) REVERT: B 288 LYS cc_start: 0.7193 (ttmt) cc_final: 0.6703 (tmmt) REVERT: B 315 LYS cc_start: 0.3565 (OUTLIER) cc_final: 0.3037 (pttm) REVERT: B 324 ILE cc_start: 0.7519 (mm) cc_final: 0.7235 (mp) REVERT: B 349 ARG cc_start: 0.6521 (mtt180) cc_final: 0.6270 (mtp-110) REVERT: B 397 GLU cc_start: 0.6038 (tt0) cc_final: 0.5544 (tm-30) REVERT: B 449 MET cc_start: 0.5262 (tpt) cc_final: 0.4882 (tpt) REVERT: B 451 ASP cc_start: 0.6803 (m-30) cc_final: 0.6594 (m-30) REVERT: B 456 LEU cc_start: 0.7013 (tp) cc_final: 0.6720 (mt) REVERT: B 491 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6409 (mm-30) REVERT: B 546 GLU cc_start: 0.8182 (tt0) cc_final: 0.7646 (tp30) REVERT: B 567 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6871 (ttm-80) REVERT: B 578 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6599 (mt-10) REVERT: B 638 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6735 (mmt-90) REVERT: B 693 ARG cc_start: 0.7021 (tpp80) cc_final: 0.6564 (mmt90) REVERT: B 741 ARG cc_start: 0.6267 (mtp-110) cc_final: 0.5565 (mmt-90) REVERT: B 753 ARG cc_start: 0.5551 (mtp180) cc_final: 0.4824 (mmm-85) REVERT: B 754 LYS cc_start: 0.5965 (mmtt) cc_final: 0.5543 (ttpt) REVERT: B 757 MET cc_start: 0.6362 (mtm) cc_final: 0.6079 (ptm) REVERT: C 39 VAL cc_start: 0.4573 (OUTLIER) cc_final: 0.4233 (m) REVERT: C 85 ASN cc_start: 0.5096 (p0) cc_final: 0.4477 (m-40) REVERT: C 215 GLN cc_start: 0.7085 (tt0) cc_final: 0.6801 (tt0) REVERT: C 221 GLU cc_start: 0.6588 (mm-30) cc_final: 0.6346 (mm-30) REVERT: C 239 ARG cc_start: 0.5525 (mtt180) cc_final: 0.5200 (mmp-170) REVERT: C 270 ASN cc_start: 0.7323 (t0) cc_final: 0.6965 (t0) REVERT: C 288 LYS cc_start: 0.7765 (tmmt) cc_final: 0.7319 (tmmt) REVERT: C 292 GLU cc_start: 0.5370 (OUTLIER) cc_final: 0.4986 (mp0) REVERT: C 305 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: C 322 ARG cc_start: 0.6248 (mpt90) cc_final: 0.4724 (ttm110) REVERT: C 340 HIS cc_start: 0.5602 (OUTLIER) cc_final: 0.5399 (m90) REVERT: C 349 ARG cc_start: 0.6459 (mtt180) cc_final: 0.6140 (mtp-110) REVERT: C 366 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7604 (tt0) REVERT: C 389 LYS cc_start: 0.5216 (tptm) cc_final: 0.4888 (tptt) REVERT: C 397 GLU cc_start: 0.6069 (tt0) cc_final: 0.5568 (tm-30) REVERT: C 401 ASN cc_start: 0.6257 (m-40) cc_final: 0.6031 (m110) REVERT: C 451 ASP cc_start: 0.6818 (m-30) cc_final: 0.6559 (m-30) REVERT: C 502 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.7134 (tppp) REVERT: C 546 GLU cc_start: 0.8180 (tt0) cc_final: 0.7670 (tp30) REVERT: C 556 GLU cc_start: 0.7402 (pm20) cc_final: 0.7037 (pm20) REVERT: C 567 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6895 (ttm-80) REVERT: C 638 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6121 (mmt-90) REVERT: C 689 GLU cc_start: 0.6909 (tm-30) cc_final: 0.6695 (tm-30) REVERT: C 693 ARG cc_start: 0.7055 (tpp80) cc_final: 0.6788 (mtt180) REVERT: C 741 ARG cc_start: 0.6122 (mtp-110) cc_final: 0.5471 (mmt-90) REVERT: C 753 ARG cc_start: 0.5510 (mtp180) cc_final: 0.5185 (mtp-110) REVERT: C 754 LYS cc_start: 0.5751 (mmtt) cc_final: 0.5442 (ttpt) REVERT: C 757 MET cc_start: 0.6492 (ttm) cc_final: 0.6118 (ptm) REVERT: D 39 VAL cc_start: 0.4530 (OUTLIER) cc_final: 0.4170 (m) REVERT: D 85 ASN cc_start: 0.5457 (p0) cc_final: 0.4746 (m-40) REVERT: D 221 GLU cc_start: 0.6611 (mm-30) cc_final: 0.6233 (mm-30) REVERT: D 239 ARG cc_start: 0.5646 (mtt180) cc_final: 0.5184 (mmp-170) REVERT: D 288 LYS cc_start: 0.7288 (ttmt) cc_final: 0.6596 (ptmm) REVERT: D 291 GLU cc_start: 0.5688 (tm-30) cc_final: 0.5411 (tm-30) REVERT: D 304 ASP cc_start: 0.7839 (p0) cc_final: 0.7348 (t70) REVERT: D 349 ARG cc_start: 0.6464 (mtt180) cc_final: 0.6110 (mtp-110) REVERT: D 360 PHE cc_start: 0.5870 (t80) cc_final: 0.5668 (t80) REVERT: D 397 GLU cc_start: 0.6030 (tt0) cc_final: 0.5636 (tm-30) REVERT: D 451 ASP cc_start: 0.6726 (m-30) cc_final: 0.6430 (m-30) REVERT: D 465 ARG cc_start: 0.5967 (mmt180) cc_final: 0.5556 (mtt-85) REVERT: D 546 GLU cc_start: 0.8182 (tt0) cc_final: 0.7658 (tp30) REVERT: D 556 GLU cc_start: 0.7370 (pm20) cc_final: 0.7044 (pm20) REVERT: D 567 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6901 (ttm-80) REVERT: D 577 ASP cc_start: 0.6384 (m-30) cc_final: 0.6145 (m-30) REVERT: D 578 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6485 (mp0) REVERT: D 627 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6508 (m-30) REVERT: D 633 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7882 (mm) REVERT: D 638 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6241 (mmt-90) REVERT: D 696 LYS cc_start: 0.7273 (ttpt) cc_final: 0.6972 (tttt) REVERT: D 741 ARG cc_start: 0.6037 (mtp-110) cc_final: 0.5389 (mmt-90) REVERT: D 753 ARG cc_start: 0.5504 (mtp180) cc_final: 0.5144 (mtp-110) REVERT: D 754 LYS cc_start: 0.5825 (mmtt) cc_final: 0.5241 (ptmt) REVERT: D 757 MET cc_start: 0.6469 (ttm) cc_final: 0.6113 (ptm) REVERT: D 758 PHE cc_start: 0.6227 (t80) cc_final: 0.5972 (t80) REVERT: E 215 GLN cc_start: 0.7074 (tt0) cc_final: 0.6648 (tt0) REVERT: E 239 ARG cc_start: 0.5490 (mtt180) cc_final: 0.5213 (mmp-170) REVERT: E 270 ASN cc_start: 0.7364 (t0) cc_final: 0.6937 (t0) REVERT: E 288 LYS cc_start: 0.7195 (ttmt) cc_final: 0.6710 (tmmt) REVERT: E 324 ILE cc_start: 0.7519 (mm) cc_final: 0.7234 (mp) REVERT: E 349 ARG cc_start: 0.6531 (mtt180) cc_final: 0.6254 (mtp-110) REVERT: E 364 ASP cc_start: 0.6707 (m-30) cc_final: 0.6503 (m-30) REVERT: E 397 GLU cc_start: 0.6041 (tt0) cc_final: 0.5549 (tm-30) REVERT: E 449 MET cc_start: 0.5257 (tpt) cc_final: 0.4875 (tpt) REVERT: E 451 ASP cc_start: 0.6797 (m-30) cc_final: 0.6589 (m-30) REVERT: E 456 LEU cc_start: 0.7011 (tp) cc_final: 0.6717 (mt) REVERT: E 465 ARG cc_start: 0.6047 (mmt180) cc_final: 0.5352 (mtt-85) REVERT: E 470 GLU cc_start: 0.7094 (pm20) cc_final: 0.6708 (pp20) REVERT: E 491 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6229 (mm-30) REVERT: E 546 GLU cc_start: 0.8184 (tt0) cc_final: 0.7647 (tp30) REVERT: E 567 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6874 (ttm-80) REVERT: E 578 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6599 (mt-10) REVERT: E 638 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6717 (mmt-90) REVERT: E 693 ARG cc_start: 0.7023 (tpp80) cc_final: 0.6559 (mmt90) REVERT: E 741 ARG cc_start: 0.6276 (mtp-110) cc_final: 0.5573 (mmt-90) REVERT: E 753 ARG cc_start: 0.5566 (mtp180) cc_final: 0.4833 (mmm-85) REVERT: E 754 LYS cc_start: 0.5966 (mmtt) cc_final: 0.5543 (ttpt) REVERT: E 757 MET cc_start: 0.6359 (mtm) cc_final: 0.6073 (ptm) REVERT: F 39 VAL cc_start: 0.4566 (OUTLIER) cc_final: 0.4228 (m) REVERT: F 85 ASN cc_start: 0.5100 (p0) cc_final: 0.4466 (m-40) REVERT: F 215 GLN cc_start: 0.7080 (tt0) cc_final: 0.6803 (tt0) REVERT: F 221 GLU cc_start: 0.6623 (mm-30) cc_final: 0.6379 (mm-30) REVERT: F 239 ARG cc_start: 0.5541 (mtt180) cc_final: 0.5195 (mmp-170) REVERT: F 270 ASN cc_start: 0.7357 (t0) cc_final: 0.7015 (t0) REVERT: F 288 LYS cc_start: 0.7249 (ttmt) cc_final: 0.6757 (tmmt) REVERT: F 305 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: F 322 ARG cc_start: 0.6238 (mpt90) cc_final: 0.4719 (ttm110) REVERT: F 340 HIS cc_start: 0.5598 (OUTLIER) cc_final: 0.5397 (m90) REVERT: F 349 ARG cc_start: 0.6428 (mtt180) cc_final: 0.6076 (mtm-85) REVERT: F 360 PHE cc_start: 0.5754 (t80) cc_final: 0.5540 (t80) REVERT: F 389 LYS cc_start: 0.5205 (tptm) cc_final: 0.4877 (tptt) REVERT: F 397 GLU cc_start: 0.6032 (tt0) cc_final: 0.5551 (tm-30) REVERT: F 401 ASN cc_start: 0.6244 (m-40) cc_final: 0.6020 (m110) REVERT: F 451 ASP cc_start: 0.6804 (m-30) cc_final: 0.6592 (m-30) REVERT: F 491 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6359 (mm-30) REVERT: F 502 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.7133 (tppp) REVERT: F 546 GLU cc_start: 0.8210 (tt0) cc_final: 0.7668 (tp30) REVERT: F 567 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6893 (ttm-80) REVERT: F 638 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6111 (mmt-90) REVERT: F 693 ARG cc_start: 0.7029 (tpp80) cc_final: 0.6550 (mmt90) REVERT: F 741 ARG cc_start: 0.6116 (mtp-110) cc_final: 0.5469 (mmt-90) REVERT: F 753 ARG cc_start: 0.5484 (mtp180) cc_final: 0.5161 (mtp-110) REVERT: F 754 LYS cc_start: 0.5750 (mmtt) cc_final: 0.5440 (ttpt) REVERT: F 757 MET cc_start: 0.6463 (ttm) cc_final: 0.6095 (ptm) outliers start: 123 outliers final: 26 residues processed: 688 average time/residue: 1.6702 time to fit residues: 1340.4997 Evaluate side-chains 581 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 523 time to evaluate : 3.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 638 ARG Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 567 ARG Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 638 ARG Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 638 ARG Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain F residue 502 LYS Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 638 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 20.0000 chunk 295 optimal weight: 30.0000 chunk 203 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 187 optimal weight: 20.0000 chunk 263 optimal weight: 10.0000 chunk 394 optimal weight: 8.9990 chunk 417 optimal weight: 40.0000 chunk 206 optimal weight: 10.0000 chunk 373 optimal weight: 0.0970 chunk 112 optimal weight: 10.0000 overall best weight: 7.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 GLN ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS B 129 ASN B 382 GLN B 401 ASN B 603 GLN ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS C 129 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 382 GLN D 401 ASN ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 HIS E 129 ASN E 382 GLN E 401 ASN ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS F 129 ASN ** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 35082 Z= 0.358 Angle : 0.854 10.415 47460 Z= 0.423 Chirality : 0.051 0.173 5322 Planarity : 0.006 0.061 6198 Dihedral : 13.710 126.303 5016 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.37 % Favored : 93.49 % Rotamer: Outliers : 5.47 % Allowed : 14.69 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.12), residues: 4314 helix: -0.55 (0.12), residues: 1614 sheet: -0.55 (0.22), residues: 606 loop : -1.56 (0.12), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 551 HIS 0.010 0.002 HIS A 340 PHE 0.032 0.003 PHE D 360 TYR 0.021 0.002 TYR F 244 ARG 0.009 0.001 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 529 time to evaluate : 3.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.5620 (mtt180) cc_final: 0.5264 (mmp-170) REVERT: A 270 ASN cc_start: 0.7425 (t0) cc_final: 0.7034 (t0) REVERT: A 288 LYS cc_start: 0.7113 (ttmt) cc_final: 0.6323 (pttm) REVERT: A 304 ASP cc_start: 0.7878 (p0) cc_final: 0.7217 (t70) REVERT: A 315 LYS cc_start: 0.3958 (OUTLIER) cc_final: 0.3474 (ptpt) REVERT: A 349 ARG cc_start: 0.6496 (mtt180) cc_final: 0.6156 (mtp-110) REVERT: A 360 PHE cc_start: 0.6211 (t80) cc_final: 0.5863 (t80) REVERT: A 397 GLU cc_start: 0.6189 (tt0) cc_final: 0.5737 (tm-30) REVERT: A 451 ASP cc_start: 0.7161 (m-30) cc_final: 0.6888 (m-30) REVERT: A 465 ARG cc_start: 0.6001 (mmt90) cc_final: 0.5168 (mtt-85) REVERT: A 546 GLU cc_start: 0.8205 (tt0) cc_final: 0.7648 (tp30) REVERT: A 608 MET cc_start: 0.8510 (mtm) cc_final: 0.8260 (mtp) REVERT: A 627 ASP cc_start: 0.7065 (OUTLIER) cc_final: 0.6584 (m-30) REVERT: A 633 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7848 (mm) REVERT: A 674 PHE cc_start: 0.6225 (t80) cc_final: 0.5827 (t80) REVERT: A 741 ARG cc_start: 0.6265 (mtp-110) cc_final: 0.5582 (mmt-90) REVERT: A 753 ARG cc_start: 0.5550 (mtp180) cc_final: 0.5144 (mtp-110) REVERT: A 754 LYS cc_start: 0.6057 (mmtt) cc_final: 0.5580 (ttpt) REVERT: A 757 MET cc_start: 0.6712 (OUTLIER) cc_final: 0.6290 (ptm) REVERT: B 89 ARG cc_start: 0.6219 (OUTLIER) cc_final: 0.4044 (ttp80) REVERT: B 198 LEU cc_start: 0.6042 (OUTLIER) cc_final: 0.5747 (mm) REVERT: B 215 GLN cc_start: 0.7119 (tt0) cc_final: 0.6738 (tt0) REVERT: B 239 ARG cc_start: 0.5598 (mtt180) cc_final: 0.5228 (mmp-170) REVERT: B 270 ASN cc_start: 0.7426 (t0) cc_final: 0.7103 (t0) REVERT: B 288 LYS cc_start: 0.7184 (ttmt) cc_final: 0.6669 (tmmt) REVERT: B 294 GLU cc_start: 0.5946 (mm-30) cc_final: 0.5566 (tp30) REVERT: B 315 LYS cc_start: 0.4334 (OUTLIER) cc_final: 0.4098 (pttp) REVERT: B 322 ARG cc_start: 0.6623 (ttp-110) cc_final: 0.5785 (mmt180) REVERT: B 349 ARG cc_start: 0.6522 (mtt180) cc_final: 0.6167 (mtm-85) REVERT: B 397 GLU cc_start: 0.6202 (tt0) cc_final: 0.5655 (tm-30) REVERT: B 404 HIS cc_start: 0.6818 (t-90) cc_final: 0.6583 (t70) REVERT: B 451 ASP cc_start: 0.7086 (m-30) cc_final: 0.6863 (m-30) REVERT: B 456 LEU cc_start: 0.7170 (tp) cc_final: 0.6962 (mt) REVERT: B 491 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6330 (mm-30) REVERT: B 546 GLU cc_start: 0.8236 (tt0) cc_final: 0.7658 (tp30) REVERT: B 567 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6928 (ttm-80) REVERT: B 577 ASP cc_start: 0.7562 (m-30) cc_final: 0.7316 (m-30) REVERT: B 627 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6506 (m-30) REVERT: B 638 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.6554 (mmt-90) REVERT: B 740 MET cc_start: 0.7501 (tpp) cc_final: 0.7259 (tpt) REVERT: B 741 ARG cc_start: 0.6338 (mtp-110) cc_final: 0.5689 (mmt-90) REVERT: B 753 ARG cc_start: 0.5606 (mtp180) cc_final: 0.4853 (mmm-85) REVERT: B 754 LYS cc_start: 0.6162 (mmtt) cc_final: 0.5777 (ttpt) REVERT: C 215 GLN cc_start: 0.7249 (tt0) cc_final: 0.7002 (tt0) REVERT: C 239 ARG cc_start: 0.5571 (mtt180) cc_final: 0.5224 (mmp-170) REVERT: C 270 ASN cc_start: 0.7391 (t0) cc_final: 0.7083 (t0) REVERT: C 321 GLU cc_start: 0.6252 (tp30) cc_final: 0.6036 (tp30) REVERT: C 349 ARG cc_start: 0.6364 (mtt180) cc_final: 0.6056 (mtp-110) REVERT: C 366 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7645 (tt0) REVERT: C 397 GLU cc_start: 0.6196 (tt0) cc_final: 0.5673 (tm-30) REVERT: C 451 ASP cc_start: 0.7033 (m-30) cc_final: 0.6775 (m-30) REVERT: C 465 ARG cc_start: 0.5701 (mmt90) cc_final: 0.5127 (mtt-85) REVERT: C 546 GLU cc_start: 0.8232 (tt0) cc_final: 0.7658 (tp30) REVERT: C 567 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6971 (ttm-80) REVERT: C 577 ASP cc_start: 0.7527 (m-30) cc_final: 0.7064 (m-30) REVERT: C 741 ARG cc_start: 0.6284 (mtp-110) cc_final: 0.5629 (mmt-90) REVERT: C 754 LYS cc_start: 0.5924 (mmtt) cc_final: 0.5500 (ttpt) REVERT: C 757 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.6265 (ptm) REVERT: D 239 ARG cc_start: 0.5610 (mtt180) cc_final: 0.5228 (mmp-170) REVERT: D 288 LYS cc_start: 0.7126 (ttmt) cc_final: 0.6295 (ptmm) REVERT: D 304 ASP cc_start: 0.7868 (p0) cc_final: 0.7227 (t70) REVERT: D 315 LYS cc_start: 0.4013 (OUTLIER) cc_final: 0.3519 (ptpt) REVERT: D 349 ARG cc_start: 0.6489 (mtt180) cc_final: 0.6149 (mtp-110) REVERT: D 360 PHE cc_start: 0.6231 (t80) cc_final: 0.5881 (t80) REVERT: D 397 GLU cc_start: 0.6172 (tt0) cc_final: 0.5738 (tm-30) REVERT: D 451 ASP cc_start: 0.7041 (m-30) cc_final: 0.6783 (m-30) REVERT: D 465 ARG cc_start: 0.5856 (mmt180) cc_final: 0.5610 (mtt-85) REVERT: D 546 GLU cc_start: 0.8208 (tt0) cc_final: 0.7653 (tp30) REVERT: D 627 ASP cc_start: 0.7025 (OUTLIER) cc_final: 0.6536 (m-30) REVERT: D 633 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7872 (mm) REVERT: D 741 ARG cc_start: 0.6311 (mtp-110) cc_final: 0.5613 (mmt-90) REVERT: D 753 ARG cc_start: 0.5560 (mtp180) cc_final: 0.5190 (mtp-110) REVERT: D 754 LYS cc_start: 0.6050 (mmtt) cc_final: 0.5756 (ttpt) REVERT: E 89 ARG cc_start: 0.6212 (OUTLIER) cc_final: 0.4033 (ttp80) REVERT: E 198 LEU cc_start: 0.6045 (OUTLIER) cc_final: 0.5725 (mm) REVERT: E 215 GLN cc_start: 0.7122 (tt0) cc_final: 0.6742 (tt0) REVERT: E 239 ARG cc_start: 0.5621 (mtt180) cc_final: 0.5328 (mmp-170) REVERT: E 270 ASN cc_start: 0.7427 (t0) cc_final: 0.7104 (t0) REVERT: E 288 LYS cc_start: 0.7197 (ttmt) cc_final: 0.6702 (tmmt) REVERT: E 294 GLU cc_start: 0.5914 (mm-30) cc_final: 0.5572 (tp30) REVERT: E 324 ILE cc_start: 0.7639 (mm) cc_final: 0.7433 (mp) REVERT: E 349 ARG cc_start: 0.6523 (mtt180) cc_final: 0.6170 (mtm-85) REVERT: E 397 GLU cc_start: 0.6202 (tt0) cc_final: 0.5656 (tm-30) REVERT: E 451 ASP cc_start: 0.7082 (m-30) cc_final: 0.6857 (m-30) REVERT: E 456 LEU cc_start: 0.7182 (tp) cc_final: 0.6971 (mt) REVERT: E 465 ARG cc_start: 0.5550 (mmt180) cc_final: 0.5330 (mtt-85) REVERT: E 491 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6339 (mm-30) REVERT: E 546 GLU cc_start: 0.8237 (tt0) cc_final: 0.7655 (tp30) REVERT: E 577 ASP cc_start: 0.7564 (m-30) cc_final: 0.7315 (m-30) REVERT: E 627 ASP cc_start: 0.7032 (OUTLIER) cc_final: 0.6511 (m-30) REVERT: E 638 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.6570 (mmt-90) REVERT: E 741 ARG cc_start: 0.6345 (mtp-110) cc_final: 0.5699 (mmt-90) REVERT: E 754 LYS cc_start: 0.6082 (mmtt) cc_final: 0.5714 (ttpt) REVERT: F 215 GLN cc_start: 0.7238 (tt0) cc_final: 0.6996 (tt0) REVERT: F 239 ARG cc_start: 0.5599 (mtt180) cc_final: 0.5261 (mmp-170) REVERT: F 270 ASN cc_start: 0.7399 (t0) cc_final: 0.7085 (t0) REVERT: F 288 LYS cc_start: 0.7263 (ttmt) cc_final: 0.6607 (ptmm) REVERT: F 294 GLU cc_start: 0.6189 (mm-30) cc_final: 0.5923 (tp30) REVERT: F 321 GLU cc_start: 0.6227 (tp30) cc_final: 0.6025 (tp30) REVERT: F 349 ARG cc_start: 0.6422 (mtt180) cc_final: 0.6105 (mtp-110) REVERT: F 397 GLU cc_start: 0.6157 (tt0) cc_final: 0.5649 (tm-30) REVERT: F 451 ASP cc_start: 0.7028 (m-30) cc_final: 0.6777 (m-30) REVERT: F 460 ASN cc_start: 0.5783 (t0) cc_final: 0.5511 (p0) REVERT: F 465 ARG cc_start: 0.5710 (mmt90) cc_final: 0.5131 (mtt-85) REVERT: F 491 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6383 (mm-30) REVERT: F 546 GLU cc_start: 0.8244 (tt0) cc_final: 0.7675 (tp30) REVERT: F 567 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6975 (ttm-80) REVERT: F 577 ASP cc_start: 0.7530 (m-30) cc_final: 0.7064 (m-30) REVERT: F 607 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8107 (mm-30) REVERT: F 669 ASP cc_start: 0.3947 (t0) cc_final: 0.3211 (OUTLIER) REVERT: F 689 GLU cc_start: 0.7343 (tt0) cc_final: 0.6631 (tm-30) REVERT: F 741 ARG cc_start: 0.6274 (mtp-110) cc_final: 0.5629 (mmt-90) REVERT: F 754 LYS cc_start: 0.5917 (mmtt) cc_final: 0.5464 (ttmt) REVERT: F 757 MET cc_start: 0.6634 (OUTLIER) cc_final: 0.6260 (ptm) outliers start: 202 outliers final: 107 residues processed: 676 average time/residue: 1.5510 time to fit residues: 1236.1116 Evaluate side-chains 610 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 479 time to evaluate : 2.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 638 ARG Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 638 ARG Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 502 LYS Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 638 ARG Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 470 GLU Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain F residue 502 LYS Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 607 GLU Chi-restraints excluded: chain F residue 638 ARG Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 8.9990 chunk 237 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 310 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 356 optimal weight: 4.9990 chunk 288 optimal weight: 30.0000 chunk 0 optimal weight: 9.9990 chunk 213 optimal weight: 0.0870 chunk 374 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 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 115 HIS A 401 ASN ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 HIS D 401 ASN D 603 GLN ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN E 404 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 35082 Z= 0.240 Angle : 0.743 9.484 47460 Z= 0.364 Chirality : 0.047 0.167 5322 Planarity : 0.005 0.059 6198 Dihedral : 12.806 113.564 5016 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.00 % Favored : 93.86 % Rotamer: Outliers : 4.53 % Allowed : 16.26 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.12), residues: 4314 helix: -0.35 (0.12), residues: 1656 sheet: -0.39 (0.23), residues: 582 loop : -1.39 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 476 HIS 0.011 0.002 HIS C 340 PHE 0.025 0.002 PHE F 360 TYR 0.009 0.002 TYR C 244 ARG 0.005 0.001 ARG F 653 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 523 time to evaluate : 3.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.4370 (OUTLIER) cc_final: 0.4169 (m) REVERT: A 236 LYS cc_start: 0.6239 (tptt) cc_final: 0.6034 (tptt) REVERT: A 239 ARG cc_start: 0.5639 (mtt180) cc_final: 0.5241 (mmp-170) REVERT: A 270 ASN cc_start: 0.7457 (t0) cc_final: 0.7032 (t0) REVERT: A 288 LYS cc_start: 0.7035 (ttmt) cc_final: 0.6400 (ptmm) REVERT: A 304 ASP cc_start: 0.7872 (p0) cc_final: 0.7268 (t70) REVERT: A 322 ARG cc_start: 0.6657 (ttp-110) cc_final: 0.5821 (mmt180) REVERT: A 349 ARG cc_start: 0.6488 (mtt180) cc_final: 0.6152 (mtp-110) REVERT: A 360 PHE cc_start: 0.6143 (t80) cc_final: 0.5746 (t80) REVERT: A 397 GLU cc_start: 0.6180 (tt0) cc_final: 0.5654 (tm-30) REVERT: A 445 LEU cc_start: 0.5223 (OUTLIER) cc_final: 0.4700 (tp) REVERT: A 451 ASP cc_start: 0.7017 (m-30) cc_final: 0.6778 (m-30) REVERT: A 458 GLN cc_start: 0.6836 (mm110) cc_final: 0.6596 (mm-40) REVERT: A 465 ARG cc_start: 0.6043 (mmt90) cc_final: 0.5199 (mtt-85) REVERT: A 546 GLU cc_start: 0.8221 (tt0) cc_final: 0.7636 (tp30) REVERT: A 567 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6857 (ttm-80) REVERT: A 633 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7865 (mm) REVERT: A 638 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.6485 (mmt-90) REVERT: A 741 ARG cc_start: 0.6228 (mtp-110) cc_final: 0.5532 (mmt-90) REVERT: A 753 ARG cc_start: 0.5585 (mtp180) cc_final: 0.4852 (mmm-85) REVERT: A 754 LYS cc_start: 0.5978 (mmtt) cc_final: 0.5586 (ttpt) REVERT: A 757 MET cc_start: 0.6613 (OUTLIER) cc_final: 0.6199 (ptm) REVERT: B 215 GLN cc_start: 0.7112 (tt0) cc_final: 0.6761 (tt0) REVERT: B 239 ARG cc_start: 0.5620 (mtt180) cc_final: 0.5335 (mmp-170) REVERT: B 270 ASN cc_start: 0.7467 (t0) cc_final: 0.7119 (t0) REVERT: B 288 LYS cc_start: 0.7214 (ttmt) cc_final: 0.6758 (tmmt) REVERT: B 294 GLU cc_start: 0.5883 (mm-30) cc_final: 0.5511 (tp30) REVERT: B 315 LYS cc_start: 0.4195 (OUTLIER) cc_final: 0.3918 (pttp) REVERT: B 322 ARG cc_start: 0.6626 (ttp-110) cc_final: 0.5789 (mmt180) REVERT: B 349 ARG cc_start: 0.6491 (mtt180) cc_final: 0.6146 (mtm-85) REVERT: B 397 GLU cc_start: 0.6210 (tt0) cc_final: 0.5630 (tm-30) REVERT: B 445 LEU cc_start: 0.5265 (OUTLIER) cc_final: 0.4798 (tp) REVERT: B 451 ASP cc_start: 0.6984 (m-30) cc_final: 0.6729 (m-30) REVERT: B 456 LEU cc_start: 0.7261 (tp) cc_final: 0.7047 (mt) REVERT: B 491 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6245 (mm-30) REVERT: B 546 GLU cc_start: 0.8246 (tt0) cc_final: 0.7683 (tp30) REVERT: B 567 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6893 (ttm-80) REVERT: B 627 ASP cc_start: 0.6941 (OUTLIER) cc_final: 0.6445 (m-30) REVERT: B 633 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7902 (mm) REVERT: B 638 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.6525 (mmt-90) REVERT: B 741 ARG cc_start: 0.6352 (mtp-110) cc_final: 0.5665 (mmt-90) REVERT: B 753 ARG cc_start: 0.5664 (mtp180) cc_final: 0.4899 (mmm-85) REVERT: B 754 LYS cc_start: 0.6046 (mmtt) cc_final: 0.5586 (ttpt) REVERT: B 757 MET cc_start: 0.6604 (mtm) cc_final: 0.6299 (ptm) REVERT: C 39 VAL cc_start: 0.4484 (OUTLIER) cc_final: 0.4232 (m) REVERT: C 215 GLN cc_start: 0.7108 (tt0) cc_final: 0.6873 (tt0) REVERT: C 221 GLU cc_start: 0.6606 (mm-30) cc_final: 0.6252 (mm-30) REVERT: C 239 ARG cc_start: 0.5586 (mtt180) cc_final: 0.5228 (mmp-170) REVERT: C 270 ASN cc_start: 0.7437 (t0) cc_final: 0.7099 (t0) REVERT: C 321 GLU cc_start: 0.6232 (tp30) cc_final: 0.5975 (tp30) REVERT: C 322 ARG cc_start: 0.6737 (mpt180) cc_final: 0.6533 (mmt180) REVERT: C 349 ARG cc_start: 0.6485 (mtt180) cc_final: 0.6130 (mtp-110) REVERT: C 366 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7628 (tt0) REVERT: C 397 GLU cc_start: 0.6160 (tt0) cc_final: 0.5654 (tm-30) REVERT: C 451 ASP cc_start: 0.7002 (m-30) cc_final: 0.6733 (m-30) REVERT: C 458 GLN cc_start: 0.6933 (mm110) cc_final: 0.6629 (mm-40) REVERT: C 465 ARG cc_start: 0.5784 (mmt90) cc_final: 0.5164 (mtt-85) REVERT: C 546 GLU cc_start: 0.8239 (tt0) cc_final: 0.7720 (tp30) REVERT: C 567 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6923 (ttm-80) REVERT: C 627 ASP cc_start: 0.6956 (OUTLIER) cc_final: 0.6431 (m-30) REVERT: C 638 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.6368 (mmt-90) REVERT: C 693 ARG cc_start: 0.7116 (tpp80) cc_final: 0.6789 (mmt180) REVERT: C 741 ARG cc_start: 0.6432 (mtp-110) cc_final: 0.5584 (mmt-90) REVERT: C 753 ARG cc_start: 0.5566 (mtp180) cc_final: 0.5209 (mtp-110) REVERT: C 754 LYS cc_start: 0.5965 (mmtt) cc_final: 0.5577 (ttpt) REVERT: C 757 MET cc_start: 0.6570 (ttm) cc_final: 0.6206 (ptm) REVERT: D 39 VAL cc_start: 0.4458 (OUTLIER) cc_final: 0.4171 (m) REVERT: D 239 ARG cc_start: 0.5594 (mtt180) cc_final: 0.5255 (mmp-170) REVERT: D 288 LYS cc_start: 0.7035 (ttmt) cc_final: 0.6431 (ptmm) REVERT: D 304 ASP cc_start: 0.7872 (p0) cc_final: 0.7242 (t70) REVERT: D 322 ARG cc_start: 0.6653 (ttp-110) cc_final: 0.5816 (mmt180) REVERT: D 349 ARG cc_start: 0.6489 (mtt180) cc_final: 0.6145 (mtp-110) REVERT: D 360 PHE cc_start: 0.6140 (t80) cc_final: 0.5757 (t80) REVERT: D 397 GLU cc_start: 0.6186 (tt0) cc_final: 0.5714 (tm-30) REVERT: D 445 LEU cc_start: 0.5262 (OUTLIER) cc_final: 0.4847 (tp) REVERT: D 449 MET cc_start: 0.5392 (tpt) cc_final: 0.5030 (tpt) REVERT: D 451 ASP cc_start: 0.6985 (m-30) cc_final: 0.6729 (m-30) REVERT: D 465 ARG cc_start: 0.5896 (mmt180) cc_final: 0.5628 (mtt-85) REVERT: D 546 GLU cc_start: 0.8222 (tt0) cc_final: 0.7687 (tp30) REVERT: D 567 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6856 (ttm-80) REVERT: D 608 MET cc_start: 0.8406 (mtm) cc_final: 0.8172 (mtp) REVERT: D 633 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7866 (mm) REVERT: D 638 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.6498 (mmt-90) REVERT: D 674 PHE cc_start: 0.6240 (t80) cc_final: 0.5849 (t80) REVERT: D 741 ARG cc_start: 0.6383 (mtp-110) cc_final: 0.5335 (mmm160) REVERT: D 753 ARG cc_start: 0.5594 (mtp180) cc_final: 0.4856 (mmm-85) REVERT: D 754 LYS cc_start: 0.6015 (mmtt) cc_final: 0.5603 (ttpt) REVERT: D 757 MET cc_start: 0.6635 (OUTLIER) cc_final: 0.6300 (ptm) REVERT: E 215 GLN cc_start: 0.7112 (tt0) cc_final: 0.6761 (tt0) REVERT: E 239 ARG cc_start: 0.5608 (mtt180) cc_final: 0.5317 (mmp-170) REVERT: E 270 ASN cc_start: 0.7469 (t0) cc_final: 0.7120 (t0) REVERT: E 288 LYS cc_start: 0.7209 (ttmt) cc_final: 0.6740 (tmmt) REVERT: E 294 GLU cc_start: 0.5892 (mm-30) cc_final: 0.5519 (tp30) REVERT: E 349 ARG cc_start: 0.6490 (mtt180) cc_final: 0.6145 (mtm-85) REVERT: E 397 GLU cc_start: 0.6212 (tt0) cc_final: 0.5631 (tm-30) REVERT: E 445 LEU cc_start: 0.5288 (OUTLIER) cc_final: 0.4817 (tp) REVERT: E 451 ASP cc_start: 0.6934 (m-30) cc_final: 0.6690 (m-30) REVERT: E 456 LEU cc_start: 0.7321 (tp) cc_final: 0.7035 (mt) REVERT: E 491 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6252 (mm-30) REVERT: E 546 GLU cc_start: 0.8254 (tt0) cc_final: 0.7705 (tp30) REVERT: E 567 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6871 (ttm-80) REVERT: E 627 ASP cc_start: 0.6960 (OUTLIER) cc_final: 0.6450 (m-30) REVERT: E 633 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7901 (mm) REVERT: E 638 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.6532 (mmt-90) REVERT: E 693 ARG cc_start: 0.7174 (tpp80) cc_final: 0.6642 (ttm-80) REVERT: E 741 ARG cc_start: 0.6307 (mtp-110) cc_final: 0.5639 (mmt-90) REVERT: E 753 ARG cc_start: 0.5614 (mtp180) cc_final: 0.4853 (mmm-85) REVERT: E 754 LYS cc_start: 0.6056 (mmtt) cc_final: 0.5589 (ttpt) REVERT: E 757 MET cc_start: 0.6612 (mtm) cc_final: 0.6305 (ptm) REVERT: F 39 VAL cc_start: 0.4487 (OUTLIER) cc_final: 0.4234 (m) REVERT: F 215 GLN cc_start: 0.7098 (tt0) cc_final: 0.6837 (tt0) REVERT: F 221 GLU cc_start: 0.6611 (mm-30) cc_final: 0.6278 (mm-30) REVERT: F 239 ARG cc_start: 0.5598 (mtt180) cc_final: 0.5265 (mmp-170) REVERT: F 270 ASN cc_start: 0.7455 (t0) cc_final: 0.7093 (t0) REVERT: F 288 LYS cc_start: 0.7167 (ttmt) cc_final: 0.6408 (pttm) REVERT: F 321 GLU cc_start: 0.6233 (tp30) cc_final: 0.5982 (tp30) REVERT: F 322 ARG cc_start: 0.6595 (mpt180) cc_final: 0.6393 (mmt180) REVERT: F 349 ARG cc_start: 0.6512 (mtt180) cc_final: 0.6153 (mtp-110) REVERT: F 397 GLU cc_start: 0.6152 (tt0) cc_final: 0.5653 (tm-30) REVERT: F 449 MET cc_start: 0.5363 (tpt) cc_final: 0.5125 (tpt) REVERT: F 451 ASP cc_start: 0.7048 (m-30) cc_final: 0.6787 (m-30) REVERT: F 458 GLN cc_start: 0.6950 (mm110) cc_final: 0.6670 (mm-40) REVERT: F 465 ARG cc_start: 0.5805 (mmt90) cc_final: 0.5174 (mtt-85) REVERT: F 491 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6285 (mm-30) REVERT: F 546 GLU cc_start: 0.8235 (tt0) cc_final: 0.7668 (tp30) REVERT: F 567 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6918 (ttm-80) REVERT: F 607 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8056 (mm-30) REVERT: F 627 ASP cc_start: 0.6971 (OUTLIER) cc_final: 0.6423 (m-30) REVERT: F 638 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6375 (mmt-90) REVERT: F 693 ARG cc_start: 0.7087 (tpp80) cc_final: 0.6582 (mmt90) REVERT: F 741 ARG cc_start: 0.6423 (mtp-110) cc_final: 0.5586 (mmt-90) REVERT: F 753 ARG cc_start: 0.5562 (mtp180) cc_final: 0.4886 (mmm-85) REVERT: F 754 LYS cc_start: 0.5961 (mmtt) cc_final: 0.5579 (ttpt) REVERT: F 757 MET cc_start: 0.6565 (ttm) cc_final: 0.6184 (ptm) outliers start: 167 outliers final: 82 residues processed: 652 average time/residue: 1.6175 time to fit residues: 1236.7704 Evaluate side-chains 605 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 488 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 638 ARG Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 567 ARG Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 638 ARG Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 470 GLU Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 502 LYS Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 638 ARG Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 470 GLU Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain F residue 502 LYS Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 607 GLU Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 638 ARG Chi-restraints excluded: chain F residue 688 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 4.9990 chunk 376 optimal weight: 0.1980 chunk 82 optimal weight: 0.3980 chunk 245 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 417 optimal weight: 20.0000 chunk 346 optimal weight: 5.9990 chunk 193 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 chunk 219 optimal weight: 0.3980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN C 129 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35082 Z= 0.166 Angle : 0.661 8.695 47460 Z= 0.320 Chirality : 0.045 0.164 5322 Planarity : 0.004 0.050 6198 Dihedral : 10.928 115.420 5016 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.63 % Favored : 94.16 % Rotamer: Outliers : 3.71 % Allowed : 17.91 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.13), residues: 4314 helix: 0.07 (0.13), residues: 1668 sheet: 0.14 (0.24), residues: 510 loop : -1.14 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.008 0.001 HIS F 340 PHE 0.029 0.001 PHE F 360 TYR 0.009 0.001 TYR F 495 ARG 0.005 0.000 ARG E 465 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 552 time to evaluate : 3.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 THR cc_start: 0.3109 (OUTLIER) cc_final: 0.2853 (p) REVERT: A 221 GLU cc_start: 0.6650 (mm-30) cc_final: 0.6237 (mm-30) REVERT: A 239 ARG cc_start: 0.5656 (mtt180) cc_final: 0.5278 (mmp-170) REVERT: A 270 ASN cc_start: 0.7482 (t0) cc_final: 0.6964 (t0) REVERT: A 288 LYS cc_start: 0.7096 (ttmt) cc_final: 0.6408 (ptmm) REVERT: A 304 ASP cc_start: 0.7796 (p0) cc_final: 0.7277 (t70) REVERT: A 349 ARG cc_start: 0.6495 (mtt180) cc_final: 0.6102 (mtm-85) REVERT: A 397 GLU cc_start: 0.6142 (tt0) cc_final: 0.5648 (tm-30) REVERT: A 445 LEU cc_start: 0.5222 (OUTLIER) cc_final: 0.4688 (tp) REVERT: A 449 MET cc_start: 0.5340 (tpt) cc_final: 0.5014 (tpt) REVERT: A 451 ASP cc_start: 0.6877 (m-30) cc_final: 0.6651 (m-30) REVERT: A 465 ARG cc_start: 0.6045 (mmt90) cc_final: 0.5130 (mtt-85) REVERT: A 491 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6419 (mm-30) REVERT: A 546 GLU cc_start: 0.8216 (tt0) cc_final: 0.7653 (tp30) REVERT: A 550 MET cc_start: 0.8478 (mtm) cc_final: 0.8133 (ttp) REVERT: A 567 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6671 (ttp-110) REVERT: A 627 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6798 (p0) REVERT: A 633 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7881 (mm) REVERT: A 638 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6676 (mmt-90) REVERT: A 674 PHE cc_start: 0.6101 (t80) cc_final: 0.5731 (t80) REVERT: A 693 ARG cc_start: 0.7089 (tpp80) cc_final: 0.6795 (mtt180) REVERT: A 696 LYS cc_start: 0.7314 (ttpt) cc_final: 0.7037 (tttt) REVERT: A 741 ARG cc_start: 0.6339 (mtp-110) cc_final: 0.5476 (mmt-90) REVERT: A 753 ARG cc_start: 0.5596 (mtp180) cc_final: 0.4812 (mmm-85) REVERT: A 754 LYS cc_start: 0.5774 (mmtt) cc_final: 0.5502 (ttpt) REVERT: A 757 MET cc_start: 0.6529 (ttm) cc_final: 0.6162 (ptm) REVERT: B 39 VAL cc_start: 0.4593 (OUTLIER) cc_final: 0.4386 (m) REVERT: B 215 GLN cc_start: 0.7098 (tt0) cc_final: 0.6696 (tt0) REVERT: B 239 ARG cc_start: 0.5597 (mtt180) cc_final: 0.5328 (mmp-170) REVERT: B 270 ASN cc_start: 0.7497 (t0) cc_final: 0.7145 (t0) REVERT: B 288 LYS cc_start: 0.7269 (ttmt) cc_final: 0.6395 (tmmt) REVERT: B 315 LYS cc_start: 0.3834 (OUTLIER) cc_final: 0.3626 (pttp) REVERT: B 349 ARG cc_start: 0.6446 (mtt180) cc_final: 0.6132 (mtm-85) REVERT: B 397 GLU cc_start: 0.6275 (tt0) cc_final: 0.5650 (tm-30) REVERT: B 427 MET cc_start: 0.4090 (tpt) cc_final: 0.3581 (tpt) REVERT: B 445 LEU cc_start: 0.5177 (OUTLIER) cc_final: 0.4664 (tp) REVERT: B 451 ASP cc_start: 0.6918 (m-30) cc_final: 0.6698 (m-30) REVERT: B 491 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6329 (mm-30) REVERT: B 546 GLU cc_start: 0.8212 (tt0) cc_final: 0.7714 (tp30) REVERT: B 550 MET cc_start: 0.8437 (mtm) cc_final: 0.8126 (ttp) REVERT: B 567 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6769 (ttm-80) REVERT: B 578 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6750 (mt-10) REVERT: B 633 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7891 (mm) REVERT: B 638 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6813 (mmt-90) REVERT: B 693 ARG cc_start: 0.7150 (tpp80) cc_final: 0.6514 (mmt90) REVERT: B 741 ARG cc_start: 0.6236 (mtp-110) cc_final: 0.5539 (mmt-90) REVERT: B 753 ARG cc_start: 0.5690 (mtp180) cc_final: 0.4910 (mmm-85) REVERT: B 754 LYS cc_start: 0.5988 (mmtt) cc_final: 0.5584 (ttpp) REVERT: B 757 MET cc_start: 0.6434 (mtm) cc_final: 0.6140 (ptm) REVERT: C 56 THR cc_start: 0.3209 (OUTLIER) cc_final: 0.2950 (p) REVERT: C 85 ASN cc_start: 0.5156 (p0) cc_final: 0.4458 (m-40) REVERT: C 215 GLN cc_start: 0.7081 (tt0) cc_final: 0.6797 (tt0) REVERT: C 221 GLU cc_start: 0.6600 (mm-30) cc_final: 0.6344 (mm-30) REVERT: C 239 ARG cc_start: 0.5563 (mtt180) cc_final: 0.5238 (mmp-170) REVERT: C 270 ASN cc_start: 0.7467 (t0) cc_final: 0.7078 (t0) REVERT: C 288 LYS cc_start: 0.7598 (tmmt) cc_final: 0.7369 (tmmt) REVERT: C 321 GLU cc_start: 0.6198 (tp30) cc_final: 0.5909 (tp30) REVERT: C 322 ARG cc_start: 0.6524 (mpt180) cc_final: 0.6081 (mmt90) REVERT: C 349 ARG cc_start: 0.6552 (mtt180) cc_final: 0.6163 (mtp180) REVERT: C 366 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7496 (tt0) REVERT: C 397 GLU cc_start: 0.6082 (tt0) cc_final: 0.5594 (tm-30) REVERT: C 465 ARG cc_start: 0.5811 (mmt90) cc_final: 0.5186 (mtt-85) REVERT: C 546 GLU cc_start: 0.8177 (tt0) cc_final: 0.7667 (tp30) REVERT: C 556 GLU cc_start: 0.7366 (pm20) cc_final: 0.7058 (pm20) REVERT: C 567 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6787 (ttm-80) REVERT: C 577 ASP cc_start: 0.6916 (m-30) cc_final: 0.6511 (m-30) REVERT: C 638 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6290 (mmt-90) REVERT: C 693 ARG cc_start: 0.7078 (tpp80) cc_final: 0.6767 (mtt180) REVERT: C 696 LYS cc_start: 0.7199 (ttpt) cc_final: 0.6942 (tttt) REVERT: C 741 ARG cc_start: 0.6465 (mtp-110) cc_final: 0.5596 (mmt-90) REVERT: C 753 ARG cc_start: 0.5556 (mtp180) cc_final: 0.4856 (mmm-85) REVERT: C 754 LYS cc_start: 0.5945 (mmtt) cc_final: 0.5591 (ttpt) REVERT: C 757 MET cc_start: 0.6478 (ttm) cc_final: 0.6212 (ptp) REVERT: D 39 VAL cc_start: 0.4413 (OUTLIER) cc_final: 0.4200 (m) REVERT: D 56 THR cc_start: 0.3219 (OUTLIER) cc_final: 0.2949 (p) REVERT: D 221 GLU cc_start: 0.6664 (mm-30) cc_final: 0.6226 (mm-30) REVERT: D 239 ARG cc_start: 0.5613 (mtt180) cc_final: 0.5254 (mmp-170) REVERT: D 288 LYS cc_start: 0.7116 (ttmt) cc_final: 0.6409 (ptmm) REVERT: D 304 ASP cc_start: 0.7800 (p0) cc_final: 0.7275 (t70) REVERT: D 349 ARG cc_start: 0.6507 (mtt180) cc_final: 0.6106 (mtm-85) REVERT: D 397 GLU cc_start: 0.6107 (tt0) cc_final: 0.5646 (tm-30) REVERT: D 445 LEU cc_start: 0.5088 (OUTLIER) cc_final: 0.4601 (tp) REVERT: D 451 ASP cc_start: 0.6822 (m-30) cc_final: 0.6577 (m-30) REVERT: D 465 ARG cc_start: 0.5811 (mmt180) cc_final: 0.5566 (mtt-85) REVERT: D 546 GLU cc_start: 0.8212 (tt0) cc_final: 0.7721 (tp30) REVERT: D 567 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6708 (tpp-160) REVERT: D 608 MET cc_start: 0.8355 (mtm) cc_final: 0.8112 (mtp) REVERT: D 627 ASP cc_start: 0.7247 (OUTLIER) cc_final: 0.6804 (p0) REVERT: D 633 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7869 (mm) REVERT: D 638 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.6765 (mmt-90) REVERT: D 696 LYS cc_start: 0.7295 (ttpt) cc_final: 0.7003 (tttt) REVERT: D 741 ARG cc_start: 0.6332 (mtp-110) cc_final: 0.5529 (mmt-90) REVERT: D 753 ARG cc_start: 0.5588 (mtp180) cc_final: 0.4786 (mmm-85) REVERT: D 754 LYS cc_start: 0.5854 (mmtt) cc_final: 0.5526 (ttpt) REVERT: D 757 MET cc_start: 0.6560 (mtm) cc_final: 0.6324 (ptm) REVERT: E 39 VAL cc_start: 0.4550 (OUTLIER) cc_final: 0.4346 (m) REVERT: E 215 GLN cc_start: 0.7100 (tt0) cc_final: 0.6697 (tt0) REVERT: E 239 ARG cc_start: 0.5640 (mtt180) cc_final: 0.5244 (mmp80) REVERT: E 270 ASN cc_start: 0.7500 (t0) cc_final: 0.7150 (t0) REVERT: E 288 LYS cc_start: 0.7284 (ttmt) cc_final: 0.6405 (tmmt) REVERT: E 294 GLU cc_start: 0.5922 (mm-30) cc_final: 0.5555 (tp30) REVERT: E 349 ARG cc_start: 0.6446 (mtt180) cc_final: 0.6133 (mtm-85) REVERT: E 397 GLU cc_start: 0.6275 (tt0) cc_final: 0.5652 (tm-30) REVERT: E 427 MET cc_start: 0.4118 (tpt) cc_final: 0.3592 (tpt) REVERT: E 445 LEU cc_start: 0.5142 (OUTLIER) cc_final: 0.4742 (tp) REVERT: E 451 ASP cc_start: 0.6886 (m-30) cc_final: 0.6631 (m-30) REVERT: E 491 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.6330 (mm-30) REVERT: E 546 GLU cc_start: 0.8213 (tt0) cc_final: 0.7714 (tp30) REVERT: E 550 MET cc_start: 0.8445 (mtm) cc_final: 0.8134 (ttp) REVERT: E 567 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6757 (ttm-80) REVERT: E 578 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6750 (mt-10) REVERT: E 633 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7890 (mm) REVERT: E 638 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6864 (mmt-90) REVERT: E 693 ARG cc_start: 0.7139 (tpp80) cc_final: 0.6521 (mmt90) REVERT: E 741 ARG cc_start: 0.6259 (mtp-110) cc_final: 0.5567 (mmt-90) REVERT: E 753 ARG cc_start: 0.5636 (mtp180) cc_final: 0.4852 (mmm-85) REVERT: E 754 LYS cc_start: 0.6018 (mmtt) cc_final: 0.5617 (ttpm) REVERT: E 757 MET cc_start: 0.6465 (mtm) cc_final: 0.6183 (ptm) REVERT: F 56 THR cc_start: 0.3212 (OUTLIER) cc_final: 0.2953 (p) REVERT: F 85 ASN cc_start: 0.5154 (p0) cc_final: 0.4455 (m-40) REVERT: F 215 GLN cc_start: 0.7134 (tt0) cc_final: 0.6877 (tt0) REVERT: F 221 GLU cc_start: 0.6618 (mm-30) cc_final: 0.6316 (mm-30) REVERT: F 239 ARG cc_start: 0.5609 (mtt180) cc_final: 0.5289 (mmp-170) REVERT: F 270 ASN cc_start: 0.7485 (t0) cc_final: 0.7094 (t0) REVERT: F 288 LYS cc_start: 0.6989 (ttmt) cc_final: 0.6442 (ptmm) REVERT: F 321 GLU cc_start: 0.6221 (tp30) cc_final: 0.5946 (tp30) REVERT: F 349 ARG cc_start: 0.6575 (mtt180) cc_final: 0.6210 (mtp-110) REVERT: F 360 PHE cc_start: 0.5958 (t80) cc_final: 0.5659 (t80) REVERT: F 397 GLU cc_start: 0.6079 (tt0) cc_final: 0.5594 (tm-30) REVERT: F 465 ARG cc_start: 0.5835 (mmt90) cc_final: 0.5235 (mtt-85) REVERT: F 491 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6272 (mm-30) REVERT: F 546 GLU cc_start: 0.8214 (tt0) cc_final: 0.7683 (tp30) REVERT: F 567 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6776 (ttm-80) REVERT: F 577 ASP cc_start: 0.6927 (m-30) cc_final: 0.6512 (m-30) REVERT: F 607 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8057 (mm-30) REVERT: F 638 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6314 (mmt-90) REVERT: F 693 ARG cc_start: 0.7040 (tpp80) cc_final: 0.6442 (mmt90) REVERT: F 696 LYS cc_start: 0.7203 (ttpt) cc_final: 0.6926 (tttt) REVERT: F 741 ARG cc_start: 0.6468 (mtp-110) cc_final: 0.5598 (mmt-90) REVERT: F 753 ARG cc_start: 0.5562 (mtp180) cc_final: 0.4858 (mmm-85) REVERT: F 754 LYS cc_start: 0.5938 (mmtt) cc_final: 0.5590 (ttpt) REVERT: F 757 MET cc_start: 0.6476 (ttm) cc_final: 0.6210 (ptp) outliers start: 137 outliers final: 42 residues processed: 654 average time/residue: 1.6750 time to fit residues: 1286.3871 Evaluate side-chains 562 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 485 time to evaluate : 3.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 638 ARG Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 567 ARG Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 638 ARG Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 638 ARG Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 607 GLU Chi-restraints excluded: chain F residue 638 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 238 optimal weight: 5.9990 chunk 305 optimal weight: 6.9990 chunk 236 optimal weight: 7.9990 chunk 351 optimal weight: 9.9990 chunk 233 optimal weight: 0.0970 chunk 416 optimal weight: 8.9990 chunk 260 optimal weight: 5.9990 chunk 253 optimal weight: 0.0470 chunk 192 optimal weight: 0.0270 overall best weight: 1.8338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35082 Z= 0.170 Angle : 0.656 8.863 47460 Z= 0.315 Chirality : 0.045 0.156 5322 Planarity : 0.004 0.047 6198 Dihedral : 9.923 102.693 5016 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.10 % Favored : 94.69 % Rotamer: Outliers : 3.79 % Allowed : 18.35 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.13), residues: 4314 helix: 0.25 (0.13), residues: 1668 sheet: 0.24 (0.24), residues: 510 loop : -1.05 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 476 HIS 0.007 0.001 HIS C 340 PHE 0.026 0.001 PHE F 360 TYR 0.008 0.001 TYR F 495 ARG 0.010 0.000 ARG E 465 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 516 time to evaluate : 4.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 GLU cc_start: 0.6652 (mm-30) cc_final: 0.6265 (mm-30) REVERT: A 239 ARG cc_start: 0.5706 (mtt180) cc_final: 0.5272 (mmp-170) REVERT: A 270 ASN cc_start: 0.7434 (t0) cc_final: 0.6916 (t0) REVERT: A 288 LYS cc_start: 0.7031 (ttmt) cc_final: 0.6366 (ptmm) REVERT: A 304 ASP cc_start: 0.7799 (p0) cc_final: 0.7268 (t70) REVERT: A 349 ARG cc_start: 0.6502 (mtt180) cc_final: 0.6107 (mtm-85) REVERT: A 397 GLU cc_start: 0.6139 (tt0) cc_final: 0.5641 (tm-30) REVERT: A 445 LEU cc_start: 0.5394 (OUTLIER) cc_final: 0.4829 (tp) REVERT: A 451 ASP cc_start: 0.6809 (m-30) cc_final: 0.6592 (m-30) REVERT: A 465 ARG cc_start: 0.6055 (mmt90) cc_final: 0.5168 (mtt-85) REVERT: A 491 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6375 (mm-30) REVERT: A 546 GLU cc_start: 0.8196 (tt0) cc_final: 0.7646 (tp30) REVERT: A 567 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6727 (tpp-160) REVERT: A 608 MET cc_start: 0.8418 (mtm) cc_final: 0.8183 (mtp) REVERT: A 627 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6867 (p0) REVERT: A 633 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7868 (mm) REVERT: A 638 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.6735 (mmt-90) REVERT: A 650 GLU cc_start: 0.5427 (mp0) cc_final: 0.4842 (mt-10) REVERT: A 674 PHE cc_start: 0.6147 (t80) cc_final: 0.5681 (t80) REVERT: A 693 ARG cc_start: 0.7108 (tpp80) cc_final: 0.6795 (mtt180) REVERT: A 696 LYS cc_start: 0.7254 (ttpt) cc_final: 0.6986 (tttt) REVERT: A 741 ARG cc_start: 0.6319 (mtp-110) cc_final: 0.5480 (mmt-90) REVERT: A 753 ARG cc_start: 0.5537 (mtp180) cc_final: 0.4747 (mmm-85) REVERT: A 754 LYS cc_start: 0.5773 (mmtt) cc_final: 0.5542 (ttpt) REVERT: A 757 MET cc_start: 0.6517 (ttm) cc_final: 0.6149 (ptm) REVERT: B 89 ARG cc_start: 0.6270 (OUTLIER) cc_final: 0.3967 (ttp80) REVERT: B 215 GLN cc_start: 0.7087 (tt0) cc_final: 0.6678 (tt0) REVERT: B 239 ARG cc_start: 0.5674 (mtt180) cc_final: 0.5347 (mmp-170) REVERT: B 270 ASN cc_start: 0.7492 (t0) cc_final: 0.7158 (t0) REVERT: B 288 LYS cc_start: 0.7158 (ttmt) cc_final: 0.6621 (tttp) REVERT: B 315 LYS cc_start: 0.3818 (OUTLIER) cc_final: 0.3513 (pttm) REVERT: B 349 ARG cc_start: 0.6436 (mtt180) cc_final: 0.6110 (mtm-85) REVERT: B 397 GLU cc_start: 0.6236 (tt0) cc_final: 0.5636 (tm-30) REVERT: B 445 LEU cc_start: 0.5121 (OUTLIER) cc_final: 0.4658 (tp) REVERT: B 491 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6387 (mm-30) REVERT: B 546 GLU cc_start: 0.8220 (tt0) cc_final: 0.7712 (tp30) REVERT: B 577 ASP cc_start: 0.6916 (m-30) cc_final: 0.6525 (m-30) REVERT: B 633 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7914 (mm) REVERT: B 634 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8028 (mt) REVERT: B 638 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6861 (mmt-90) REVERT: B 693 ARG cc_start: 0.7120 (tpp80) cc_final: 0.6494 (mmt90) REVERT: B 741 ARG cc_start: 0.6130 (mtp-110) cc_final: 0.5168 (mmm160) REVERT: B 753 ARG cc_start: 0.5655 (mtp180) cc_final: 0.4877 (mmm-85) REVERT: B 754 LYS cc_start: 0.5959 (mmtt) cc_final: 0.5615 (ttpp) REVERT: B 757 MET cc_start: 0.6426 (mtm) cc_final: 0.6159 (ptm) REVERT: C 56 THR cc_start: 0.3120 (OUTLIER) cc_final: 0.2874 (p) REVERT: C 85 ASN cc_start: 0.5193 (p0) cc_final: 0.4464 (m-40) REVERT: C 215 GLN cc_start: 0.7101 (tt0) cc_final: 0.6813 (tt0) REVERT: C 221 GLU cc_start: 0.6616 (mm-30) cc_final: 0.6361 (mm-30) REVERT: C 239 ARG cc_start: 0.5589 (mtt180) cc_final: 0.5272 (mmp-170) REVERT: C 270 ASN cc_start: 0.7461 (t0) cc_final: 0.7058 (t0) REVERT: C 288 LYS cc_start: 0.7632 (tmmt) cc_final: 0.7423 (tmmt) REVERT: C 321 GLU cc_start: 0.6277 (tp30) cc_final: 0.6023 (tp30) REVERT: C 322 ARG cc_start: 0.6532 (mpt180) cc_final: 0.6156 (mmt90) REVERT: C 349 ARG cc_start: 0.6554 (mtt180) cc_final: 0.6215 (mtp-110) REVERT: C 366 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7543 (tt0) REVERT: C 397 GLU cc_start: 0.6105 (tt0) cc_final: 0.5607 (tm-30) REVERT: C 465 ARG cc_start: 0.5786 (mmt90) cc_final: 0.5200 (mtt-85) REVERT: C 546 GLU cc_start: 0.8187 (tt0) cc_final: 0.7673 (tp30) REVERT: C 577 ASP cc_start: 0.7006 (m-30) cc_final: 0.6597 (m-30) REVERT: C 638 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6302 (mmt-90) REVERT: C 693 ARG cc_start: 0.7094 (tpp80) cc_final: 0.6774 (mtt180) REVERT: C 696 LYS cc_start: 0.7204 (ttpt) cc_final: 0.6944 (tttt) REVERT: C 741 ARG cc_start: 0.6453 (mtp-110) cc_final: 0.5609 (mmt-90) REVERT: C 753 ARG cc_start: 0.5577 (mtp180) cc_final: 0.4886 (mmm-85) REVERT: C 754 LYS cc_start: 0.5886 (mmtt) cc_final: 0.5606 (ttpt) REVERT: C 757 MET cc_start: 0.6463 (OUTLIER) cc_final: 0.6094 (ptm) REVERT: D 221 GLU cc_start: 0.6661 (mm-30) cc_final: 0.6270 (mm-30) REVERT: D 239 ARG cc_start: 0.5699 (mtt180) cc_final: 0.5305 (mmp-170) REVERT: D 288 LYS cc_start: 0.7093 (ttmt) cc_final: 0.6421 (ptmm) REVERT: D 304 ASP cc_start: 0.7790 (p0) cc_final: 0.7250 (t70) REVERT: D 349 ARG cc_start: 0.6518 (mtt180) cc_final: 0.6121 (mtm-85) REVERT: D 397 GLU cc_start: 0.6151 (tt0) cc_final: 0.5694 (tm-30) REVERT: D 427 MET cc_start: 0.4222 (tpt) cc_final: 0.3696 (tpt) REVERT: D 445 LEU cc_start: 0.5117 (OUTLIER) cc_final: 0.4799 (tp) REVERT: D 449 MET cc_start: 0.5306 (tpt) cc_final: 0.4989 (tpt) REVERT: D 451 ASP cc_start: 0.6796 (m-30) cc_final: 0.6559 (m-30) REVERT: D 465 ARG cc_start: 0.5879 (mmt180) cc_final: 0.5572 (mtt-85) REVERT: D 546 GLU cc_start: 0.8223 (tt0) cc_final: 0.7711 (tp30) REVERT: D 567 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6722 (tpp-160) REVERT: D 627 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.6881 (p0) REVERT: D 633 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7884 (mm) REVERT: D 638 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.6770 (mmt-90) REVERT: D 674 PHE cc_start: 0.6059 (t80) cc_final: 0.5731 (t80) REVERT: D 696 LYS cc_start: 0.7247 (ttpt) cc_final: 0.6910 (tttt) REVERT: D 741 ARG cc_start: 0.6303 (mtp-110) cc_final: 0.5519 (mmt-90) REVERT: D 753 ARG cc_start: 0.5575 (mtp180) cc_final: 0.4797 (mmm-85) REVERT: D 754 LYS cc_start: 0.5823 (mmtt) cc_final: 0.5548 (ttpt) REVERT: D 757 MET cc_start: 0.6473 (mtm) cc_final: 0.6218 (ptm) REVERT: E 89 ARG cc_start: 0.6262 (OUTLIER) cc_final: 0.3961 (ttp80) REVERT: E 215 GLN cc_start: 0.7108 (tt0) cc_final: 0.6721 (tt0) REVERT: E 239 ARG cc_start: 0.5617 (mtt180) cc_final: 0.5240 (mmp-170) REVERT: E 270 ASN cc_start: 0.7490 (t0) cc_final: 0.7156 (t0) REVERT: E 288 LYS cc_start: 0.7161 (ttmt) cc_final: 0.6590 (pttm) REVERT: E 349 ARG cc_start: 0.6435 (mtt180) cc_final: 0.6111 (mtm-85) REVERT: E 397 GLU cc_start: 0.6231 (tt0) cc_final: 0.5664 (tm-30) REVERT: E 445 LEU cc_start: 0.5263 (OUTLIER) cc_final: 0.4677 (tp) REVERT: E 449 MET cc_start: 0.5538 (tpt) cc_final: 0.5248 (tpt) REVERT: E 491 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6377 (mm-30) REVERT: E 546 GLU cc_start: 0.8217 (tt0) cc_final: 0.7705 (tp30) REVERT: E 567 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6682 (ttp-110) REVERT: E 577 ASP cc_start: 0.6914 (m-30) cc_final: 0.6521 (m-30) REVERT: E 633 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7913 (mm) REVERT: E 634 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8023 (mt) REVERT: E 638 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.6919 (mmt-90) REVERT: E 693 ARG cc_start: 0.7128 (tpp80) cc_final: 0.6517 (mmt90) REVERT: E 741 ARG cc_start: 0.6118 (mtp-110) cc_final: 0.5145 (mmm160) REVERT: E 753 ARG cc_start: 0.5657 (mtp180) cc_final: 0.4861 (mmm-85) REVERT: E 754 LYS cc_start: 0.6001 (mmtt) cc_final: 0.5617 (ttpp) REVERT: E 757 MET cc_start: 0.6456 (mtm) cc_final: 0.6195 (ptm) REVERT: F 56 THR cc_start: 0.3123 (OUTLIER) cc_final: 0.2879 (p) REVERT: F 85 ASN cc_start: 0.5191 (p0) cc_final: 0.4459 (m-40) REVERT: F 215 GLN cc_start: 0.7052 (tt0) cc_final: 0.6790 (tt0) REVERT: F 221 GLU cc_start: 0.6647 (mm-30) cc_final: 0.6402 (mm-30) REVERT: F 236 LYS cc_start: 0.6091 (tptt) cc_final: 0.5522 (ttpm) REVERT: F 239 ARG cc_start: 0.5521 (mtt180) cc_final: 0.5169 (mmp-170) REVERT: F 270 ASN cc_start: 0.7484 (t0) cc_final: 0.7074 (t0) REVERT: F 288 LYS cc_start: 0.6988 (ttmt) cc_final: 0.5997 (ptmm) REVERT: F 321 GLU cc_start: 0.6326 (tp30) cc_final: 0.6125 (mp0) REVERT: F 322 ARG cc_start: 0.6579 (mmt180) cc_final: 0.6253 (mmt90) REVERT: F 349 ARG cc_start: 0.6568 (mtt180) cc_final: 0.6235 (mtp-110) REVERT: F 360 PHE cc_start: 0.5985 (t80) cc_final: 0.5753 (t80) REVERT: F 397 GLU cc_start: 0.6111 (tt0) cc_final: 0.5621 (tm-30) REVERT: F 458 GLN cc_start: 0.6920 (mm110) cc_final: 0.6641 (mm-40) REVERT: F 465 ARG cc_start: 0.5776 (mmt90) cc_final: 0.5271 (mtt-85) REVERT: F 491 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.6284 (mm-30) REVERT: F 546 GLU cc_start: 0.8236 (tt0) cc_final: 0.7710 (tp30) REVERT: F 577 ASP cc_start: 0.7001 (m-30) cc_final: 0.6591 (m-30) REVERT: F 607 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8026 (mm-30) REVERT: F 638 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6345 (mmt-90) REVERT: F 693 ARG cc_start: 0.7062 (tpp80) cc_final: 0.6453 (mmt90) REVERT: F 696 LYS cc_start: 0.7177 (ttpt) cc_final: 0.6894 (tttt) REVERT: F 741 ARG cc_start: 0.6453 (mtp-110) cc_final: 0.5612 (mmt-90) REVERT: F 753 ARG cc_start: 0.5582 (mtp180) cc_final: 0.4888 (mmm-85) REVERT: F 754 LYS cc_start: 0.5860 (mmtt) cc_final: 0.5588 (ttpt) REVERT: F 757 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.6095 (ptm) outliers start: 140 outliers final: 59 residues processed: 629 average time/residue: 1.6043 time to fit residues: 1185.0712 Evaluate side-chains 582 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 490 time to evaluate : 4.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 638 ARG Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 567 ARG Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 638 ARG Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 638 ARG Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 607 GLU Chi-restraints excluded: chain F residue 638 ARG Chi-restraints excluded: chain F residue 752 ILE Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 0.0980 chunk 166 optimal weight: 0.5980 chunk 248 optimal weight: 20.0000 chunk 125 optimal weight: 0.8980 chunk 81 optimal weight: 0.0060 chunk 80 optimal weight: 6.9990 chunk 264 optimal weight: 9.9990 chunk 283 optimal weight: 9.9990 chunk 205 optimal weight: 0.6980 chunk 38 optimal weight: 20.0000 chunk 327 optimal weight: 7.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN B 129 ASN B 538 ASN B 603 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN E 538 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 35082 Z= 0.146 Angle : 0.622 8.527 47460 Z= 0.298 Chirality : 0.044 0.157 5322 Planarity : 0.004 0.045 6198 Dihedral : 8.275 75.828 5016 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.05 % Favored : 94.69 % Rotamer: Outliers : 3.06 % Allowed : 18.94 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.13), residues: 4314 helix: 0.72 (0.14), residues: 1590 sheet: -0.16 (0.22), residues: 576 loop : -1.02 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 476 HIS 0.005 0.001 HIS D 340 PHE 0.022 0.001 PHE F 360 TYR 0.011 0.001 TYR A 495 ARG 0.009 0.000 ARG E 465 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 528 time to evaluate : 3.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 THR cc_start: 0.3121 (OUTLIER) cc_final: 0.2849 (p) REVERT: A 85 ASN cc_start: 0.5412 (p0) cc_final: 0.4636 (m-40) REVERT: A 221 GLU cc_start: 0.6646 (mm-30) cc_final: 0.6297 (mm-30) REVERT: A 239 ARG cc_start: 0.5619 (mtt180) cc_final: 0.5219 (mmp-170) REVERT: A 270 ASN cc_start: 0.7479 (t0) cc_final: 0.6959 (t0) REVERT: A 278 LEU cc_start: 0.5291 (mm) cc_final: 0.4384 (tt) REVERT: A 288 LYS cc_start: 0.7077 (ttmt) cc_final: 0.6375 (ptmm) REVERT: A 304 ASP cc_start: 0.7767 (p0) cc_final: 0.7282 (t70) REVERT: A 349 ARG cc_start: 0.6485 (mtt180) cc_final: 0.6116 (mtm-85) REVERT: A 389 LYS cc_start: 0.5668 (tmtm) cc_final: 0.4866 (tptt) REVERT: A 397 GLU cc_start: 0.6138 (tt0) cc_final: 0.5646 (tm-30) REVERT: A 427 MET cc_start: 0.4083 (tpt) cc_final: 0.3598 (tpt) REVERT: A 445 LEU cc_start: 0.5369 (OUTLIER) cc_final: 0.4785 (tp) REVERT: A 451 ASP cc_start: 0.6709 (m-30) cc_final: 0.6475 (m-30) REVERT: A 477 GLU cc_start: 0.7099 (mp0) cc_final: 0.6835 (mm-30) REVERT: A 491 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.6272 (mm-30) REVERT: A 546 GLU cc_start: 0.8177 (tt0) cc_final: 0.7657 (tp30) REVERT: A 550 MET cc_start: 0.8413 (mtm) cc_final: 0.8130 (ttp) REVERT: A 567 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6556 (ttp-110) REVERT: A 638 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6767 (mmt-90) REVERT: A 650 GLU cc_start: 0.5372 (mp0) cc_final: 0.4865 (mt-10) REVERT: A 674 PHE cc_start: 0.6158 (t80) cc_final: 0.5694 (t80) REVERT: A 693 ARG cc_start: 0.7096 (tpp80) cc_final: 0.6821 (mtt180) REVERT: A 733 ARG cc_start: 0.6066 (tpt170) cc_final: 0.5828 (tpt170) REVERT: A 741 ARG cc_start: 0.6295 (mtp-110) cc_final: 0.5451 (mmt-90) REVERT: A 753 ARG cc_start: 0.5565 (mtp180) cc_final: 0.4807 (mmm-85) REVERT: A 757 MET cc_start: 0.6338 (ttm) cc_final: 0.6029 (ptm) REVERT: B 215 GLN cc_start: 0.7068 (tt0) cc_final: 0.6670 (tt0) REVERT: B 239 ARG cc_start: 0.5649 (mtt180) cc_final: 0.5309 (mmp-170) REVERT: B 270 ASN cc_start: 0.7453 (t0) cc_final: 0.7171 (t0) REVERT: B 288 LYS cc_start: 0.7191 (ttmt) cc_final: 0.6511 (tmmt) REVERT: B 315 LYS cc_start: 0.3607 (OUTLIER) cc_final: 0.3391 (pttm) REVERT: B 349 ARG cc_start: 0.6480 (mtt180) cc_final: 0.6204 (mtp-110) REVERT: B 397 GLU cc_start: 0.6254 (tt0) cc_final: 0.5637 (tm-30) REVERT: B 427 MET cc_start: 0.4264 (tpt) cc_final: 0.3709 (tpt) REVERT: B 445 LEU cc_start: 0.5325 (OUTLIER) cc_final: 0.4668 (tp) REVERT: B 491 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6135 (mm-30) REVERT: B 546 GLU cc_start: 0.8195 (tt0) cc_final: 0.7711 (tp30) REVERT: B 578 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6682 (mt-10) REVERT: B 627 ASP cc_start: 0.7185 (OUTLIER) cc_final: 0.6781 (p0) REVERT: B 638 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6693 (mmt-90) REVERT: B 693 ARG cc_start: 0.7117 (tpp80) cc_final: 0.6518 (mmt90) REVERT: B 741 ARG cc_start: 0.6201 (mtp-110) cc_final: 0.5501 (mmt-90) REVERT: B 753 ARG cc_start: 0.5620 (mtp180) cc_final: 0.4861 (mmm-85) REVERT: B 757 MET cc_start: 0.6172 (mtm) cc_final: 0.5970 (ptm) REVERT: C 56 THR cc_start: 0.2959 (OUTLIER) cc_final: 0.2734 (p) REVERT: C 85 ASN cc_start: 0.5137 (p0) cc_final: 0.4498 (m-40) REVERT: C 215 GLN cc_start: 0.7084 (tt0) cc_final: 0.6884 (tt0) REVERT: C 239 ARG cc_start: 0.5593 (mtt180) cc_final: 0.5364 (mmp-170) REVERT: C 270 ASN cc_start: 0.7459 (t0) cc_final: 0.7038 (t0) REVERT: C 288 LYS cc_start: 0.7414 (tmmt) cc_final: 0.7158 (tmmt) REVERT: C 322 ARG cc_start: 0.6356 (mpt180) cc_final: 0.6125 (mmt90) REVERT: C 349 ARG cc_start: 0.6550 (mtt180) cc_final: 0.6139 (mtm-85) REVERT: C 389 LYS cc_start: 0.5431 (tptm) cc_final: 0.5123 (tptt) REVERT: C 397 GLU cc_start: 0.6082 (tt0) cc_final: 0.5592 (tm-30) REVERT: C 465 ARG cc_start: 0.5757 (mmt90) cc_final: 0.5163 (mtt-85) REVERT: C 502 LYS cc_start: 0.7486 (tppp) cc_final: 0.7250 (tppp) REVERT: C 546 GLU cc_start: 0.8147 (tt0) cc_final: 0.7647 (tp30) REVERT: C 550 MET cc_start: 0.7976 (mtm) cc_final: 0.7698 (ttp) REVERT: C 567 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6678 (tpp-160) REVERT: C 577 ASP cc_start: 0.6652 (m-30) cc_final: 0.6288 (m-30) REVERT: C 627 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.6746 (p0) REVERT: C 638 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6154 (mmt-90) REVERT: C 693 ARG cc_start: 0.7011 (tpp80) cc_final: 0.6738 (mtt180) REVERT: C 696 LYS cc_start: 0.7214 (ttpt) cc_final: 0.6910 (tttt) REVERT: C 733 ARG cc_start: 0.6095 (tpt170) cc_final: 0.5851 (tpt170) REVERT: C 741 ARG cc_start: 0.6463 (mtp-110) cc_final: 0.5619 (mmt-90) REVERT: C 753 ARG cc_start: 0.5529 (mtp180) cc_final: 0.4832 (mmm-85) REVERT: C 754 LYS cc_start: 0.5740 (mmtt) cc_final: 0.5503 (ttpp) REVERT: C 757 MET cc_start: 0.6525 (OUTLIER) cc_final: 0.6295 (ptp) REVERT: D 56 THR cc_start: 0.3107 (OUTLIER) cc_final: 0.2852 (p) REVERT: D 85 ASN cc_start: 0.5387 (p0) cc_final: 0.4583 (m-40) REVERT: D 221 GLU cc_start: 0.6611 (mm-30) cc_final: 0.6271 (mm-30) REVERT: D 239 ARG cc_start: 0.5691 (mtt180) cc_final: 0.5310 (mmp-170) REVERT: D 278 LEU cc_start: 0.5427 (mm) cc_final: 0.4517 (tt) REVERT: D 288 LYS cc_start: 0.7063 (ttmt) cc_final: 0.6369 (ptmm) REVERT: D 304 ASP cc_start: 0.7740 (p0) cc_final: 0.7259 (t70) REVERT: D 349 ARG cc_start: 0.6493 (mtt180) cc_final: 0.6115 (mtm-85) REVERT: D 397 GLU cc_start: 0.6135 (tt0) cc_final: 0.5665 (tm-30) REVERT: D 427 MET cc_start: 0.4091 (tpt) cc_final: 0.3584 (tpt) REVERT: D 445 LEU cc_start: 0.5188 (OUTLIER) cc_final: 0.4733 (tp) REVERT: D 449 MET cc_start: 0.5377 (tpt) cc_final: 0.4936 (tpt) REVERT: D 451 ASP cc_start: 0.6618 (m-30) cc_final: 0.6386 (m-30) REVERT: D 546 GLU cc_start: 0.8188 (tt0) cc_final: 0.7704 (tp30) REVERT: D 550 MET cc_start: 0.8191 (mtm) cc_final: 0.7864 (ttp) REVERT: D 567 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6550 (ttp-110) REVERT: D 627 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6909 (p0) REVERT: D 638 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6800 (mmt-90) REVERT: D 674 PHE cc_start: 0.6067 (t80) cc_final: 0.5701 (t80) REVERT: D 741 ARG cc_start: 0.6263 (mtp-110) cc_final: 0.5436 (mmt-90) REVERT: D 753 ARG cc_start: 0.5548 (mtp180) cc_final: 0.4793 (mmm-85) REVERT: D 754 LYS cc_start: 0.5689 (mmtt) cc_final: 0.5439 (ttpp) REVERT: D 757 MET cc_start: 0.6269 (OUTLIER) cc_final: 0.6058 (ptm) REVERT: E 215 GLN cc_start: 0.7057 (tt0) cc_final: 0.6638 (tt0) REVERT: E 236 LYS cc_start: 0.5924 (tptt) cc_final: 0.5444 (tttm) REVERT: E 239 ARG cc_start: 0.5641 (mtt180) cc_final: 0.5255 (mmp80) REVERT: E 270 ASN cc_start: 0.7453 (t0) cc_final: 0.7171 (t0) REVERT: E 288 LYS cc_start: 0.7080 (ttmt) cc_final: 0.6346 (tmmt) REVERT: E 349 ARG cc_start: 0.6490 (mtt180) cc_final: 0.6209 (mtp-110) REVERT: E 397 GLU cc_start: 0.6256 (tt0) cc_final: 0.5647 (tm-30) REVERT: E 427 MET cc_start: 0.4234 (tpt) cc_final: 0.3669 (tpt) REVERT: E 445 LEU cc_start: 0.5346 (OUTLIER) cc_final: 0.4670 (tp) REVERT: E 449 MET cc_start: 0.5556 (tpt) cc_final: 0.5265 (tpt) REVERT: E 491 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.6132 (mm-30) REVERT: E 546 GLU cc_start: 0.8195 (tt0) cc_final: 0.7720 (tp30) REVERT: E 567 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6567 (ttp-110) REVERT: E 578 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6681 (mt-10) REVERT: E 627 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6851 (p0) REVERT: E 638 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6694 (mmt-90) REVERT: E 674 PHE cc_start: 0.6307 (t80) cc_final: 0.6094 (t80) REVERT: E 693 ARG cc_start: 0.7057 (tpp80) cc_final: 0.6507 (mmt90) REVERT: E 740 MET cc_start: 0.7453 (tpp) cc_final: 0.7162 (tpt) REVERT: E 741 ARG cc_start: 0.6147 (mtp-110) cc_final: 0.5109 (mmm160) REVERT: E 753 ARG cc_start: 0.5638 (mtp180) cc_final: 0.4853 (mmm-85) REVERT: E 754 LYS cc_start: 0.5857 (mmtt) cc_final: 0.5554 (ttpp) REVERT: E 757 MET cc_start: 0.6260 (mtm) cc_final: 0.6058 (ptm) REVERT: F 56 THR cc_start: 0.2956 (OUTLIER) cc_final: 0.2733 (p) REVERT: F 85 ASN cc_start: 0.5137 (p0) cc_final: 0.4507 (m-40) REVERT: F 162 GLU cc_start: 0.4592 (OUTLIER) cc_final: 0.4041 (mm-30) REVERT: F 215 GLN cc_start: 0.7020 (tt0) cc_final: 0.6777 (tt0) REVERT: F 239 ARG cc_start: 0.5606 (mtt180) cc_final: 0.5372 (mmp-170) REVERT: F 270 ASN cc_start: 0.7493 (t0) cc_final: 0.7060 (t0) REVERT: F 288 LYS cc_start: 0.6858 (ttmt) cc_final: 0.6094 (ptmm) REVERT: F 349 ARG cc_start: 0.6549 (mtt180) cc_final: 0.6151 (mtm-85) REVERT: F 389 LYS cc_start: 0.5433 (tptm) cc_final: 0.5125 (tptt) REVERT: F 397 GLU cc_start: 0.6084 (tt0) cc_final: 0.5598 (tm-30) REVERT: F 465 ARG cc_start: 0.5719 (mmt90) cc_final: 0.5208 (mtt-85) REVERT: F 491 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6148 (mm-30) REVERT: F 502 LYS cc_start: 0.7410 (tppp) cc_final: 0.7105 (tppp) REVERT: F 546 GLU cc_start: 0.8198 (tt0) cc_final: 0.7721 (tp30) REVERT: F 567 ARG cc_start: 0.7003 (OUTLIER) cc_final: 0.6689 (ttm-80) REVERT: F 577 ASP cc_start: 0.6647 (m-30) cc_final: 0.6286 (m-30) REVERT: F 627 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.6744 (p0) REVERT: F 638 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6174 (mmt-90) REVERT: F 693 ARG cc_start: 0.6981 (tpp80) cc_final: 0.6455 (mmt90) REVERT: F 696 LYS cc_start: 0.7185 (ttpt) cc_final: 0.6856 (tttt) REVERT: F 733 ARG cc_start: 0.6094 (tpt170) cc_final: 0.5834 (tpt-90) REVERT: F 741 ARG cc_start: 0.6464 (mtp-110) cc_final: 0.5624 (mmt-90) REVERT: F 753 ARG cc_start: 0.5523 (mtp180) cc_final: 0.4823 (mmm-85) REVERT: F 757 MET cc_start: 0.6507 (OUTLIER) cc_final: 0.6267 (ptp) outliers start: 113 outliers final: 41 residues processed: 614 average time/residue: 1.7429 time to fit residues: 1245.6251 Evaluate side-chains 566 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 492 time to evaluate : 3.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 638 ARG Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 567 ARG Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 638 ARG Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 638 ARG Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 638 ARG Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 30.0000 chunk 398 optimal weight: 30.0000 chunk 363 optimal weight: 9.9990 chunk 388 optimal weight: 20.0000 chunk 233 optimal weight: 30.0000 chunk 169 optimal weight: 20.0000 chunk 304 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 350 optimal weight: 0.9980 chunk 366 optimal weight: 8.9990 chunk 386 optimal weight: 7.9990 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 35082 Z= 0.330 Angle : 0.815 9.887 47460 Z= 0.401 Chirality : 0.050 0.189 5322 Planarity : 0.006 0.057 6198 Dihedral : 9.735 96.513 5016 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.26 % Favored : 93.69 % Rotamer: Outliers : 3.79 % Allowed : 18.64 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.12), residues: 4314 helix: 0.07 (0.13), residues: 1626 sheet: -0.21 (0.24), residues: 528 loop : -1.30 (0.12), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 551 HIS 0.010 0.002 HIS D 340 PHE 0.020 0.003 PHE D 139 TYR 0.012 0.002 TYR C 644 ARG 0.014 0.001 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 498 time to evaluate : 3.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 GLU cc_start: 0.6608 (mm-30) cc_final: 0.6246 (mm-30) REVERT: A 239 ARG cc_start: 0.5703 (mtt180) cc_final: 0.5289 (mmp-170) REVERT: A 270 ASN cc_start: 0.7408 (t0) cc_final: 0.6973 (t0) REVERT: A 288 LYS cc_start: 0.6973 (ttmt) cc_final: 0.6360 (ptmm) REVERT: A 304 ASP cc_start: 0.7858 (p0) cc_final: 0.7248 (t70) REVERT: A 349 ARG cc_start: 0.6514 (mtt180) cc_final: 0.6159 (mtm-85) REVERT: A 397 GLU cc_start: 0.6258 (tt0) cc_final: 0.5751 (tm-30) REVERT: A 427 MET cc_start: 0.4282 (tpt) cc_final: 0.3765 (tpt) REVERT: A 445 LEU cc_start: 0.5389 (OUTLIER) cc_final: 0.4887 (tp) REVERT: A 451 ASP cc_start: 0.7064 (m-30) cc_final: 0.6804 (m-30) REVERT: A 458 GLN cc_start: 0.6859 (mm110) cc_final: 0.6600 (mm-40) REVERT: A 546 GLU cc_start: 0.8225 (tt0) cc_final: 0.7664 (tp30) REVERT: A 567 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6784 (ttp-110) REVERT: A 577 ASP cc_start: 0.7614 (m-30) cc_final: 0.7406 (m-30) REVERT: A 608 MET cc_start: 0.8460 (mtm) cc_final: 0.8229 (mtp) REVERT: A 627 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.6904 (p0) REVERT: A 638 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.6649 (mmt-90) REVERT: A 650 GLU cc_start: 0.5522 (mp0) cc_final: 0.4880 (mt-10) REVERT: A 674 PHE cc_start: 0.6191 (t80) cc_final: 0.5885 (t80) REVERT: A 741 ARG cc_start: 0.6441 (mtp-110) cc_final: 0.5613 (mmt-90) REVERT: A 753 ARG cc_start: 0.5533 (mtp180) cc_final: 0.5153 (mtp-110) REVERT: A 757 MET cc_start: 0.6522 (OUTLIER) cc_final: 0.6224 (ptm) REVERT: B 215 GLN cc_start: 0.7130 (tt0) cc_final: 0.6758 (tt0) REVERT: B 239 ARG cc_start: 0.5704 (mtt180) cc_final: 0.5358 (mmp-170) REVERT: B 270 ASN cc_start: 0.7371 (t0) cc_final: 0.7075 (t0) REVERT: B 288 LYS cc_start: 0.7215 (ttmt) cc_final: 0.6629 (pttm) REVERT: B 349 ARG cc_start: 0.6463 (mtt180) cc_final: 0.6102 (mtm-85) REVERT: B 397 GLU cc_start: 0.6318 (tt0) cc_final: 0.5764 (tm-30) REVERT: B 491 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6661 (mm-30) REVERT: B 546 GLU cc_start: 0.8288 (tt0) cc_final: 0.7729 (tp30) REVERT: B 567 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6861 (ttm-80) REVERT: B 627 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.6924 (p0) REVERT: B 638 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.6811 (mmt-90) REVERT: B 741 ARG cc_start: 0.6304 (mtp-110) cc_final: 0.5423 (mmp-170) REVERT: B 753 ARG cc_start: 0.5585 (mtp180) cc_final: 0.4877 (mmm-85) REVERT: B 757 MET cc_start: 0.6575 (mtm) cc_final: 0.6282 (ptm) REVERT: C 215 GLN cc_start: 0.7148 (tt0) cc_final: 0.6888 (tt0) REVERT: C 239 ARG cc_start: 0.5685 (mtt180) cc_final: 0.5345 (mmp-170) REVERT: C 270 ASN cc_start: 0.7432 (t0) cc_final: 0.7077 (t0) REVERT: C 322 ARG cc_start: 0.6648 (mpt180) cc_final: 0.4940 (ttp-110) REVERT: C 349 ARG cc_start: 0.6447 (mtt180) cc_final: 0.6144 (mtp-110) REVERT: C 359 ARG cc_start: 0.6418 (OUTLIER) cc_final: 0.6051 (ttt180) REVERT: C 397 GLU cc_start: 0.6167 (tt0) cc_final: 0.5686 (tm-30) REVERT: C 458 GLN cc_start: 0.6954 (mm110) cc_final: 0.6633 (mm-40) REVERT: C 465 ARG cc_start: 0.5810 (mmt90) cc_final: 0.5220 (mtt-85) REVERT: C 546 GLU cc_start: 0.8222 (tt0) cc_final: 0.7669 (tp30) REVERT: C 567 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6904 (ttm-80) REVERT: C 627 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.6843 (p0) REVERT: C 638 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.6578 (mmt-90) REVERT: C 696 LYS cc_start: 0.7156 (ttpt) cc_final: 0.6842 (tttt) REVERT: C 741 ARG cc_start: 0.6545 (mtp-110) cc_final: 0.5744 (mmt-90) REVERT: C 753 ARG cc_start: 0.5512 (mtp180) cc_final: 0.4851 (mmm-85) REVERT: C 754 LYS cc_start: 0.5964 (mmtt) cc_final: 0.5640 (ttpt) REVERT: C 757 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.6193 (ptm) REVERT: D 56 THR cc_start: 0.3114 (OUTLIER) cc_final: 0.2801 (p) REVERT: D 221 GLU cc_start: 0.6662 (mm-30) cc_final: 0.6283 (mm-30) REVERT: D 239 ARG cc_start: 0.5749 (mtt180) cc_final: 0.5347 (mmp-170) REVERT: D 288 LYS cc_start: 0.6969 (ttmt) cc_final: 0.6360 (ptmm) REVERT: D 304 ASP cc_start: 0.7860 (p0) cc_final: 0.7237 (t70) REVERT: D 349 ARG cc_start: 0.6513 (mtt180) cc_final: 0.6154 (mtm-85) REVERT: D 397 GLU cc_start: 0.6264 (tt0) cc_final: 0.5781 (tm-30) REVERT: D 427 MET cc_start: 0.4262 (tpt) cc_final: 0.3733 (tpt) REVERT: D 445 LEU cc_start: 0.5391 (OUTLIER) cc_final: 0.4901 (tp) REVERT: D 451 ASP cc_start: 0.7019 (m-30) cc_final: 0.6771 (m-30) REVERT: D 546 GLU cc_start: 0.8206 (tt0) cc_final: 0.7671 (tp30) REVERT: D 567 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6780 (ttp-110) REVERT: D 627 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.6906 (p0) REVERT: D 638 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.6613 (mmt-90) REVERT: D 674 PHE cc_start: 0.6177 (t80) cc_final: 0.5722 (t80) REVERT: D 741 ARG cc_start: 0.6439 (mtp-110) cc_final: 0.5609 (mmt-90) REVERT: D 753 ARG cc_start: 0.5557 (mtp180) cc_final: 0.4801 (mmm-85) REVERT: D 754 LYS cc_start: 0.6038 (mmtt) cc_final: 0.5732 (ttpt) REVERT: D 757 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.6340 (ptm) REVERT: E 215 GLN cc_start: 0.7134 (tt0) cc_final: 0.6764 (tt0) REVERT: E 239 ARG cc_start: 0.5681 (mtt180) cc_final: 0.5239 (mmp-170) REVERT: E 270 ASN cc_start: 0.7371 (t0) cc_final: 0.7071 (t0) REVERT: E 288 LYS cc_start: 0.7090 (ttmt) cc_final: 0.6585 (pttm) REVERT: E 349 ARG cc_start: 0.6464 (mtt180) cc_final: 0.6102 (mtm-85) REVERT: E 397 GLU cc_start: 0.6331 (tt0) cc_final: 0.5744 (tm-30) REVERT: E 491 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6661 (mm-30) REVERT: E 546 GLU cc_start: 0.8291 (tt0) cc_final: 0.7731 (tp30) REVERT: E 567 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6872 (ttm-80) REVERT: E 627 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.6960 (p0) REVERT: E 638 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.6855 (mmt-90) REVERT: E 740 MET cc_start: 0.7559 (tpp) cc_final: 0.7353 (tpt) REVERT: E 741 ARG cc_start: 0.6353 (mtp-110) cc_final: 0.5678 (mmt-90) REVERT: E 753 ARG cc_start: 0.5598 (mtp180) cc_final: 0.4871 (mmm-85) REVERT: E 754 LYS cc_start: 0.6086 (mmtt) cc_final: 0.5717 (ttpt) REVERT: E 757 MET cc_start: 0.6622 (mtm) cc_final: 0.6285 (ptm) REVERT: F 215 GLN cc_start: 0.7180 (tt0) cc_final: 0.6967 (tt0) REVERT: F 239 ARG cc_start: 0.5666 (mtt180) cc_final: 0.5331 (mmp-170) REVERT: F 270 ASN cc_start: 0.7450 (t0) cc_final: 0.7085 (t0) REVERT: F 288 LYS cc_start: 0.6825 (ttmt) cc_final: 0.6145 (ptmm) REVERT: F 322 ARG cc_start: 0.6739 (mmt180) cc_final: 0.6351 (mpt-90) REVERT: F 349 ARG cc_start: 0.6471 (mtt180) cc_final: 0.6163 (mtp-110) REVERT: F 397 GLU cc_start: 0.6192 (tt0) cc_final: 0.5699 (tm-30) REVERT: F 458 GLN cc_start: 0.6964 (mm110) cc_final: 0.6629 (mm-40) REVERT: F 465 ARG cc_start: 0.5782 (mmt90) cc_final: 0.5197 (mtt-85) REVERT: F 491 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6312 (mm-30) REVERT: F 546 GLU cc_start: 0.8263 (tt0) cc_final: 0.7703 (tp30) REVERT: F 567 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6901 (ttm-80) REVERT: F 607 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7968 (mm-30) REVERT: F 627 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.6855 (p0) REVERT: F 638 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.6495 (mmt-90) REVERT: F 689 GLU cc_start: 0.7286 (tt0) cc_final: 0.6590 (tm-30) REVERT: F 696 LYS cc_start: 0.7162 (ttpt) cc_final: 0.6846 (tttt) REVERT: F 741 ARG cc_start: 0.6582 (mtp-110) cc_final: 0.5781 (mmt-90) REVERT: F 757 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.6199 (ptm) outliers start: 140 outliers final: 62 residues processed: 606 average time/residue: 1.6225 time to fit residues: 1163.7828 Evaluate side-chains 575 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 483 time to evaluate : 3.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 638 ARG Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 567 ARG Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 638 ARG Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 752 ILE Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 470 GLU Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 638 ARG Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 470 GLU Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 607 GLU Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 638 ARG Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 20.0000 chunk 410 optimal weight: 5.9990 chunk 250 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 285 optimal weight: 9.9990 chunk 430 optimal weight: 9.9990 chunk 396 optimal weight: 1.9990 chunk 342 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 264 optimal weight: 0.7980 chunk 210 optimal weight: 7.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 35082 Z= 0.232 Angle : 0.710 9.393 47460 Z= 0.349 Chirality : 0.047 0.158 5322 Planarity : 0.005 0.051 6198 Dihedral : 9.390 94.918 5016 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.91 % Favored : 94.04 % Rotamer: Outliers : 2.79 % Allowed : 19.97 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.12), residues: 4314 helix: 0.13 (0.13), residues: 1638 sheet: -0.23 (0.24), residues: 522 loop : -1.19 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 551 HIS 0.009 0.001 HIS A 340 PHE 0.018 0.002 PHE D 265 TYR 0.018 0.002 TYR A 495 ARG 0.009 0.001 ARG E 465 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 483 time to evaluate : 3.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 GLU cc_start: 0.6604 (mm-30) cc_final: 0.6257 (mm-30) REVERT: A 239 ARG cc_start: 0.5658 (mtt180) cc_final: 0.5356 (mmp-170) REVERT: A 270 ASN cc_start: 0.7402 (t0) cc_final: 0.6868 (t0) REVERT: A 288 LYS cc_start: 0.6974 (ttmt) cc_final: 0.6025 (ptmm) REVERT: A 304 ASP cc_start: 0.7848 (p0) cc_final: 0.7240 (t70) REVERT: A 349 ARG cc_start: 0.6509 (mtt180) cc_final: 0.6112 (mtm-85) REVERT: A 397 GLU cc_start: 0.6224 (tt0) cc_final: 0.5756 (tm-30) REVERT: A 427 MET cc_start: 0.4271 (tpt) cc_final: 0.3728 (tpt) REVERT: A 445 LEU cc_start: 0.5419 (OUTLIER) cc_final: 0.4890 (tp) REVERT: A 451 ASP cc_start: 0.6985 (m-30) cc_final: 0.6698 (m-30) REVERT: A 458 GLN cc_start: 0.6877 (mm110) cc_final: 0.6620 (mm-40) REVERT: A 546 GLU cc_start: 0.8249 (tt0) cc_final: 0.7677 (tp30) REVERT: A 567 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6792 (ttm-80) REVERT: A 608 MET cc_start: 0.8457 (mtm) cc_final: 0.8213 (mtp) REVERT: A 627 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.6928 (p0) REVERT: A 638 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.6641 (mmt-90) REVERT: A 650 GLU cc_start: 0.5452 (mp0) cc_final: 0.4943 (mt-10) REVERT: A 674 PHE cc_start: 0.6161 (t80) cc_final: 0.5813 (t80) REVERT: A 741 ARG cc_start: 0.6355 (mtp-110) cc_final: 0.5551 (mmt-90) REVERT: A 753 ARG cc_start: 0.5607 (mtp180) cc_final: 0.4840 (mmm-85) REVERT: A 757 MET cc_start: 0.6487 (OUTLIER) cc_final: 0.6166 (ptm) REVERT: B 215 GLN cc_start: 0.7065 (tt0) cc_final: 0.6702 (tt0) REVERT: B 239 ARG cc_start: 0.5642 (mtt180) cc_final: 0.5337 (mmp-170) REVERT: B 270 ASN cc_start: 0.7428 (t0) cc_final: 0.7113 (t0) REVERT: B 288 LYS cc_start: 0.7125 (ttmt) cc_final: 0.6575 (ptmm) REVERT: B 349 ARG cc_start: 0.6420 (mtt180) cc_final: 0.6098 (mtm-85) REVERT: B 397 GLU cc_start: 0.6334 (tt0) cc_final: 0.5737 (tm-30) REVERT: B 427 MET cc_start: 0.4219 (tpt) cc_final: 0.3641 (tpt) REVERT: B 443 ASN cc_start: 0.4050 (m110) cc_final: 0.3723 (t160) REVERT: B 491 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6461 (mm-30) REVERT: B 546 GLU cc_start: 0.8285 (tt0) cc_final: 0.7743 (tp30) REVERT: B 627 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.6907 (p0) REVERT: B 633 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7925 (mm) REVERT: B 634 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8069 (mt) REVERT: B 638 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.6881 (mmt-90) REVERT: B 650 GLU cc_start: 0.5600 (mp0) cc_final: 0.4820 (mt-10) REVERT: B 740 MET cc_start: 0.7446 (tpp) cc_final: 0.7173 (tpt) REVERT: B 741 ARG cc_start: 0.6204 (mtp-110) cc_final: 0.5228 (mmm160) REVERT: B 753 ARG cc_start: 0.5600 (mtp180) cc_final: 0.4826 (mmm-85) REVERT: B 757 MET cc_start: 0.6546 (mtm) cc_final: 0.6249 (ptm) REVERT: C 56 THR cc_start: 0.3100 (OUTLIER) cc_final: 0.2815 (p) REVERT: C 215 GLN cc_start: 0.7035 (tt0) cc_final: 0.6802 (tt0) REVERT: C 239 ARG cc_start: 0.5658 (mtt180) cc_final: 0.5327 (mmp-170) REVERT: C 270 ASN cc_start: 0.7463 (t0) cc_final: 0.7067 (t0) REVERT: C 322 ARG cc_start: 0.6628 (mpt180) cc_final: 0.5017 (ttp-110) REVERT: C 349 ARG cc_start: 0.6544 (mtt180) cc_final: 0.6195 (mtp-110) REVERT: C 359 ARG cc_start: 0.6492 (OUTLIER) cc_final: 0.6103 (ttt180) REVERT: C 397 GLU cc_start: 0.6126 (tt0) cc_final: 0.5692 (tm-30) REVERT: C 449 MET cc_start: 0.5284 (tpt) cc_final: 0.5015 (tpt) REVERT: C 458 GLN cc_start: 0.6914 (mm110) cc_final: 0.6609 (mm-40) REVERT: C 465 ARG cc_start: 0.5828 (mmt90) cc_final: 0.5195 (mtt-85) REVERT: C 546 GLU cc_start: 0.8240 (tt0) cc_final: 0.7659 (tp30) REVERT: C 567 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6842 (ttm-80) REVERT: C 607 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7782 (mm-30) REVERT: C 627 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.6813 (p0) REVERT: C 638 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.6454 (mmt-90) REVERT: C 693 ARG cc_start: 0.7094 (tpp80) cc_final: 0.6748 (mtt180) REVERT: C 696 LYS cc_start: 0.7180 (ttpt) cc_final: 0.6911 (tttt) REVERT: C 741 ARG cc_start: 0.6547 (mtp-110) cc_final: 0.5708 (mmt-90) REVERT: C 753 ARG cc_start: 0.5554 (mtp180) cc_final: 0.4878 (mmm-85) REVERT: C 754 LYS cc_start: 0.5904 (mmtt) cc_final: 0.5592 (ttpt) REVERT: C 757 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.6289 (ptp) REVERT: D 56 THR cc_start: 0.3121 (OUTLIER) cc_final: 0.2818 (p) REVERT: D 221 GLU cc_start: 0.6657 (mm-30) cc_final: 0.6279 (mm-30) REVERT: D 239 ARG cc_start: 0.5674 (mtt180) cc_final: 0.5390 (mmp-170) REVERT: D 288 LYS cc_start: 0.6965 (ttmt) cc_final: 0.6017 (ptmm) REVERT: D 304 ASP cc_start: 0.7892 (p0) cc_final: 0.7229 (t70) REVERT: D 349 ARG cc_start: 0.6545 (mtt180) cc_final: 0.6150 (mtm-85) REVERT: D 397 GLU cc_start: 0.6194 (tt0) cc_final: 0.5799 (tm-30) REVERT: D 427 MET cc_start: 0.4120 (tpt) cc_final: 0.3639 (tpt) REVERT: D 445 LEU cc_start: 0.5359 (OUTLIER) cc_final: 0.4847 (tp) REVERT: D 451 ASP cc_start: 0.6995 (m-30) cc_final: 0.6774 (m-30) REVERT: D 546 GLU cc_start: 0.8222 (tt0) cc_final: 0.7698 (tp30) REVERT: D 567 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6802 (ttm-80) REVERT: D 608 MET cc_start: 0.8443 (mtm) cc_final: 0.8219 (mtp) REVERT: D 615 LYS cc_start: 0.4320 (mmmt) cc_final: 0.4098 (mtpp) REVERT: D 627 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.6933 (p0) REVERT: D 638 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.6618 (mmt-90) REVERT: D 650 GLU cc_start: 0.5603 (mp0) cc_final: 0.4899 (mt-10) REVERT: D 674 PHE cc_start: 0.6121 (t80) cc_final: 0.5669 (t80) REVERT: D 741 ARG cc_start: 0.6376 (mtp-110) cc_final: 0.5570 (mmt-90) REVERT: D 753 ARG cc_start: 0.5608 (mtp180) cc_final: 0.4820 (mmm-85) REVERT: D 754 LYS cc_start: 0.6025 (mmtt) cc_final: 0.5712 (ttpt) REVERT: D 757 MET cc_start: 0.6643 (OUTLIER) cc_final: 0.6331 (ptm) REVERT: E 215 GLN cc_start: 0.7069 (tt0) cc_final: 0.6703 (tt0) REVERT: E 239 ARG cc_start: 0.5662 (mtt180) cc_final: 0.5258 (mmp-170) REVERT: E 270 ASN cc_start: 0.7430 (t0) cc_final: 0.7120 (t0) REVERT: E 288 LYS cc_start: 0.7180 (ttmt) cc_final: 0.6479 (pttm) REVERT: E 349 ARG cc_start: 0.6424 (mtt180) cc_final: 0.6093 (mtm-85) REVERT: E 397 GLU cc_start: 0.6361 (tt0) cc_final: 0.5727 (tm-30) REVERT: E 427 MET cc_start: 0.4210 (tpt) cc_final: 0.3650 (tpt) REVERT: E 491 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6458 (mm-30) REVERT: E 546 GLU cc_start: 0.8283 (tt0) cc_final: 0.7742 (tp30) REVERT: E 567 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6790 (ttm-80) REVERT: E 627 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.6940 (p0) REVERT: E 633 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7925 (mm) REVERT: E 634 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8072 (mt) REVERT: E 638 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6887 (mmt-90) REVERT: E 740 MET cc_start: 0.7549 (tpp) cc_final: 0.7290 (tpt) REVERT: E 741 ARG cc_start: 0.6300 (mtp-110) cc_final: 0.5614 (mmt-90) REVERT: E 753 ARG cc_start: 0.5637 (mtp180) cc_final: 0.4867 (mmm-85) REVERT: E 754 LYS cc_start: 0.6002 (mmtt) cc_final: 0.5662 (ttpt) REVERT: E 757 MET cc_start: 0.6539 (mtm) cc_final: 0.6228 (ptm) REVERT: F 56 THR cc_start: 0.3100 (OUTLIER) cc_final: 0.2816 (p) REVERT: F 215 GLN cc_start: 0.7058 (tt0) cc_final: 0.6826 (tt0) REVERT: F 239 ARG cc_start: 0.5621 (mtt180) cc_final: 0.5313 (mmp-170) REVERT: F 270 ASN cc_start: 0.7465 (t0) cc_final: 0.7067 (t0) REVERT: F 288 LYS cc_start: 0.6825 (ttmt) cc_final: 0.6303 (pttm) REVERT: F 322 ARG cc_start: 0.6710 (mmt180) cc_final: 0.6450 (mpt-90) REVERT: F 349 ARG cc_start: 0.6558 (mtt180) cc_final: 0.6207 (mtp-110) REVERT: F 397 GLU cc_start: 0.6166 (tt0) cc_final: 0.5709 (tm-30) REVERT: F 458 GLN cc_start: 0.6928 (mm110) cc_final: 0.6646 (mm-40) REVERT: F 465 ARG cc_start: 0.5858 (mmt90) cc_final: 0.5192 (mtt-85) REVERT: F 491 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6314 (mm-30) REVERT: F 546 GLU cc_start: 0.8263 (tt0) cc_final: 0.7704 (tp30) REVERT: F 567 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6838 (ttm-80) REVERT: F 607 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7910 (mm-30) REVERT: F 627 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.6834 (p0) REVERT: F 638 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6494 (mmt-90) REVERT: F 693 ARG cc_start: 0.7076 (tpp80) cc_final: 0.6485 (mtm-85) REVERT: F 696 LYS cc_start: 0.7180 (ttpt) cc_final: 0.6883 (tttt) REVERT: F 741 ARG cc_start: 0.6543 (mtp-110) cc_final: 0.5727 (mmt-90) REVERT: F 753 ARG cc_start: 0.5568 (mtp180) cc_final: 0.4898 (mmm-85) REVERT: F 757 MET cc_start: 0.6526 (OUTLIER) cc_final: 0.6284 (ptp) outliers start: 103 outliers final: 52 residues processed: 564 average time/residue: 1.6417 time to fit residues: 1084.7965 Evaluate side-chains 565 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 477 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 638 ARG Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 567 ARG Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 638 ARG Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 752 ILE Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 638 ARG Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 470 GLU Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 607 GLU Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 638 ARG Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 9.9990 chunk 365 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 316 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 343 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 352 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.238149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.215173 restraints weight = 41677.581| |-----------------------------------------------------------------------------| r_work (start): 0.4451 rms_B_bonded: 1.45 r_work: 0.4262 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.4172 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 35082 Z= 0.257 Angle : 0.740 9.430 47460 Z= 0.364 Chirality : 0.048 0.182 5322 Planarity : 0.005 0.047 6198 Dihedral : 9.627 97.823 5016 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.91 % Favored : 93.05 % Rotamer: Outliers : 3.01 % Allowed : 19.89 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.12), residues: 4314 helix: 0.07 (0.13), residues: 1632 sheet: -0.35 (0.23), residues: 522 loop : -1.26 (0.12), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 551 HIS 0.010 0.002 HIS A 340 PHE 0.019 0.002 PHE D 265 TYR 0.017 0.002 TYR A 495 ARG 0.009 0.001 ARG E 465 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17838.05 seconds wall clock time: 312 minutes 37.29 seconds (18757.29 seconds total)