Starting phenix.real_space_refine on Sun Aug 11 04:28:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r0e_18790/08_2024/8r0e_18790.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r0e_18790/08_2024/8r0e_18790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r0e_18790/08_2024/8r0e_18790.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r0e_18790/08_2024/8r0e_18790.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r0e_18790/08_2024/8r0e_18790.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r0e_18790/08_2024/8r0e_18790.cif" } resolution = 2.7 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= 0.006 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: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 19954 2.51 5 N 5808 2.21 5 O 6156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 225": "NH1" <-> "NH2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A ARG 635": "NH1" <-> "NH2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A ARG 766": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B GLU 470": "OE1" <-> "OE2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "B GLU 578": "OE1" <-> "OE2" Residue "B GLU 607": "OE1" <-> "OE2" Residue "B ARG 635": "NH1" <-> "NH2" Residue "B GLU 673": "OE1" <-> "OE2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B ARG 766": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C GLU 417": "OE1" <-> "OE2" Residue "C GLU 440": "OE1" <-> "OE2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C GLU 470": "OE1" <-> "OE2" Residue "C ARG 487": "NH1" <-> "NH2" Residue "C GLU 578": "OE1" <-> "OE2" Residue "C GLU 607": "OE1" <-> "OE2" Residue "C ARG 635": "NH1" <-> "NH2" Residue "C GLU 673": "OE1" <-> "OE2" Residue "C ARG 711": "NH1" <-> "NH2" Residue "C ARG 766": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D GLU 294": "OE1" <-> "OE2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D GLU 417": "OE1" <-> "OE2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D ARG 453": "NH1" <-> "NH2" Residue "D GLU 470": "OE1" <-> "OE2" Residue "D ARG 487": "NH1" <-> "NH2" Residue "D GLU 578": "OE1" <-> "OE2" Residue "D GLU 607": "OE1" <-> "OE2" Residue "D ARG 635": "NH1" <-> "NH2" Residue "D GLU 673": "OE1" <-> "OE2" Residue "D ARG 711": "NH1" <-> "NH2" Residue "D ARG 766": "NH1" <-> "NH2" Residue "E ARG 225": "NH1" <-> "NH2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "E ARG 313": "NH1" <-> "NH2" Residue "E GLU 417": "OE1" <-> "OE2" Residue "E GLU 440": "OE1" <-> "OE2" Residue "E ARG 453": "NH1" <-> "NH2" Residue "E GLU 470": "OE1" <-> "OE2" Residue "E ARG 487": "NH1" <-> "NH2" Residue "E GLU 578": "OE1" <-> "OE2" Residue "E GLU 607": "OE1" <-> "OE2" Residue "E ARG 635": "NH1" <-> "NH2" Residue "E GLU 673": "OE1" <-> "OE2" Residue "E ARG 711": "NH1" <-> "NH2" Residue "E ARG 766": "NH1" <-> "NH2" Residue "F ARG 225": "NH1" <-> "NH2" Residue "F GLU 294": "OE1" <-> "OE2" Residue "F ARG 313": "NH1" <-> "NH2" Residue "F GLU 417": "OE1" <-> "OE2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "F ARG 453": "NH1" <-> "NH2" Residue "F GLU 470": "OE1" <-> "OE2" Residue "F ARG 487": "NH1" <-> "NH2" Residue "F GLU 578": "OE1" <-> "OE2" Residue "F GLU 607": "OE1" <-> "OE2" Residue "F ARG 635": "NH1" <-> "NH2" Residue "F GLU 673": "OE1" <-> "OE2" Residue "F ARG 711": "NH1" <-> "NH2" Residue "F ARG 766": "NH1" <-> "NH2" Time to flip residues: 0.56s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 32056 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5342 Classifications: {'peptide': 754} Incomplete info: {'truncation_to_alanine': 171} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 711} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 594 Unresolved non-hydrogen angles: 754 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 10, 'ASP:plan': 16, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 318 Chain: "B" Number of atoms: 5342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5342 Classifications: {'peptide': 754} Incomplete info: {'truncation_to_alanine': 171} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 711} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 594 Unresolved non-hydrogen angles: 754 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 10, 'ASP:plan': 16, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 318 Chain: "C" Number of atoms: 5342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5342 Classifications: {'peptide': 754} Incomplete info: {'truncation_to_alanine': 171} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 711} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 594 Unresolved non-hydrogen angles: 754 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 10, 'ASP:plan': 16, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 318 Chain: "D" Number of atoms: 5344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5344 Classifications: {'peptide': 754} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 711} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 592 Unresolved non-hydrogen angles: 751 Unresolved non-hydrogen dihedrals: 473 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 10, 'ASP:plan': 16, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 318 Chain: "E" Number of atoms: 5344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5344 Classifications: {'peptide': 754} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 711} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 592 Unresolved non-hydrogen angles: 751 Unresolved non-hydrogen dihedrals: 473 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 10, 'ASP:plan': 16, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 318 Chain: "F" Number of atoms: 5342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5342 Classifications: {'peptide': 754} Incomplete info: {'truncation_to_alanine': 171} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 711} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 594 Unresolved non-hydrogen angles: 754 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 10, 'ASP:plan': 16, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 318 Time building chain proxies: 16.62, per 1000 atoms: 0.52 Number of scatterers: 32056 At special positions: 0 Unit cell: (176.3, 178.02, 118.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 6156 8.00 N 5808 7.00 C 19954 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: 11.00 Conformation dependent library (CDL) restraints added in 6.0 seconds 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8448 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 24 sheets defined 48.8% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 85 through 90 removed outlier: 3.608A pdb=" N ASN A 90 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 200 Processing helix chain 'A' and resid 209 through 226 removed outlier: 5.018A 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 226 through 234 removed outlier: 3.836A pdb=" N GLY A 234 " --> pdb=" O PHE A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 278 through 296 removed outlier: 4.162A pdb=" N GLU A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 4.074A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 334 removed outlier: 3.608A pdb=" N ARG A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.560A pdb=" N SER A 352 " --> pdb=" O ARG A 349 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 349 through 353' Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 407 through 427 removed outlier: 4.285A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 433 removed outlier: 3.789A pdb=" N GLU A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 443 removed outlier: 4.112A pdb=" N GLU A 440 " --> pdb=" O THR A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.587A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 457 " --> pdb=" O ARG A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.391A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 506 removed outlier: 3.866A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.810A pdb=" N LEU A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.518A pdb=" N LEU A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 598 through 609 removed outlier: 3.586A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.923A pdb=" N ILE A 629 " --> pdb=" O PRO A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.807A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 662 Processing helix chain 'A' and resid 671 through 678 removed outlier: 3.719A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 716 Processing helix chain 'A' and resid 732 through 741 removed outlier: 3.636A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 765 removed outlier: 3.775A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A 762 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.608A pdb=" N ASN B 90 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 200 removed outlier: 3.751A pdb=" N GLU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLU B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N SER B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 226 removed outlier: 5.019A 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 226 through 234 removed outlier: 3.836A pdb=" N GLY B 234 " --> pdb=" O PHE B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 278 through 296 removed outlier: 4.162A pdb=" N GLU B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 4.074A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 334 removed outlier: 3.608A pdb=" N ARG B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.560A pdb=" N SER B 352 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 349 through 353' Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 407 through 427 removed outlier: 4.285A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 433 removed outlier: 3.789A pdb=" N GLU B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 443 removed outlier: 4.112A pdb=" N GLU B 440 " --> pdb=" O THR B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 removed outlier: 3.588A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 457 " --> pdb=" O ARG B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 removed outlier: 4.391A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 506 removed outlier: 3.866A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.810A pdb=" N LEU B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.517A pdb=" N LEU B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 569 Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 598 through 609 removed outlier: 3.576A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.923A pdb=" N ILE B 629 " --> pdb=" O PRO B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.807A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 662 Processing helix chain 'B' and resid 671 through 678 removed outlier: 3.719A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 716 Processing helix chain 'B' and resid 732 through 741 removed outlier: 3.635A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 765 removed outlier: 3.775A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU B 762 " --> pdb=" O PHE B 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 46 Processing helix chain 'C' and resid 85 through 90 removed outlier: 3.609A pdb=" N ASN C 90 " --> pdb=" O VAL C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 200 removed outlier: 3.984A pdb=" N GLU C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 226 removed outlier: 5.018A 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 226 through 234 removed outlier: 3.837A pdb=" N GLY C 234 " --> pdb=" O PHE C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 278 through 296 removed outlier: 4.162A pdb=" N GLU C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 4.073A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 334 removed outlier: 3.608A pdb=" N ARG C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.559A pdb=" N SER C 352 " --> pdb=" O ARG C 349 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 349 through 353' Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 386 through 388 No H-bonds generated for 'chain 'C' and resid 386 through 388' Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 407 through 427 removed outlier: 4.284A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 433 removed outlier: 3.789A pdb=" N GLU C 433 " --> pdb=" O LEU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 443 removed outlier: 4.112A pdb=" N GLU C 440 " --> pdb=" O THR C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.588A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER C 457 " --> pdb=" O ARG C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 removed outlier: 4.391A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 506 removed outlier: 3.867A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.810A pdb=" N LEU C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 removed outlier: 3.518A pdb=" N LEU C 547 " --> pdb=" O LYS C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 609 removed outlier: 3.583A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 629 removed outlier: 3.924A pdb=" N ILE C 629 " --> pdb=" O PRO C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.807A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 662 Processing helix chain 'C' and resid 671 through 678 removed outlier: 3.719A pdb=" N LEU C 675 " --> pdb=" O ASP C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 716 Processing helix chain 'C' and resid 732 through 741 removed outlier: 3.635A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 765 removed outlier: 3.776A pdb=" N ILE C 752 " --> pdb=" O SER C 748 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU C 762 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 46 Processing helix chain 'D' and resid 85 through 90 removed outlier: 3.607A pdb=" N ASN D 90 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 199 removed outlier: 3.711A pdb=" N GLU D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLU D 196 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N SER D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 226 removed outlier: 5.019A 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 226 through 234 removed outlier: 3.837A pdb=" N GLY D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 278 through 296 removed outlier: 4.162A pdb=" N GLU D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.074A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 334 removed outlier: 3.608A pdb=" N ARG D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.560A pdb=" N SER D 352 " --> pdb=" O ARG D 349 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 349 through 353' Processing helix chain 'D' and resid 354 through 358 Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 407 through 427 removed outlier: 4.285A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 433 removed outlier: 3.790A pdb=" N GLU D 433 " --> pdb=" O LEU D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 443 removed outlier: 4.112A pdb=" N GLU D 440 " --> pdb=" O THR D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.588A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 457 " --> pdb=" O ARG D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 499 removed outlier: 4.391A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 506 removed outlier: 3.866A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.810A pdb=" N LEU D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 removed outlier: 3.517A pdb=" N LEU D 547 " --> pdb=" O LYS D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 569 Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 609 removed outlier: 3.617A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 629 removed outlier: 3.923A pdb=" N ILE D 629 " --> pdb=" O PRO D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.807A pdb=" N ARG D 635 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 662 Processing helix chain 'D' and resid 671 through 678 removed outlier: 3.720A pdb=" N LEU D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 716 Processing helix chain 'D' and resid 732 through 741 removed outlier: 3.636A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 765 removed outlier: 3.775A pdb=" N ILE D 752 " --> pdb=" O SER D 748 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU D 762 " --> pdb=" O PHE D 758 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 46 Processing helix chain 'E' and resid 85 through 90 removed outlier: 3.608A pdb=" N ASN E 90 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 200 removed outlier: 3.711A pdb=" N GLU E 194 " --> pdb=" O LYS E 190 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU E 196 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N SER E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 226 removed outlier: 5.019A 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 226 through 234 removed outlier: 3.836A pdb=" N GLY E 234 " --> pdb=" O PHE E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 278 through 296 removed outlier: 4.162A pdb=" N GLU E 283 " --> pdb=" O ALA E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 4.074A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 334 removed outlier: 3.608A pdb=" N ARG E 323 " --> pdb=" O GLU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.560A pdb=" N SER E 352 " --> pdb=" O ARG E 349 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 349 through 353' Processing helix chain 'E' and resid 354 through 358 Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 407 through 427 removed outlier: 4.285A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 433 removed outlier: 3.789A pdb=" N GLU E 433 " --> pdb=" O LEU E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 443 removed outlier: 4.112A pdb=" N GLU E 440 " --> pdb=" O THR E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 458 removed outlier: 3.587A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER E 457 " --> pdb=" O ARG E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 499 removed outlier: 4.391A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 506 removed outlier: 3.867A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.810A pdb=" N LEU E 527 " --> pdb=" O GLY E 523 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 553 removed outlier: 3.518A pdb=" N LEU E 547 " --> pdb=" O LYS E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 569 Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 609 removed outlier: 3.562A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 629 removed outlier: 3.923A pdb=" N ILE E 629 " --> pdb=" O PRO E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.807A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 662 Processing helix chain 'E' and resid 671 through 678 removed outlier: 3.719A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 716 Processing helix chain 'E' and resid 732 through 741 removed outlier: 3.636A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 765 removed outlier: 3.775A pdb=" N ILE E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU E 762 " --> pdb=" O PHE E 758 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 46 Processing helix chain 'F' and resid 85 through 90 removed outlier: 3.608A pdb=" N ASN F 90 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 200 removed outlier: 3.751A pdb=" N GLU F 194 " --> pdb=" O LYS F 190 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU F 196 " --> pdb=" O GLU F 192 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N SER F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 226 removed outlier: 5.018A 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 226 through 234 removed outlier: 3.836A pdb=" N GLY F 234 " --> pdb=" O PHE F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 278 through 296 removed outlier: 4.162A pdb=" N GLU F 283 " --> pdb=" O ALA F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 4.074A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 334 removed outlier: 3.608A pdb=" N ARG F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.560A pdb=" N SER F 352 " --> pdb=" O ARG F 349 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 349 through 353' Processing helix chain 'F' and resid 354 through 358 Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 386 through 388 No H-bonds generated for 'chain 'F' and resid 386 through 388' Processing helix chain 'F' and resid 395 through 402 Processing helix chain 'F' and resid 407 through 427 removed outlier: 4.285A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 433 removed outlier: 3.789A pdb=" N GLU F 433 " --> pdb=" O LEU F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 443 removed outlier: 4.112A pdb=" N GLU F 440 " --> pdb=" O THR F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.587A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER F 457 " --> pdb=" O ARG F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 removed outlier: 4.391A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 506 removed outlier: 3.867A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.810A pdb=" N LEU F 527 " --> pdb=" O GLY F 523 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS F 535 " --> pdb=" O ILE F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 553 removed outlier: 3.518A pdb=" N LEU F 547 " --> pdb=" O LYS F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 569 Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 609 removed outlier: 3.591A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 625 through 629 removed outlier: 3.923A pdb=" N ILE F 629 " --> pdb=" O PRO F 626 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.808A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 662 Processing helix chain 'F' and resid 671 through 678 removed outlier: 3.719A pdb=" N LEU F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 716 Processing helix chain 'F' and resid 732 through 741 removed outlier: 3.636A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 765 removed outlier: 3.776A pdb=" N ILE F 752 " --> pdb=" O SER F 748 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU F 762 " --> pdb=" O PHE F 758 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.749A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY A 240 " --> pdb=" O PHE A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.669A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 27 through 29 Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 60 Processing sheet with id=AA7, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.750A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY B 240 " --> pdb=" O PHE B 363 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.669A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 27 through 29 Processing sheet with id=AB1, first strand: chain 'C' and resid 58 through 60 Processing sheet with id=AB2, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.749A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY C 240 " --> pdb=" O PHE C 363 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.669A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 27 through 29 Processing sheet with id=AB5, first strand: chain 'D' and resid 58 through 60 Processing sheet with id=AB6, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.750A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY D 240 " --> pdb=" O PHE D 363 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.668A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 27 through 29 Processing sheet with id=AB9, first strand: chain 'E' and resid 58 through 60 Processing sheet with id=AC1, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.748A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY E 240 " --> pdb=" O PHE E 363 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.669A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 27 through 29 Processing sheet with id=AC4, first strand: chain 'F' and resid 58 through 60 Processing sheet with id=AC5, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.749A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY F 240 " --> pdb=" O PHE F 363 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.668A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) 1408 hydrogen bonds defined for protein. 3990 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: 10.49 Time building geometry restraints manager: 12.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7127 1.33 - 1.45: 6572 1.45 - 1.57: 18571 1.57 - 1.69: 2 1.69 - 1.81: 234 Bond restraints: 32506 Sorted by residual: bond pdb=" C LEU C 117 " pdb=" N PRO C 118 " ideal model delta sigma weight residual 1.326 1.389 -0.063 1.44e-02 4.82e+03 1.89e+01 bond pdb=" C LEU D 117 " pdb=" N PRO D 118 " ideal model delta sigma weight residual 1.326 1.389 -0.062 1.44e-02 4.82e+03 1.88e+01 bond pdb=" C LEU A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 1.326 1.388 -0.062 1.44e-02 4.82e+03 1.85e+01 bond pdb=" C LEU B 117 " pdb=" N PRO B 118 " ideal model delta sigma weight residual 1.326 1.388 -0.062 1.44e-02 4.82e+03 1.84e+01 bond pdb=" C LEU E 117 " pdb=" N PRO E 118 " ideal model delta sigma weight residual 1.326 1.388 -0.062 1.44e-02 4.82e+03 1.84e+01 ... (remaining 32501 not shown) Histogram of bond angle deviations from ideal: 96.86 - 104.31: 557 104.31 - 111.76: 13471 111.76 - 119.21: 12977 119.21 - 126.67: 16860 126.67 - 134.12: 253 Bond angle restraints: 44118 Sorted by residual: angle pdb=" N LYS E 190 " pdb=" CA LYS E 190 " pdb=" C LYS E 190 " ideal model delta sigma weight residual 108.78 118.93 -10.15 8.20e-01 1.49e+00 1.53e+02 angle pdb=" N GLU C 200 " pdb=" CA GLU C 200 " pdb=" C GLU C 200 " ideal model delta sigma weight residual 111.52 96.95 14.57 1.40e+00 5.10e-01 1.08e+02 angle pdb=" N LYS B 190 " pdb=" CA LYS B 190 " pdb=" C LYS B 190 " ideal model delta sigma weight residual 108.75 118.37 -9.62 9.60e-01 1.09e+00 1.00e+02 angle pdb=" N LYS F 190 " pdb=" CA LYS F 190 " pdb=" C LYS F 190 " ideal model delta sigma weight residual 108.75 117.94 -9.19 9.60e-01 1.09e+00 9.16e+01 angle pdb=" C LEU E 117 " pdb=" N PRO E 118 " pdb=" CA PRO E 118 " ideal model delta sigma weight residual 120.98 111.66 9.32 1.07e+00 8.73e-01 7.59e+01 ... (remaining 44113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 17867 16.98 - 33.96: 1686 33.96 - 50.94: 284 50.94 - 67.92: 79 67.92 - 84.90: 48 Dihedral angle restraints: 19964 sinusoidal: 6962 harmonic: 13002 Sorted by residual: dihedral pdb=" CA ASP A 169 " pdb=" C ASP A 169 " pdb=" N PRO A 170 " pdb=" CA PRO A 170 " ideal model delta harmonic sigma weight residual 180.00 153.61 26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ASP D 169 " pdb=" C ASP D 169 " pdb=" N PRO D 170 " pdb=" CA PRO D 170 " ideal model delta harmonic sigma weight residual 180.00 153.61 26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ASP B 169 " pdb=" C ASP B 169 " pdb=" N PRO B 170 " pdb=" CA PRO B 170 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 19961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.339: 5100 0.339 - 0.678: 8 0.678 - 1.017: 0 1.017 - 1.357: 0 1.357 - 1.696: 6 Chirality restraints: 5114 Sorted by residual: chirality pdb=" CG LEU B 222 " pdb=" CB LEU B 222 " pdb=" CD1 LEU B 222 " pdb=" CD2 LEU B 222 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.19e+01 chirality pdb=" CG LEU E 222 " pdb=" CB LEU E 222 " pdb=" CD1 LEU E 222 " pdb=" CD2 LEU E 222 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.18e+01 chirality pdb=" CG LEU F 222 " pdb=" CB LEU F 222 " pdb=" CD1 LEU F 222 " pdb=" CD2 LEU F 222 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.17e+01 ... (remaining 5111 not shown) Planarity restraints: 5976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 371 " 0.051 5.00e-02 4.00e+02 7.76e-02 9.64e+00 pdb=" N PRO D 372 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO D 372 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 372 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 371 " 0.051 5.00e-02 4.00e+02 7.76e-02 9.62e+00 pdb=" N PRO A 372 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 372 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 372 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 371 " 0.051 5.00e-02 4.00e+02 7.76e-02 9.62e+00 pdb=" N PRO F 372 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO F 372 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO F 372 " 0.042 5.00e-02 4.00e+02 ... (remaining 5973 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 177 2.57 - 3.15: 26105 3.15 - 3.74: 44697 3.74 - 4.32: 61209 4.32 - 4.90: 101740 Nonbonded interactions: 233928 Sorted by model distance: nonbonded pdb=" O ARG E 313 " pdb=" OG1 THR E 316 " model vdw 1.990 3.040 nonbonded pdb=" O ARG F 313 " pdb=" OG1 THR F 316 " model vdw 1.991 3.040 nonbonded pdb=" O ARG B 313 " pdb=" OG1 THR B 316 " model vdw 1.991 3.040 nonbonded pdb=" O ARG D 313 " pdb=" OG1 THR D 316 " model vdw 1.991 3.040 nonbonded pdb=" O ARG A 313 " pdb=" OG1 THR A 316 " model vdw 1.991 3.040 ... (remaining 233923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = (chain 'D' and ((resid 21 through 201 and (name N or name CA or name C or name O \ or name CB )) or resid 202 through 774)) selection = (chain 'E' and ((resid 21 through 201 and (name N or name CA or name C or name O \ or name CB )) or resid 202 through 774)) 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: 0.730 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: 0.040 Extract box with map and model: 1.080 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 77.460 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.130 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:10.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.164 32506 Z= 0.831 Angle : 1.204 14.569 44118 Z= 0.703 Chirality : 0.089 1.696 5114 Planarity : 0.008 0.078 5976 Dihedral : 14.995 84.898 11516 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.69 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % 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: -4.61 (0.10), residues: 4512 helix: -2.88 (0.09), residues: 1992 sheet: -0.27 (0.24), residues: 438 loop : -3.92 (0.11), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP B 454 HIS 0.009 0.002 HIS C 406 PHE 0.030 0.003 PHE C 575 TYR 0.014 0.002 TYR D 244 ARG 0.008 0.001 ARG C 708 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 543 time to evaluate : 3.721 Fit side-chains REVERT: A 211 LYS cc_start: 0.7056 (mtpt) cc_final: 0.6834 (mtmm) REVERT: A 295 LYS cc_start: 0.6466 (mttp) cc_final: 0.6143 (mmtt) REVERT: A 742 PHE cc_start: 0.6763 (m-10) cc_final: 0.6267 (m-80) REVERT: A 753 ARG cc_start: 0.6163 (mtm110) cc_final: 0.5869 (mmp80) REVERT: B 225 ARG cc_start: 0.6599 (ttm-80) cc_final: 0.6306 (ttp80) REVERT: B 295 LYS cc_start: 0.6700 (mttp) cc_final: 0.6239 (mmtt) REVERT: B 340 HIS cc_start: 0.6506 (m90) cc_final: 0.6133 (m-70) REVERT: B 753 ARG cc_start: 0.6180 (mtm110) cc_final: 0.5763 (mmp80) REVERT: C 560 ARG cc_start: 0.6907 (ttm170) cc_final: 0.6544 (ttm-80) REVERT: C 753 ARG cc_start: 0.6045 (mtm110) cc_final: 0.5807 (mmp80) REVERT: D 211 LYS cc_start: 0.6954 (mtpt) cc_final: 0.6624 (mmpt) REVERT: D 753 ARG cc_start: 0.6161 (mtm110) cc_final: 0.5609 (mmp80) REVERT: E 225 ARG cc_start: 0.6523 (ttm-80) cc_final: 0.6232 (ttp80) REVERT: E 285 ASN cc_start: 0.6817 (m110) cc_final: 0.6611 (m110) REVERT: E 295 LYS cc_start: 0.6707 (mttp) cc_final: 0.6238 (mmtt) REVERT: E 340 HIS cc_start: 0.6593 (m90) cc_final: 0.6261 (m-70) REVERT: E 560 ARG cc_start: 0.6809 (ttm170) cc_final: 0.6451 (ttm-80) REVERT: E 753 ARG cc_start: 0.6045 (mtm110) cc_final: 0.5806 (mmp80) REVERT: F 560 ARG cc_start: 0.7016 (ttm170) cc_final: 0.6643 (ttm-80) REVERT: F 753 ARG cc_start: 0.6052 (mtm110) cc_final: 0.5779 (mmp80) outliers start: 2 outliers final: 0 residues processed: 545 average time/residue: 1.8432 time to fit residues: 1141.0868 Evaluate side-chains 403 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 379 optimal weight: 50.0000 chunk 341 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 230 optimal weight: 0.0070 chunk 182 optimal weight: 10.0000 chunk 352 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 214 optimal weight: 0.0970 chunk 262 optimal weight: 0.0980 chunk 408 optimal weight: 1.9990 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 340 HIS C 260 ASN C 533 ASN C 624 ASN D 285 ASN D 340 HIS F 260 ASN F 533 ASN F 624 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32506 Z= 0.188 Angle : 0.621 6.754 44118 Z= 0.332 Chirality : 0.045 0.205 5114 Planarity : 0.004 0.045 5976 Dihedral : 5.182 24.545 4800 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.94 % Allowed : 11.39 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % 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: -2.38 (0.12), residues: 4512 helix: -0.56 (0.11), residues: 1932 sheet: -0.08 (0.24), residues: 522 loop : -3.09 (0.12), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 454 HIS 0.006 0.001 HIS C 317 PHE 0.020 0.001 PHE D 265 TYR 0.012 0.001 TYR D 203 ARG 0.004 0.000 ARG F 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 428 time to evaluate : 3.492 Fit side-chains REVERT: A 211 LYS cc_start: 0.6795 (mtpt) cc_final: 0.6522 (mmpt) REVERT: A 275 MET cc_start: 0.8492 (mmm) cc_final: 0.8265 (mmm) REVERT: A 295 LYS cc_start: 0.6167 (mttp) cc_final: 0.5771 (mmtt) REVERT: A 442 MET cc_start: 0.4495 (ptp) cc_final: 0.3541 (tmm) REVERT: A 678 MET cc_start: 0.5762 (mmp) cc_final: 0.5203 (mpm) REVERT: A 733 ARG cc_start: 0.6604 (mtp85) cc_final: 0.6246 (mtp180) REVERT: A 742 PHE cc_start: 0.6660 (m-10) cc_final: 0.5716 (m-80) REVERT: A 753 ARG cc_start: 0.6186 (mtm110) cc_final: 0.5801 (mmp80) REVERT: B 210 ARG cc_start: 0.5138 (tpm170) cc_final: 0.4927 (tpm170) REVERT: B 256 ARG cc_start: 0.7277 (mpt-90) cc_final: 0.7073 (mpp80) REVERT: B 295 LYS cc_start: 0.6209 (mttp) cc_final: 0.5910 (mmtm) REVERT: B 324 ILE cc_start: 0.7984 (tt) cc_final: 0.7736 (tp) REVERT: B 340 HIS cc_start: 0.6582 (m90) cc_final: 0.6076 (m-70) REVERT: B 554 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: B 720 MET cc_start: 0.2609 (OUTLIER) cc_final: 0.2108 (mpm) REVERT: B 742 PHE cc_start: 0.6681 (m-10) cc_final: 0.5872 (m-80) REVERT: B 753 ARG cc_start: 0.6151 (mtm110) cc_final: 0.5699 (mmp80) REVERT: C 256 ARG cc_start: 0.7364 (mpt-90) cc_final: 0.7069 (mpt-90) REVERT: C 295 LYS cc_start: 0.6384 (mttp) cc_final: 0.6057 (mmpt) REVERT: C 508 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.6908 (ttt) REVERT: C 560 ARG cc_start: 0.7088 (ttm170) cc_final: 0.6881 (ttm-80) REVERT: C 753 ARG cc_start: 0.5987 (mtm110) cc_final: 0.5739 (mmp80) REVERT: D 210 ARG cc_start: 0.5448 (tpm170) cc_final: 0.4909 (ttp-110) REVERT: D 211 LYS cc_start: 0.6736 (mtpt) cc_final: 0.6496 (mmmm) REVERT: D 256 ARG cc_start: 0.7408 (mpt-90) cc_final: 0.7138 (mpp80) REVERT: D 288 LYS cc_start: 0.7299 (mttt) cc_final: 0.7019 (mmmt) REVERT: D 295 LYS cc_start: 0.6196 (mttp) cc_final: 0.5872 (mmtt) REVERT: D 324 ILE cc_start: 0.8086 (tt) cc_final: 0.7868 (tp) REVERT: D 442 MET cc_start: 0.4489 (ptp) cc_final: 0.3586 (tmm) REVERT: D 508 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.6925 (ttt) REVERT: D 753 ARG cc_start: 0.6193 (mtm110) cc_final: 0.5678 (mmp80) REVERT: E 295 LYS cc_start: 0.6229 (mttp) cc_final: 0.5946 (mmtm) REVERT: E 324 ILE cc_start: 0.8040 (tt) cc_final: 0.7747 (tp) REVERT: E 340 HIS cc_start: 0.6695 (m90) cc_final: 0.6233 (m-70) REVERT: E 554 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: E 560 ARG cc_start: 0.6899 (ttm170) cc_final: 0.6589 (ttm170) REVERT: E 720 MET cc_start: 0.2614 (OUTLIER) cc_final: 0.2098 (mpm) REVERT: E 742 PHE cc_start: 0.6683 (m-10) cc_final: 0.5924 (m-80) REVERT: E 753 ARG cc_start: 0.6034 (mtm110) cc_final: 0.5747 (mmp80) REVERT: F 219 MET cc_start: 0.7665 (mtt) cc_final: 0.7402 (mtm) REVERT: F 256 ARG cc_start: 0.7337 (mpt-90) cc_final: 0.7071 (mpt-90) REVERT: F 295 LYS cc_start: 0.6373 (mttp) cc_final: 0.6130 (mmtm) REVERT: F 508 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.6701 (ttt) REVERT: F 560 ARG cc_start: 0.7202 (ttm170) cc_final: 0.6986 (ttm-80) REVERT: F 753 ARG cc_start: 0.5964 (mtm110) cc_final: 0.5700 (mmp80) outliers start: 55 outliers final: 19 residues processed: 458 average time/residue: 1.7727 time to fit residues: 927.4780 Evaluate side-chains 391 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 365 time to evaluate : 3.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 741 ARG Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 741 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 720 MET Chi-restraints excluded: chain E residue 741 ARG Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 741 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 227 optimal weight: 30.0000 chunk 126 optimal weight: 7.9990 chunk 340 optimal weight: 8.9990 chunk 278 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 409 optimal weight: 5.9990 chunk 442 optimal weight: 9.9990 chunk 364 optimal weight: 7.9990 chunk 405 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 328 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 ASN C 285 ASN C 327 GLN E 260 ASN E 285 ASN F 285 ASN F 327 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 32506 Z= 0.398 Angle : 0.794 9.036 44118 Z= 0.420 Chirality : 0.053 0.226 5114 Planarity : 0.006 0.045 5976 Dihedral : 5.493 26.364 4800 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 3.18 % Allowed : 13.44 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % 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: -2.25 (0.12), residues: 4512 helix: -0.54 (0.11), residues: 1944 sheet: 0.15 (0.24), residues: 522 loop : -2.97 (0.12), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 476 HIS 0.007 0.002 HIS E 317 PHE 0.025 0.003 PHE D 265 TYR 0.023 0.003 TYR D 203 ARG 0.006 0.001 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 389 time to evaluate : 3.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.7052 (mtpt) cc_final: 0.6817 (mtmm) REVERT: A 295 LYS cc_start: 0.6367 (mttp) cc_final: 0.5958 (mmtt) REVERT: A 442 MET cc_start: 0.4608 (ptp) cc_final: 0.3706 (tmm) REVERT: A 599 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8110 (ptm160) REVERT: A 678 MET cc_start: 0.5898 (mmp) cc_final: 0.5288 (mpm) REVERT: A 742 PHE cc_start: 0.6751 (m-10) cc_final: 0.5922 (m-80) REVERT: A 753 ARG cc_start: 0.6326 (mtm110) cc_final: 0.5879 (mmp80) REVERT: B 256 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7222 (mpp80) REVERT: B 295 LYS cc_start: 0.6218 (mttp) cc_final: 0.6017 (mmtm) REVERT: B 321 GLU cc_start: 0.7474 (mp0) cc_final: 0.7146 (mm-30) REVERT: B 554 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: B 641 GLN cc_start: 0.6970 (OUTLIER) cc_final: 0.6670 (mt0) REVERT: B 720 MET cc_start: 0.2897 (OUTLIER) cc_final: 0.2249 (mpm) REVERT: B 742 PHE cc_start: 0.6757 (m-10) cc_final: 0.5943 (m-80) REVERT: C 218 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7091 (tt0) REVERT: C 256 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7196 (mpt-90) REVERT: C 417 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6660 (tp30) REVERT: C 508 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.6974 (ttt) REVERT: C 753 ARG cc_start: 0.6258 (mtm110) cc_final: 0.5903 (mmp80) REVERT: D 211 LYS cc_start: 0.7038 (mtpt) cc_final: 0.6487 (tmtt) REVERT: D 256 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7264 (mpp80) REVERT: D 295 LYS cc_start: 0.6302 (mttp) cc_final: 0.5937 (mmtt) REVERT: D 442 MET cc_start: 0.4506 (ptp) cc_final: 0.3638 (tmm) REVERT: D 678 MET cc_start: 0.5918 (mmp) cc_final: 0.5321 (mpm) REVERT: D 742 PHE cc_start: 0.6814 (m-10) cc_final: 0.6016 (m-80) REVERT: D 753 ARG cc_start: 0.6428 (mtm110) cc_final: 0.5839 (mmp80) REVERT: E 321 GLU cc_start: 0.7309 (mp0) cc_final: 0.7081 (mm-30) REVERT: E 554 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: E 560 ARG cc_start: 0.7414 (ttm170) cc_final: 0.7157 (ttm170) REVERT: E 641 GLN cc_start: 0.6988 (OUTLIER) cc_final: 0.6691 (mt0) REVERT: E 720 MET cc_start: 0.2911 (OUTLIER) cc_final: 0.2251 (mpm) REVERT: E 742 PHE cc_start: 0.6788 (m-10) cc_final: 0.6004 (m-80) REVERT: F 218 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6995 (tt0) REVERT: F 256 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7172 (mpt-90) REVERT: F 417 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6816 (tp30) REVERT: F 508 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.6762 (ttt) REVERT: F 753 ARG cc_start: 0.6241 (mtm110) cc_final: 0.5873 (mmp80) outliers start: 90 outliers final: 27 residues processed: 438 average time/residue: 1.7132 time to fit residues: 853.6298 Evaluate side-chains 406 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 362 time to evaluate : 3.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 641 GLN Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain E residue 641 GLN Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 720 MET Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 256 ARG Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 615 LYS Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 404 optimal weight: 4.9990 chunk 307 optimal weight: 50.0000 chunk 212 optimal weight: 6.9990 chunk 45 optimal weight: 0.2980 chunk 195 optimal weight: 0.5980 chunk 274 optimal weight: 2.9990 chunk 410 optimal weight: 0.4980 chunk 434 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 389 optimal weight: 40.0000 chunk 117 optimal weight: 7.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 GLN C 624 ASN D 260 ASN D 327 GLN D 624 ASN F 327 GLN F 624 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32506 Z= 0.193 Angle : 0.585 7.275 44118 Z= 0.310 Chirality : 0.045 0.210 5114 Planarity : 0.004 0.042 5976 Dihedral : 4.709 20.442 4800 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.25 % Allowed : 14.92 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % 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: -1.21 (0.12), residues: 4512 helix: 0.44 (0.12), residues: 1944 sheet: 0.62 (0.25), residues: 516 loop : -2.51 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 454 HIS 0.003 0.001 HIS E 317 PHE 0.023 0.001 PHE D 265 TYR 0.014 0.001 TYR D 203 ARG 0.004 0.000 ARG F 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 377 time to evaluate : 3.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.5989 (mm-30) REVERT: A 427 MET cc_start: 0.5090 (mpm) cc_final: 0.4398 (mmt) REVERT: A 599 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7921 (ptm160) REVERT: A 674 PHE cc_start: 0.7240 (t80) cc_final: 0.6826 (t80) REVERT: A 678 MET cc_start: 0.5949 (mmp) cc_final: 0.5298 (mpm) REVERT: A 742 PHE cc_start: 0.6928 (m-80) cc_final: 0.6019 (m-80) REVERT: A 756 GLU cc_start: 0.6275 (mm-30) cc_final: 0.5741 (mt-10) REVERT: B 211 LYS cc_start: 0.6771 (mtpt) cc_final: 0.6121 (tptm) REVERT: B 534 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7270 (tt0) REVERT: B 554 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6701 (mp0) REVERT: B 611 MET cc_start: 0.7816 (ptt) cc_final: 0.7572 (ptp) REVERT: B 720 MET cc_start: 0.2566 (OUTLIER) cc_final: 0.2034 (mpm) REVERT: B 742 PHE cc_start: 0.6700 (m-10) cc_final: 0.5882 (m-80) REVERT: B 744 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6644 (ttm170) REVERT: B 756 GLU cc_start: 0.6085 (mm-30) cc_final: 0.5542 (mt-10) REVERT: C 218 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6980 (tt0) REVERT: C 256 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7250 (mpt-90) REVERT: C 364 ASP cc_start: 0.7411 (p0) cc_final: 0.7143 (p0) REVERT: C 417 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6578 (tp30) REVERT: C 427 MET cc_start: 0.5419 (mmt) cc_final: 0.4312 (mmt) REVERT: C 508 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.6919 (ttt) REVERT: C 756 GLU cc_start: 0.6331 (mm-30) cc_final: 0.5845 (mt-10) REVERT: D 210 ARG cc_start: 0.5707 (tpm170) cc_final: 0.5468 (ttp-110) REVERT: D 211 LYS cc_start: 0.6911 (mtpt) cc_final: 0.6705 (mtmm) REVERT: D 321 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.5919 (mm-30) REVERT: D 427 MET cc_start: 0.5139 (mpm) cc_final: 0.4345 (mmt) REVERT: D 678 MET cc_start: 0.5971 (mmp) cc_final: 0.5439 (mpm) REVERT: D 742 PHE cc_start: 0.6872 (m-80) cc_final: 0.6116 (m-80) REVERT: D 753 ARG cc_start: 0.6442 (mtm110) cc_final: 0.6140 (mtm-85) REVERT: D 756 GLU cc_start: 0.6112 (mm-30) cc_final: 0.5700 (mt-10) REVERT: E 211 LYS cc_start: 0.6627 (mtpt) cc_final: 0.6060 (tptt) REVERT: E 554 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: E 560 ARG cc_start: 0.7334 (ttm170) cc_final: 0.7030 (ttm170) REVERT: E 611 MET cc_start: 0.7787 (ptt) cc_final: 0.7545 (ptp) REVERT: E 720 MET cc_start: 0.2579 (OUTLIER) cc_final: 0.2041 (mpm) REVERT: E 742 PHE cc_start: 0.6752 (m-10) cc_final: 0.5946 (m-80) REVERT: E 744 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6785 (ttm170) REVERT: E 756 GLU cc_start: 0.6054 (mm-30) cc_final: 0.5513 (mt-10) REVERT: F 218 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6876 (tt0) REVERT: F 364 ASP cc_start: 0.7692 (p0) cc_final: 0.7436 (p0) REVERT: F 417 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6757 (tp30) REVERT: F 427 MET cc_start: 0.5323 (mmt) cc_final: 0.4255 (mmt) REVERT: F 508 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6703 (ttt) REVERT: F 756 GLU cc_start: 0.6200 (mm-30) cc_final: 0.5732 (mt-10) REVERT: F 772 ARG cc_start: 0.6386 (OUTLIER) cc_final: 0.5368 (mmt180) outliers start: 92 outliers final: 28 residues processed: 425 average time/residue: 1.7391 time to fit residues: 847.0311 Evaluate side-chains 403 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 357 time to evaluate : 3.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 744 ARG Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 720 MET Chi-restraints excluded: chain E residue 744 ARG Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain F residue 772 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 362 optimal weight: 7.9990 chunk 246 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 323 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 371 optimal weight: 5.9990 chunk 300 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 222 optimal weight: 2.9990 chunk 390 optimal weight: 0.9980 chunk 109 optimal weight: 0.0670 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN C 327 GLN D 327 GLN E 327 GLN F 327 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32506 Z= 0.223 Angle : 0.600 8.098 44118 Z= 0.317 Chirality : 0.046 0.200 5114 Planarity : 0.004 0.046 5976 Dihedral : 4.606 20.579 4800 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 3.85 % Allowed : 15.66 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % 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: -0.95 (0.12), residues: 4512 helix: 0.61 (0.12), residues: 1944 sheet: 1.40 (0.26), residues: 450 loop : -2.41 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 454 HIS 0.002 0.001 HIS E 317 PHE 0.020 0.002 PHE D 265 TYR 0.014 0.001 TYR D 203 ARG 0.004 0.000 ARG E 772 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 366 time to evaluate : 3.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6061 (mm-30) REVERT: A 427 MET cc_start: 0.5160 (mpm) cc_final: 0.4329 (mmt) REVERT: A 599 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7981 (ptm160) REVERT: A 608 MET cc_start: 0.8611 (mtm) cc_final: 0.8327 (mtm) REVERT: A 678 MET cc_start: 0.5939 (mmp) cc_final: 0.5303 (mpm) REVERT: A 742 PHE cc_start: 0.6831 (m-80) cc_final: 0.6043 (m-80) REVERT: A 757 MET cc_start: 0.6274 (mtt) cc_final: 0.6072 (mmt) REVERT: B 211 LYS cc_start: 0.6851 (mtpt) cc_final: 0.6255 (tptt) REVERT: B 534 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7304 (tt0) REVERT: B 554 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: B 720 MET cc_start: 0.2599 (OUTLIER) cc_final: 0.2062 (mpm) REVERT: B 742 PHE cc_start: 0.6688 (m-80) cc_final: 0.5870 (m-80) REVERT: B 744 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6718 (ttm170) REVERT: C 218 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6974 (tt0) REVERT: C 364 ASP cc_start: 0.7310 (p0) cc_final: 0.7030 (p0) REVERT: C 417 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6632 (tp30) REVERT: C 427 MET cc_start: 0.5336 (mmt) cc_final: 0.4233 (mmt) REVERT: C 504 LEU cc_start: 0.7848 (mt) cc_final: 0.7622 (tp) REVERT: C 508 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.6908 (ttt) REVERT: C 611 MET cc_start: 0.7792 (ptt) cc_final: 0.7450 (ptm) REVERT: C 756 GLU cc_start: 0.6376 (mm-30) cc_final: 0.5937 (mt-10) REVERT: D 211 LYS cc_start: 0.6966 (mtpt) cc_final: 0.6763 (mtmm) REVERT: D 295 LYS cc_start: 0.5895 (mttp) cc_final: 0.5575 (mmtt) REVERT: D 321 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6014 (mm-30) REVERT: D 427 MET cc_start: 0.5060 (mpm) cc_final: 0.4438 (mmt) REVERT: D 678 MET cc_start: 0.6028 (mmp) cc_final: 0.5395 (mpm) REVERT: D 742 PHE cc_start: 0.6897 (m-80) cc_final: 0.6137 (m-80) REVERT: D 753 ARG cc_start: 0.6431 (mtm110) cc_final: 0.6021 (mtm-85) REVERT: E 211 LYS cc_start: 0.6673 (mtpt) cc_final: 0.6076 (tptm) REVERT: E 534 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7371 (tt0) REVERT: E 554 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: E 560 ARG cc_start: 0.7362 (ttm170) cc_final: 0.7080 (ttm170) REVERT: E 720 MET cc_start: 0.2557 (OUTLIER) cc_final: 0.2044 (mpm) REVERT: E 742 PHE cc_start: 0.6730 (m-80) cc_final: 0.5934 (m-80) REVERT: F 218 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6877 (tt0) REVERT: F 364 ASP cc_start: 0.7611 (p0) cc_final: 0.7330 (p0) REVERT: F 417 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6813 (tp30) REVERT: F 427 MET cc_start: 0.5279 (mmt) cc_final: 0.4183 (mmt) REVERT: F 508 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6693 (ttt) REVERT: F 611 MET cc_start: 0.7772 (ptt) cc_final: 0.7422 (ptm) REVERT: F 756 GLU cc_start: 0.6227 (mm-30) cc_final: 0.5812 (mt-10) outliers start: 109 outliers final: 36 residues processed: 434 average time/residue: 1.7697 time to fit residues: 878.3465 Evaluate side-chains 404 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 352 time to evaluate : 3.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 741 ARG Chi-restraints excluded: chain B residue 744 ARG Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 741 ARG Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 720 MET Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 741 ARG Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 146 optimal weight: 8.9990 chunk 391 optimal weight: 0.0570 chunk 85 optimal weight: 50.0000 chunk 255 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 435 optimal weight: 5.9990 chunk 361 optimal weight: 0.0770 chunk 201 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 chunk 228 optimal weight: 40.0000 overall best weight: 1.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 760 GLN B 760 GLN D 327 GLN D 760 GLN E 760 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32506 Z= 0.182 Angle : 0.546 6.378 44118 Z= 0.290 Chirality : 0.045 0.205 5114 Planarity : 0.004 0.046 5976 Dihedral : 4.325 19.484 4800 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.08 % Allowed : 16.65 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % 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: -0.58 (0.13), residues: 4512 helix: 0.96 (0.12), residues: 1944 sheet: 1.52 (0.26), residues: 450 loop : -2.23 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 454 HIS 0.001 0.000 HIS E 317 PHE 0.019 0.001 PHE D 265 TYR 0.012 0.001 TYR D 203 ARG 0.004 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 357 time to evaluate : 3.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6008 (mm-30) REVERT: A 427 MET cc_start: 0.5183 (mpm) cc_final: 0.4562 (mmt) REVERT: A 508 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7144 (ttt) REVERT: A 599 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7908 (ptm160) REVERT: A 608 MET cc_start: 0.8616 (mtm) cc_final: 0.8321 (mtm) REVERT: A 678 MET cc_start: 0.5925 (mmp) cc_final: 0.5261 (mpm) REVERT: A 742 PHE cc_start: 0.6802 (m-80) cc_final: 0.5974 (m-80) REVERT: A 756 GLU cc_start: 0.6263 (mm-30) cc_final: 0.5727 (mt-10) REVERT: B 211 LYS cc_start: 0.6800 (mtpt) cc_final: 0.6177 (tptm) REVERT: B 534 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7261 (tt0) REVERT: B 554 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6785 (mp0) REVERT: B 720 MET cc_start: 0.2674 (OUTLIER) cc_final: 0.2075 (mpm) REVERT: B 742 PHE cc_start: 0.6671 (m-80) cc_final: 0.5862 (m-80) REVERT: B 756 GLU cc_start: 0.6230 (mm-30) cc_final: 0.5675 (mt-10) REVERT: C 218 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6943 (tt0) REVERT: C 359 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.6620 (ttm170) REVERT: C 417 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6635 (tp30) REVERT: C 427 MET cc_start: 0.5276 (mmt) cc_final: 0.4196 (mmt) REVERT: C 508 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.6932 (ttt) REVERT: C 534 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7059 (tt0) REVERT: C 611 MET cc_start: 0.7792 (ptt) cc_final: 0.7474 (ptm) REVERT: C 756 GLU cc_start: 0.6310 (mm-30) cc_final: 0.5895 (mt-10) REVERT: D 321 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.5947 (mm-30) REVERT: D 427 MET cc_start: 0.5153 (mpm) cc_final: 0.4518 (mmt) REVERT: D 534 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7329 (tt0) REVERT: D 658 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7769 (mtmt) REVERT: D 678 MET cc_start: 0.6019 (mmp) cc_final: 0.5353 (mpm) REVERT: D 742 PHE cc_start: 0.6869 (m-80) cc_final: 0.6138 (m-80) REVERT: D 753 ARG cc_start: 0.6448 (mtm110) cc_final: 0.6070 (mtm-85) REVERT: D 756 GLU cc_start: 0.6162 (mm-30) cc_final: 0.5727 (mt-10) REVERT: E 211 LYS cc_start: 0.6672 (mtpt) cc_final: 0.6107 (tptm) REVERT: E 554 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: E 560 ARG cc_start: 0.7350 (ttm170) cc_final: 0.7040 (ttm170) REVERT: E 720 MET cc_start: 0.2606 (OUTLIER) cc_final: 0.2030 (mpm) REVERT: E 742 PHE cc_start: 0.6782 (m-80) cc_final: 0.5949 (m-80) REVERT: E 756 GLU cc_start: 0.6208 (mm-30) cc_final: 0.5649 (mt-10) REVERT: F 218 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6875 (tt0) REVERT: F 359 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.6641 (ttm170) REVERT: F 417 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6804 (tp30) REVERT: F 427 MET cc_start: 0.5216 (mmt) cc_final: 0.4143 (mmt) REVERT: F 508 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6712 (ttt) REVERT: F 534 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7156 (tt0) REVERT: F 611 MET cc_start: 0.7760 (ptt) cc_final: 0.7433 (ptm) REVERT: F 756 GLU cc_start: 0.6159 (mm-30) cc_final: 0.5781 (mt-10) outliers start: 87 outliers final: 39 residues processed: 409 average time/residue: 1.7427 time to fit residues: 818.9068 Evaluate side-chains 411 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 351 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 741 ARG Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 720 MET Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 359 ARG Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 419 optimal weight: 0.0170 chunk 49 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 317 optimal weight: 8.9990 chunk 246 optimal weight: 0.5980 chunk 366 optimal weight: 9.9990 chunk 243 optimal weight: 0.2980 chunk 433 optimal weight: 1.9990 chunk 271 optimal weight: 6.9990 chunk 264 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 32506 Z= 0.153 Angle : 0.501 5.138 44118 Z= 0.266 Chirality : 0.044 0.203 5114 Planarity : 0.003 0.045 5976 Dihedral : 3.982 19.397 4800 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.86 % Allowed : 17.33 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % 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: -0.17 (0.13), residues: 4512 helix: 1.38 (0.12), residues: 1938 sheet: 1.67 (0.26), residues: 450 loop : -2.06 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 454 HIS 0.001 0.000 HIS B 404 PHE 0.018 0.001 PHE F 265 TYR 0.010 0.001 TYR D 203 ARG 0.004 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 381 time to evaluate : 3.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.5861 (mm-30) REVERT: A 427 MET cc_start: 0.5342 (mpm) cc_final: 0.4764 (mmt) REVERT: A 488 GLU cc_start: 0.7170 (tt0) cc_final: 0.6813 (tt0) REVERT: A 508 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7087 (ttt) REVERT: A 599 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7915 (ptm160) REVERT: A 674 PHE cc_start: 0.7320 (t80) cc_final: 0.7013 (t80) REVERT: A 678 MET cc_start: 0.6023 (mmp) cc_final: 0.5395 (mpm) REVERT: A 742 PHE cc_start: 0.6848 (m-80) cc_final: 0.5952 (m-80) REVERT: A 756 GLU cc_start: 0.6220 (mm-30) cc_final: 0.5796 (mt-10) REVERT: B 211 LYS cc_start: 0.6753 (mtpt) cc_final: 0.6180 (tptm) REVERT: B 340 HIS cc_start: 0.6785 (m90) cc_final: 0.6221 (m-70) REVERT: B 427 MET cc_start: 0.5401 (mmt) cc_final: 0.4520 (mmt) REVERT: B 678 MET cc_start: 0.6230 (mmp) cc_final: 0.5996 (mmm) REVERT: B 720 MET cc_start: 0.2539 (OUTLIER) cc_final: 0.1985 (mpm) REVERT: B 742 PHE cc_start: 0.6654 (m-80) cc_final: 0.5822 (m-80) REVERT: C 218 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6944 (tt0) REVERT: C 417 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6631 (tp30) REVERT: C 427 MET cc_start: 0.5314 (mmt) cc_final: 0.4353 (mmt) REVERT: C 508 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.6895 (ttt) REVERT: C 534 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7053 (tt0) REVERT: C 611 MET cc_start: 0.7792 (ptt) cc_final: 0.7514 (ptm) REVERT: C 678 MET cc_start: 0.6211 (mmp) cc_final: 0.5865 (mmm) REVERT: C 756 GLU cc_start: 0.6262 (mm-30) cc_final: 0.5933 (mt-10) REVERT: D 321 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.5826 (mm-30) REVERT: D 427 MET cc_start: 0.5212 (mpm) cc_final: 0.4644 (mmt) REVERT: D 658 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7713 (mtmt) REVERT: D 674 PHE cc_start: 0.7256 (t80) cc_final: 0.7007 (t80) REVERT: D 678 MET cc_start: 0.6127 (mmp) cc_final: 0.5488 (mpm) REVERT: D 742 PHE cc_start: 0.6850 (m-80) cc_final: 0.6085 (m-80) REVERT: D 753 ARG cc_start: 0.6449 (mtm110) cc_final: 0.6173 (mtm-85) REVERT: D 756 GLU cc_start: 0.6076 (mm-30) cc_final: 0.5737 (mt-10) REVERT: E 211 LYS cc_start: 0.6613 (mtpt) cc_final: 0.6083 (tptm) REVERT: E 340 HIS cc_start: 0.6901 (m90) cc_final: 0.6377 (m-70) REVERT: E 427 MET cc_start: 0.5408 (mmt) cc_final: 0.4501 (mmt) REVERT: E 534 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7029 (tt0) REVERT: E 560 ARG cc_start: 0.7321 (ttm170) cc_final: 0.6973 (ttm170) REVERT: E 678 MET cc_start: 0.6250 (mmp) cc_final: 0.6011 (mmm) REVERT: E 720 MET cc_start: 0.2465 (OUTLIER) cc_final: 0.1946 (mpm) REVERT: E 742 PHE cc_start: 0.6765 (m-80) cc_final: 0.5877 (m-80) REVERT: F 218 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6847 (tt0) REVERT: F 417 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6804 (tp30) REVERT: F 427 MET cc_start: 0.5252 (mmt) cc_final: 0.4296 (mmt) REVERT: F 508 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.6687 (ttt) REVERT: F 534 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7148 (tt0) REVERT: F 611 MET cc_start: 0.7753 (ptt) cc_final: 0.7484 (ptm) REVERT: F 678 MET cc_start: 0.6063 (mmp) cc_final: 0.5760 (mmm) REVERT: F 756 GLU cc_start: 0.6113 (mm-30) cc_final: 0.5801 (mt-10) outliers start: 81 outliers final: 33 residues processed: 429 average time/residue: 1.7339 time to fit residues: 860.4419 Evaluate side-chains 412 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 363 time to evaluate : 3.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 741 ARG Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 741 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 720 MET Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 741 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 268 optimal weight: 9.9990 chunk 173 optimal weight: 0.7980 chunk 259 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 85 optimal weight: 50.0000 chunk 84 optimal weight: 40.0000 chunk 275 optimal weight: 0.9990 chunk 295 optimal weight: 9.9990 chunk 214 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 340 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN C 327 GLN D 327 GLN F 327 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32506 Z= 0.214 Angle : 0.566 5.328 44118 Z= 0.300 Chirality : 0.046 0.203 5114 Planarity : 0.004 0.047 5976 Dihedral : 4.229 19.998 4800 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.25 % Allowed : 17.64 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % 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: -0.47 (0.13), residues: 4512 helix: 1.02 (0.12), residues: 1980 sheet: 1.75 (0.26), residues: 444 loop : -2.23 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 454 HIS 0.002 0.001 HIS A 406 PHE 0.020 0.001 PHE E 265 TYR 0.014 0.002 TYR D 203 ARG 0.003 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 363 time to evaluate : 3.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6027 (mm-30) REVERT: A 348 ASN cc_start: 0.8030 (t0) cc_final: 0.7824 (m-40) REVERT: A 427 MET cc_start: 0.5368 (mpm) cc_final: 0.4665 (mmt) REVERT: A 599 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7995 (ptm160) REVERT: A 651 LYS cc_start: 0.7453 (mmtt) cc_final: 0.7172 (mppt) REVERT: A 674 PHE cc_start: 0.7369 (t80) cc_final: 0.7108 (t80) REVERT: A 678 MET cc_start: 0.6051 (mmp) cc_final: 0.5532 (mpm) REVERT: A 742 PHE cc_start: 0.6808 (m-80) cc_final: 0.5997 (m-80) REVERT: B 211 LYS cc_start: 0.6847 (mtpt) cc_final: 0.6225 (tptm) REVERT: B 359 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6758 (ttm170) REVERT: B 534 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7306 (tt0) REVERT: B 560 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7384 (ttm170) REVERT: B 678 MET cc_start: 0.6175 (mmp) cc_final: 0.5939 (mmm) REVERT: B 720 MET cc_start: 0.2582 (OUTLIER) cc_final: 0.2081 (mpm) REVERT: B 742 PHE cc_start: 0.6648 (m-80) cc_final: 0.5828 (m-80) REVERT: C 218 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6962 (tt0) REVERT: C 417 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6636 (tp30) REVERT: C 504 LEU cc_start: 0.7963 (mp) cc_final: 0.7734 (tp) REVERT: C 508 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.6952 (ttt) REVERT: C 534 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7159 (tt0) REVERT: C 611 MET cc_start: 0.7846 (ptt) cc_final: 0.7573 (ptm) REVERT: C 756 GLU cc_start: 0.6272 (mm-30) cc_final: 0.5887 (mt-10) REVERT: D 321 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6009 (mm-30) REVERT: D 359 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6640 (ttm170) REVERT: D 427 MET cc_start: 0.5328 (mpm) cc_final: 0.4642 (mmt) REVERT: D 658 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7750 (mtmt) REVERT: D 678 MET cc_start: 0.6107 (mmp) cc_final: 0.5457 (mpm) REVERT: D 742 PHE cc_start: 0.6795 (m-80) cc_final: 0.6105 (m-80) REVERT: D 753 ARG cc_start: 0.6452 (mtm110) cc_final: 0.6113 (mtm-85) REVERT: D 756 GLU cc_start: 0.6087 (mm-30) cc_final: 0.5714 (mt-10) REVERT: E 211 LYS cc_start: 0.6681 (mtpt) cc_final: 0.6122 (tptm) REVERT: E 348 ASN cc_start: 0.7881 (t0) cc_final: 0.7631 (m110) REVERT: E 359 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6734 (ttm170) REVERT: E 534 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7118 (tt0) REVERT: E 560 ARG cc_start: 0.7347 (ttm170) cc_final: 0.7024 (ttm-80) REVERT: E 678 MET cc_start: 0.6178 (mmp) cc_final: 0.5930 (mmm) REVERT: E 720 MET cc_start: 0.2645 (OUTLIER) cc_final: 0.2170 (mpm) REVERT: E 742 PHE cc_start: 0.6742 (m-80) cc_final: 0.5957 (m-80) REVERT: F 218 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6942 (tt0) REVERT: F 359 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6696 (ttm170) REVERT: F 417 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6783 (tp30) REVERT: F 427 MET cc_start: 0.5276 (mmt) cc_final: 0.4156 (mmt) REVERT: F 508 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6741 (ttt) REVERT: F 534 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: F 611 MET cc_start: 0.7824 (ptt) cc_final: 0.7554 (ptm) REVERT: F 756 GLU cc_start: 0.6128 (mm-30) cc_final: 0.5774 (mt-10) outliers start: 92 outliers final: 49 residues processed: 424 average time/residue: 1.7254 time to fit residues: 839.4746 Evaluate side-chains 426 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 356 time to evaluate : 3.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 560 ARG Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 741 ARG Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 741 ARG Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 359 ARG Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 720 MET Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 359 ARG Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 741 ARG Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 394 optimal weight: 0.9980 chunk 415 optimal weight: 5.9990 chunk 379 optimal weight: 20.0000 chunk 404 optimal weight: 6.9990 chunk 243 optimal weight: 0.0870 chunk 176 optimal weight: 1.9990 chunk 317 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 365 optimal weight: 10.0000 chunk 382 optimal weight: 50.0000 chunk 402 optimal weight: 8.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN D 327 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32506 Z= 0.206 Angle : 0.560 5.304 44118 Z= 0.297 Chirality : 0.046 0.201 5114 Planarity : 0.004 0.047 5976 Dihedral : 4.225 19.743 4800 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.32 % Allowed : 18.03 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % 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: -0.47 (0.13), residues: 4512 helix: 1.00 (0.12), residues: 1980 sheet: 1.61 (0.26), residues: 450 loop : -2.18 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 454 HIS 0.002 0.000 HIS E 317 PHE 0.021 0.001 PHE C 265 TYR 0.012 0.001 TYR D 203 ARG 0.004 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 356 time to evaluate : 3.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6033 (mm-30) REVERT: A 348 ASN cc_start: 0.8033 (t0) cc_final: 0.7830 (m-40) REVERT: A 427 MET cc_start: 0.5379 (mpm) cc_final: 0.4715 (mmt) REVERT: A 599 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7950 (ptm160) REVERT: A 611 MET cc_start: 0.7501 (ptt) cc_final: 0.6959 (ptm) REVERT: A 674 PHE cc_start: 0.7337 (t80) cc_final: 0.7066 (t80) REVERT: A 678 MET cc_start: 0.5997 (mmp) cc_final: 0.5496 (mpm) REVERT: A 742 PHE cc_start: 0.6789 (m-80) cc_final: 0.6003 (m-80) REVERT: A 756 GLU cc_start: 0.6238 (mm-30) cc_final: 0.5764 (mt-10) REVERT: B 211 LYS cc_start: 0.6836 (mtpt) cc_final: 0.6223 (tptm) REVERT: B 359 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.6755 (ttm170) REVERT: B 454 TRP cc_start: 0.7581 (OUTLIER) cc_final: 0.6735 (t-100) REVERT: B 534 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7293 (tt0) REVERT: B 678 MET cc_start: 0.6165 (mmp) cc_final: 0.5938 (mmm) REVERT: B 720 MET cc_start: 0.2584 (OUTLIER) cc_final: 0.2137 (mpm) REVERT: B 742 PHE cc_start: 0.6719 (m-80) cc_final: 0.5862 (m-80) REVERT: C 218 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6950 (tt0) REVERT: C 359 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6818 (ttm170) REVERT: C 417 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6632 (tp30) REVERT: C 427 MET cc_start: 0.5349 (mmt) cc_final: 0.4355 (mmt) REVERT: C 508 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.6886 (ttt) REVERT: C 534 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7132 (tt0) REVERT: C 611 MET cc_start: 0.7884 (ptt) cc_final: 0.7621 (ptm) REVERT: C 756 GLU cc_start: 0.6331 (mm-30) cc_final: 0.5957 (mt-10) REVERT: D 321 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6033 (mm-30) REVERT: D 414 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8315 (tt) REVERT: D 427 MET cc_start: 0.5329 (mpm) cc_final: 0.4639 (mmt) REVERT: D 611 MET cc_start: 0.7599 (ptt) cc_final: 0.7211 (ptm) REVERT: D 658 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7761 (mtmt) REVERT: D 678 MET cc_start: 0.6110 (mmp) cc_final: 0.5453 (mpm) REVERT: D 742 PHE cc_start: 0.6775 (m-80) cc_final: 0.6093 (m-80) REVERT: D 753 ARG cc_start: 0.6416 (mtm110) cc_final: 0.6134 (mtm-85) REVERT: D 756 GLU cc_start: 0.6095 (mm-30) cc_final: 0.5699 (mt-10) REVERT: E 211 LYS cc_start: 0.6710 (mtpt) cc_final: 0.6134 (tptm) REVERT: E 348 ASN cc_start: 0.7900 (t0) cc_final: 0.7642 (m110) REVERT: E 359 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6836 (ttm170) REVERT: E 454 TRP cc_start: 0.7523 (OUTLIER) cc_final: 0.6673 (t-100) REVERT: E 534 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7092 (tt0) REVERT: E 560 ARG cc_start: 0.7352 (ttm170) cc_final: 0.7046 (ttm170) REVERT: E 678 MET cc_start: 0.6162 (mmp) cc_final: 0.5926 (mmm) REVERT: E 720 MET cc_start: 0.2571 (OUTLIER) cc_final: 0.2145 (mpm) REVERT: E 742 PHE cc_start: 0.6762 (m-80) cc_final: 0.5945 (m-80) REVERT: F 218 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6903 (tt0) REVERT: F 359 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6816 (ttm170) REVERT: F 417 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6801 (tp30) REVERT: F 508 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6676 (ttt) REVERT: F 534 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7210 (tt0) REVERT: F 611 MET cc_start: 0.7861 (ptt) cc_final: 0.7597 (ptm) REVERT: F 756 GLU cc_start: 0.6189 (mm-30) cc_final: 0.5850 (mt-10) outliers start: 94 outliers final: 48 residues processed: 421 average time/residue: 1.7937 time to fit residues: 866.9532 Evaluate side-chains 420 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 349 time to evaluate : 3.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 454 TRP Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 741 ARG Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 741 ARG Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 359 ARG Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 454 TRP Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 720 MET Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 359 ARG Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 265 optimal weight: 9.9990 chunk 427 optimal weight: 9.9990 chunk 260 optimal weight: 10.0000 chunk 202 optimal weight: 4.9990 chunk 297 optimal weight: 8.9990 chunk 448 optimal weight: 2.9990 chunk 412 optimal weight: 9.9990 chunk 356 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 275 optimal weight: 4.9990 chunk 218 optimal weight: 10.0000 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 327 GLN ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN ** E 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 401 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 32506 Z= 0.332 Angle : 0.691 6.724 44118 Z= 0.367 Chirality : 0.050 0.202 5114 Planarity : 0.005 0.049 5976 Dihedral : 4.788 23.890 4800 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 3.08 % Allowed : 18.71 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % 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: 4512 helix: 0.49 (0.11), residues: 1980 sheet: 1.35 (0.26), residues: 456 loop : -2.37 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 454 HIS 0.003 0.001 HIS A 404 PHE 0.022 0.002 PHE C 265 TYR 0.021 0.003 TYR D 203 ARG 0.007 0.001 ARG E 662 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 365 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6305 (mm-30) REVERT: A 348 ASN cc_start: 0.8014 (t0) cc_final: 0.7776 (m-40) REVERT: A 427 MET cc_start: 0.5293 (mpm) cc_final: 0.4654 (mmt) REVERT: A 599 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.8056 (ptm160) REVERT: A 678 MET cc_start: 0.6054 (mmp) cc_final: 0.5460 (mpm) REVERT: A 742 PHE cc_start: 0.6887 (m-80) cc_final: 0.6065 (m-80) REVERT: B 321 GLU cc_start: 0.7529 (mp0) cc_final: 0.7139 (mm-30) REVERT: B 454 TRP cc_start: 0.7681 (OUTLIER) cc_final: 0.6800 (t-100) REVERT: B 534 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: B 560 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7475 (ttm170) REVERT: B 742 PHE cc_start: 0.6773 (m-80) cc_final: 0.5890 (m-80) REVERT: C 218 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7088 (tt0) REVERT: C 359 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6835 (ttm170) REVERT: C 417 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6663 (tp30) REVERT: C 427 MET cc_start: 0.5432 (mmt) cc_final: 0.4424 (mmt) REVERT: C 508 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.6980 (ttt) REVERT: C 534 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7242 (tt0) REVERT: C 611 MET cc_start: 0.7898 (ptt) cc_final: 0.7618 (ptm) REVERT: C 756 GLU cc_start: 0.6363 (mm-30) cc_final: 0.5882 (mt-10) REVERT: D 321 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6249 (mm-30) REVERT: D 348 ASN cc_start: 0.7952 (t0) cc_final: 0.7720 (m-40) REVERT: D 359 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6806 (ttm170) REVERT: D 427 MET cc_start: 0.5283 (mpm) cc_final: 0.4627 (mmt) REVERT: D 611 MET cc_start: 0.7732 (ptt) cc_final: 0.7473 (ptm) REVERT: D 658 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7720 (mtmt) REVERT: D 678 MET cc_start: 0.6098 (mmp) cc_final: 0.5418 (mpm) REVERT: D 742 PHE cc_start: 0.6851 (m-80) cc_final: 0.6148 (m-80) REVERT: D 753 ARG cc_start: 0.6414 (mtm110) cc_final: 0.6137 (mtm-85) REVERT: E 211 LYS cc_start: 0.6752 (mtpt) cc_final: 0.6208 (tptt) REVERT: E 292 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6096 (mp0) REVERT: E 321 GLU cc_start: 0.7400 (mp0) cc_final: 0.7097 (mm-30) REVERT: E 348 ASN cc_start: 0.7923 (t0) cc_final: 0.7683 (t0) REVERT: E 359 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6929 (ttm170) REVERT: E 454 TRP cc_start: 0.7619 (OUTLIER) cc_final: 0.6732 (t-100) REVERT: E 534 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7183 (tt0) REVERT: E 560 ARG cc_start: 0.7408 (ttm170) cc_final: 0.7139 (ttm170) REVERT: E 742 PHE cc_start: 0.6818 (m-80) cc_final: 0.5974 (m-80) REVERT: F 218 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.7006 (tt0) REVERT: F 359 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6846 (ttm170) REVERT: F 417 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6833 (tp30) REVERT: F 427 MET cc_start: 0.5357 (mmt) cc_final: 0.4385 (mmt) REVERT: F 508 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.6774 (ttt) REVERT: F 534 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7322 (tt0) REVERT: F 611 MET cc_start: 0.7879 (ptt) cc_final: 0.7605 (ptm) REVERT: F 756 GLU cc_start: 0.6249 (mm-30) cc_final: 0.5778 (mt-10) outliers start: 87 outliers final: 43 residues processed: 419 average time/residue: 1.7916 time to fit residues: 867.7108 Evaluate side-chains 414 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 349 time to evaluate : 5.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 454 TRP Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 560 ARG Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 741 ARG Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 741 ARG Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 359 ARG Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 454 TRP Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 359 ARG Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 283 optimal weight: 0.9980 chunk 380 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 329 optimal weight: 0.0570 chunk 52 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 357 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 367 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 overall best weight: 1.3100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN B 226 HIS B 760 GLN C 401 ASN D 260 ASN D 327 GLN E 760 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.214115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.181677 restraints weight = 32801.576| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.34 r_work: 0.3655 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 32506 Z= 0.162 Angle : 0.531 5.289 44118 Z= 0.283 Chirality : 0.044 0.200 5114 Planarity : 0.004 0.046 5976 Dihedral : 4.163 20.351 4800 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.44 % Allowed : 19.45 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % 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: -0.41 (0.13), residues: 4512 helix: 1.07 (0.12), residues: 1980 sheet: 1.53 (0.26), residues: 450 loop : -2.14 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 454 HIS 0.001 0.000 HIS B 317 PHE 0.019 0.001 PHE C 265 TYR 0.012 0.001 TYR D 203 ARG 0.003 0.000 ARG C 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12927.08 seconds wall clock time: 317 minutes 7.56 seconds (19027.56 seconds total)