Starting phenix.real_space_refine on Sat Mar 16 10:56:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d1w_7786/03_2024/6d1w_7786.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d1w_7786/03_2024/6d1w_7786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d1w_7786/03_2024/6d1w_7786.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d1w_7786/03_2024/6d1w_7786.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d1w_7786/03_2024/6d1w_7786.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d1w_7786/03_2024/6d1w_7786.pdb" } resolution = 3.54 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= 0.001 sd= 0.008 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 72 5.16 5 C 9620 2.51 5 N 2312 2.21 5 O 2488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 251": "NH1" <-> "NH2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 361": "NH1" <-> "NH2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 397": "NH1" <-> "NH2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 592": "NH1" <-> "NH2" Residue "A ARG 654": "NH1" <-> "NH2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 361": "NH1" <-> "NH2" Residue "B TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 397": "NH1" <-> "NH2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "B ARG 528": "NH1" <-> "NH2" Residue "B PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 592": "NH1" <-> "NH2" Residue "B ARG 654": "NH1" <-> "NH2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 361": "NH1" <-> "NH2" Residue "C TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 397": "NH1" <-> "NH2" Residue "C ARG 399": "NH1" <-> "NH2" Residue "C PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 504": "NH1" <-> "NH2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 592": "NH1" <-> "NH2" Residue "C ARG 654": "NH1" <-> "NH2" Residue "D ARG 251": "NH1" <-> "NH2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 361": "NH1" <-> "NH2" Residue "D TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 397": "NH1" <-> "NH2" Residue "D ARG 399": "NH1" <-> "NH2" Residue "D PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 504": "NH1" <-> "NH2" Residue "D ARG 528": "NH1" <-> "NH2" Residue "D PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 592": "NH1" <-> "NH2" Residue "D ARG 654": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14492 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3581 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'CIS': 3, 'PTRANS': 11, 'TRANS': 436} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 10} Unresolved non-hydrogen planarities: 96 Chain: "B" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3581 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'CIS': 3, 'PTRANS': 11, 'TRANS': 436} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 10} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3581 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'CIS': 3, 'PTRANS': 11, 'TRANS': 436} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 10} Unresolved non-hydrogen planarities: 96 Chain: "D" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3581 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'CIS': 3, 'PTRANS': 11, 'TRANS': 436} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 10} Unresolved non-hydrogen planarities: 96 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.12, per 1000 atoms: 0.49 Number of scatterers: 14492 At special positions: 0 Unit cell: (110.62, 110.62, 92.3856, 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 72 16.00 O 2488 8.00 N 2312 7.00 C 9620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 344 " distance=2.02 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=2.02 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " distance=2.01 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 344 " distance=2.01 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 Links applied NAG-ASN " NAG A 801 " - " ASN A 328 " " NAG A 802 " - " ASN A 362 " " NAG A 803 " - " ASN A 375 " " NAG B 801 " - " ASN B 328 " " NAG B 802 " - " ASN B 362 " " NAG B 803 " - " ASN B 375 " " NAG C 801 " - " ASN C 328 " " NAG C 802 " - " ASN C 362 " " NAG C 803 " - " ASN C 375 " " NAG D 801 " - " ASN D 328 " " NAG D 802 " - " ASN D 362 " " NAG D 803 " - " ASN D 375 " Time building additional restraints: 5.82 Conformation dependent library (CDL) restraints added in 2.4 seconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3456 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 60.4% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 216 through 242 removed outlier: 3.518A pdb=" N ILE A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.825A pdb=" N TYR A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 285 through 291 removed outlier: 3.577A pdb=" N ASP A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 331 removed outlier: 3.614A pdb=" N SER A 330 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N CYS A 331 " --> pdb=" O ASN A 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 327 through 331' Processing helix chain 'A' and resid 398 through 412 Processing helix chain 'A' and resid 467 through 491 removed outlier: 3.505A pdb=" N ILE A 484 " --> pdb=" O PHE A 480 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 490 " --> pdb=" O TYR A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 528 removed outlier: 3.793A pdb=" N VAL A 513 " --> pdb=" O CYS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 532 through 541 removed outlier: 3.691A pdb=" N ASP A 541 " --> pdb=" O GLN A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 572 Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.769A pdb=" N ILE A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE A 579 " --> pdb=" O LYS A 575 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 619 removed outlier: 3.901A pdb=" N THR A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N THR A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG A 592 " --> pdb=" O THR A 588 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY A 599 " --> pdb=" O LYS A 595 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N MET A 603 " --> pdb=" O GLY A 599 " (cutoff:3.500A) Proline residue: A 604 - end of helix Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 628 through 642 Processing helix chain 'A' and resid 645 through 653 removed outlier: 4.009A pdb=" N ILE A 649 " --> pdb=" O ASN A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 681 removed outlier: 3.653A pdb=" N PHE A 669 " --> pdb=" O VAL A 665 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN A 674 " --> pdb=" O PHE A 670 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 242 removed outlier: 3.518A pdb=" N ILE B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 258 removed outlier: 3.824A pdb=" N TYR B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 275 through 285 Processing helix chain 'B' and resid 285 through 291 removed outlier: 3.578A pdb=" N ASP B 289 " --> pdb=" O GLY B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 331 removed outlier: 3.615A pdb=" N SER B 330 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N CYS B 331 " --> pdb=" O ASN B 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 327 through 331' Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 467 through 491 removed outlier: 3.505A pdb=" N ILE B 484 " --> pdb=" O PHE B 480 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL B 489 " --> pdb=" O PHE B 485 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 490 " --> pdb=" O TYR B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 528 removed outlier: 3.793A pdb=" N VAL B 513 " --> pdb=" O CYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 531 No H-bonds generated for 'chain 'B' and resid 529 through 531' Processing helix chain 'B' and resid 532 through 541 removed outlier: 3.691A pdb=" N ASP B 541 " --> pdb=" O GLN B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 572 Processing helix chain 'B' and resid 573 through 581 removed outlier: 3.768A pdb=" N ILE B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE B 579 " --> pdb=" O LYS B 575 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG B 581 " --> pdb=" O ILE B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 619 removed outlier: 3.902A pdb=" N THR B 588 " --> pdb=" O SER B 584 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N THR B 589 " --> pdb=" O GLN B 585 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 592 " --> pdb=" O THR B 588 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY B 599 " --> pdb=" O LYS B 595 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N MET B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) Proline residue: B 604 - end of helix Processing helix chain 'B' and resid 623 through 627 Processing helix chain 'B' and resid 628 through 642 Processing helix chain 'B' and resid 645 through 653 removed outlier: 4.009A pdb=" N ILE B 649 " --> pdb=" O ASN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 681 removed outlier: 3.652A pdb=" N PHE B 669 " --> pdb=" O VAL B 665 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN B 674 " --> pdb=" O PHE B 670 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 242 removed outlier: 3.519A pdb=" N ILE C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.825A pdb=" N TYR C 249 " --> pdb=" O ASN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 275 through 285 Processing helix chain 'C' and resid 285 through 291 removed outlier: 3.578A pdb=" N ASP C 289 " --> pdb=" O GLY C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 331 removed outlier: 3.615A pdb=" N SER C 330 " --> pdb=" O ARG C 327 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N CYS C 331 " --> pdb=" O ASN C 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 327 through 331' Processing helix chain 'C' and resid 398 through 412 Processing helix chain 'C' and resid 467 through 491 removed outlier: 3.505A pdb=" N ILE C 484 " --> pdb=" O PHE C 480 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL C 489 " --> pdb=" O PHE C 485 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU C 490 " --> pdb=" O TYR C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 528 removed outlier: 3.793A pdb=" N VAL C 513 " --> pdb=" O CYS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 531 No H-bonds generated for 'chain 'C' and resid 529 through 531' Processing helix chain 'C' and resid 532 through 541 removed outlier: 3.692A pdb=" N ASP C 541 " --> pdb=" O GLN C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 572 Processing helix chain 'C' and resid 573 through 581 removed outlier: 3.769A pdb=" N ILE C 577 " --> pdb=" O LEU C 573 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE C 579 " --> pdb=" O LYS C 575 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG C 581 " --> pdb=" O ILE C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 619 removed outlier: 3.901A pdb=" N THR C 588 " --> pdb=" O SER C 584 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N THR C 589 " --> pdb=" O GLN C 585 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG C 592 " --> pdb=" O THR C 588 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE C 598 " --> pdb=" O ALA C 594 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY C 599 " --> pdb=" O LYS C 595 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N MET C 603 " --> pdb=" O GLY C 599 " (cutoff:3.500A) Proline residue: C 604 - end of helix Processing helix chain 'C' and resid 623 through 627 Processing helix chain 'C' and resid 628 through 642 Processing helix chain 'C' and resid 645 through 653 removed outlier: 4.010A pdb=" N ILE C 649 " --> pdb=" O ASN C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 681 removed outlier: 3.652A pdb=" N PHE C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN C 674 " --> pdb=" O PHE C 670 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 242 removed outlier: 3.519A pdb=" N ILE D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 258 removed outlier: 3.826A pdb=" N TYR D 249 " --> pdb=" O ASN D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 285 through 291 removed outlier: 3.578A pdb=" N ASP D 289 " --> pdb=" O GLY D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.614A pdb=" N SER D 330 " --> pdb=" O ARG D 327 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N CYS D 331 " --> pdb=" O ASN D 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 327 through 331' Processing helix chain 'D' and resid 398 through 412 Processing helix chain 'D' and resid 467 through 491 removed outlier: 3.505A pdb=" N ILE D 484 " --> pdb=" O PHE D 480 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL D 489 " --> pdb=" O PHE D 485 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU D 490 " --> pdb=" O TYR D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 528 removed outlier: 3.793A pdb=" N VAL D 513 " --> pdb=" O CYS D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 531 No H-bonds generated for 'chain 'D' and resid 529 through 531' Processing helix chain 'D' and resid 532 through 541 removed outlier: 3.691A pdb=" N ASP D 541 " --> pdb=" O GLN D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 572 Processing helix chain 'D' and resid 573 through 581 removed outlier: 3.769A pdb=" N ILE D 577 " --> pdb=" O LEU D 573 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE D 579 " --> pdb=" O LYS D 575 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG D 581 " --> pdb=" O ILE D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 619 removed outlier: 3.901A pdb=" N THR D 588 " --> pdb=" O SER D 584 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N THR D 589 " --> pdb=" O GLN D 585 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG D 592 " --> pdb=" O THR D 588 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE D 598 " --> pdb=" O ALA D 594 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY D 599 " --> pdb=" O LYS D 595 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N MET D 603 " --> pdb=" O GLY D 599 " (cutoff:3.500A) Proline residue: D 604 - end of helix Processing helix chain 'D' and resid 623 through 627 Processing helix chain 'D' and resid 628 through 642 Processing helix chain 'D' and resid 645 through 653 removed outlier: 4.009A pdb=" N ILE D 649 " --> pdb=" O ASN D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 681 removed outlier: 3.653A pdb=" N PHE D 669 " --> pdb=" O VAL D 665 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN D 674 " --> pdb=" O PHE D 670 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 309 Processing sheet with id=AA2, first strand: chain 'A' and resid 308 through 309 removed outlier: 6.310A pdb=" N LEU A 316 " --> pdb=" O TYR A 429 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR A 429 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL A 318 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N SER A 427 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 435 " --> pdb=" O ASN A 430 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA4, first strand: chain 'B' and resid 308 through 309 Processing sheet with id=AA5, first strand: chain 'B' and resid 308 through 309 removed outlier: 6.310A pdb=" N LEU B 316 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TYR B 429 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL B 318 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N SER B 427 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 435 " --> pdb=" O ASN B 430 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 379 through 380 Processing sheet with id=AA7, first strand: chain 'C' and resid 308 through 309 Processing sheet with id=AA8, first strand: chain 'C' and resid 308 through 309 removed outlier: 6.309A pdb=" N LEU C 316 " --> pdb=" O TYR C 429 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TYR C 429 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL C 318 " --> pdb=" O SER C 427 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N SER C 427 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 435 " --> pdb=" O ASN C 430 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 379 through 380 Processing sheet with id=AB1, first strand: chain 'D' and resid 308 through 309 Processing sheet with id=AB2, first strand: chain 'D' and resid 308 through 309 removed outlier: 6.309A pdb=" N LEU D 316 " --> pdb=" O TYR D 429 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TYR D 429 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL D 318 " --> pdb=" O SER D 427 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N SER D 427 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU D 435 " --> pdb=" O ASN D 430 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 379 through 380 837 hydrogen bonds defined for protein. 2403 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: 4.14 Time building geometry restraints manager: 6.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 2136 1.28 - 1.41: 4296 1.41 - 1.54: 8324 1.54 - 1.68: 12 1.68 - 1.81: 108 Bond restraints: 14876 Sorted by residual: bond pdb=" C ALA C 356 " pdb=" N PRO C 357 " ideal model delta sigma weight residual 1.334 1.145 0.189 2.34e-02 1.83e+03 6.54e+01 bond pdb=" C ALA D 356 " pdb=" N PRO D 357 " ideal model delta sigma weight residual 1.334 1.145 0.189 2.34e-02 1.83e+03 6.49e+01 bond pdb=" C ALA A 356 " pdb=" N PRO A 357 " ideal model delta sigma weight residual 1.334 1.145 0.189 2.34e-02 1.83e+03 6.49e+01 bond pdb=" C ALA B 356 " pdb=" N PRO B 357 " ideal model delta sigma weight residual 1.334 1.145 0.188 2.34e-02 1.83e+03 6.49e+01 bond pdb=" CA ALA D 303 " pdb=" C ALA D 303 " ideal model delta sigma weight residual 1.524 1.550 -0.026 1.29e-02 6.01e+03 4.13e+00 ... (remaining 14871 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.53: 257 106.53 - 113.40: 8307 113.40 - 120.27: 5292 120.27 - 127.13: 6270 127.13 - 134.00: 134 Bond angle restraints: 20260 Sorted by residual: angle pdb=" N ALA B 303 " pdb=" CA ALA B 303 " pdb=" C ALA B 303 " ideal model delta sigma weight residual 111.36 118.10 -6.74 1.09e+00 8.42e-01 3.83e+01 angle pdb=" N ALA C 303 " pdb=" CA ALA C 303 " pdb=" C ALA C 303 " ideal model delta sigma weight residual 111.36 118.08 -6.72 1.09e+00 8.42e-01 3.80e+01 angle pdb=" N ALA A 303 " pdb=" CA ALA A 303 " pdb=" C ALA A 303 " ideal model delta sigma weight residual 111.36 118.05 -6.69 1.09e+00 8.42e-01 3.77e+01 angle pdb=" N ALA D 303 " pdb=" CA ALA D 303 " pdb=" C ALA D 303 " ideal model delta sigma weight residual 111.36 118.03 -6.67 1.09e+00 8.42e-01 3.75e+01 angle pdb=" C LYS D 294 " pdb=" N MET D 295 " pdb=" CA MET D 295 " ideal model delta sigma weight residual 121.70 128.13 -6.43 1.80e+00 3.09e-01 1.28e+01 ... (remaining 20255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 8436 16.03 - 32.07: 144 32.07 - 48.10: 76 48.10 - 64.13: 4 64.13 - 80.16: 12 Dihedral angle restraints: 8672 sinusoidal: 3336 harmonic: 5336 Sorted by residual: dihedral pdb=" CA ILE A 644 " pdb=" C ILE A 644 " pdb=" N ASN A 645 " pdb=" CA ASN A 645 " ideal model delta harmonic sigma weight residual 180.00 155.09 24.91 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ILE D 644 " pdb=" C ILE D 644 " pdb=" N ASN D 645 " pdb=" CA ASN D 645 " ideal model delta harmonic sigma weight residual 180.00 155.09 24.91 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ILE C 644 " pdb=" C ILE C 644 " pdb=" N ASN C 645 " pdb=" CA ASN C 645 " ideal model delta harmonic sigma weight residual 180.00 155.14 24.86 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 8669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1342 0.030 - 0.059: 636 0.059 - 0.089: 251 0.089 - 0.118: 123 0.118 - 0.148: 16 Chirality restraints: 2368 Sorted by residual: chirality pdb=" CA ILE C 644 " pdb=" N ILE C 644 " pdb=" C ILE C 644 " pdb=" CB ILE C 644 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA ILE A 644 " pdb=" N ILE A 644 " pdb=" C ILE A 644 " pdb=" CB ILE A 644 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA ILE D 644 " pdb=" N ILE D 644 " pdb=" C ILE D 644 " pdb=" CB ILE D 644 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 2365 not shown) Planarity restraints: 2496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 458 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO A 459 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 459 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 459 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 458 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO B 459 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 459 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 459 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 458 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO D 459 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 459 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 459 " -0.025 5.00e-02 4.00e+02 ... (remaining 2493 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 550 2.70 - 3.25: 17063 3.25 - 3.80: 25388 3.80 - 4.35: 30939 4.35 - 4.90: 49131 Nonbonded interactions: 123071 Sorted by model distance: nonbonded pdb=" O ALA B 562 " pdb=" OG1 THR B 565 " model vdw 2.154 2.440 nonbonded pdb=" O ALA C 562 " pdb=" OG1 THR C 565 " model vdw 2.154 2.440 nonbonded pdb=" O ALA D 562 " pdb=" OG1 THR D 565 " model vdw 2.154 2.440 nonbonded pdb=" O ALA A 562 " pdb=" OG1 THR A 565 " model vdw 2.155 2.440 nonbonded pdb=" OH TYR C 227 " pdb=" O VAL C 569 " model vdw 2.181 2.440 ... (remaining 123066 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 0.010 Extract box with map and model: 2.280 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 37.470 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.189 14876 Z= 0.501 Angle : 0.772 9.254 20260 Z= 0.442 Chirality : 0.043 0.148 2368 Planarity : 0.004 0.046 2484 Dihedral : 9.069 80.164 5204 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.52 % Favored : 93.26 % Rotamer: Outliers : 0.27 % Allowed : 0.82 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.16), residues: 1780 helix: -3.02 (0.11), residues: 884 sheet: 0.77 (0.34), residues: 184 loop : -1.48 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 380 HIS 0.002 0.001 HIS A 550 PHE 0.014 0.002 PHE B 436 TYR 0.014 0.002 TYR C 527 ARG 0.011 0.001 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 425 time to evaluate : 1.801 Fit side-chains REVERT: A 249 TYR cc_start: 0.8485 (t80) cc_final: 0.7821 (t80) REVERT: A 590 MET cc_start: 0.5614 (mmm) cc_final: 0.5023 (mmt) REVERT: A 616 TYR cc_start: 0.8617 (t80) cc_final: 0.8320 (t80) REVERT: B 249 TYR cc_start: 0.8492 (t80) cc_final: 0.7809 (t80) REVERT: B 590 MET cc_start: 0.5647 (mmm) cc_final: 0.4923 (mmt) REVERT: B 616 TYR cc_start: 0.8644 (t80) cc_final: 0.8399 (t80) REVERT: B 654 ARG cc_start: 0.8421 (mtp180) cc_final: 0.8158 (mtm-85) REVERT: C 249 TYR cc_start: 0.8504 (t80) cc_final: 0.7840 (t80) REVERT: C 616 TYR cc_start: 0.8658 (t80) cc_final: 0.8377 (t80) REVERT: D 249 TYR cc_start: 0.8504 (t80) cc_final: 0.7829 (t80) REVERT: D 570 TRP cc_start: 0.8350 (m100) cc_final: 0.8143 (m100) REVERT: D 616 TYR cc_start: 0.8616 (t80) cc_final: 0.8355 (t80) outliers start: 4 outliers final: 4 residues processed: 425 average time/residue: 0.2564 time to fit residues: 160.7902 Evaluate side-chains 218 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 141 optimal weight: 0.0570 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN A 458 GLN A 543 ASN A 636 GLN A 645 ASN B 323 GLN B 458 GLN B 543 ASN B 636 GLN C 323 GLN C 458 GLN C 543 ASN C 636 GLN C 645 ASN D 323 GLN D 458 GLN D 543 ASN D 636 GLN D 645 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14876 Z= 0.226 Angle : 0.619 7.559 20260 Z= 0.344 Chirality : 0.042 0.149 2368 Planarity : 0.004 0.047 2484 Dihedral : 5.843 50.860 2228 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.87 % Favored : 96.91 % Rotamer: Outliers : 2.24 % Allowed : 10.19 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -0.23 (0.18), residues: 1780 helix: 0.36 (0.15), residues: 960 sheet: 0.73 (0.33), residues: 176 loop : -1.08 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 380 HIS 0.002 0.001 HIS C 550 PHE 0.027 0.002 PHE D 472 TYR 0.022 0.002 TYR C 247 ARG 0.005 0.000 ARG D 654 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 280 time to evaluate : 1.591 Fit side-chains REVERT: A 249 TYR cc_start: 0.8506 (t80) cc_final: 0.7792 (t80) REVERT: B 249 TYR cc_start: 0.8408 (t80) cc_final: 0.7656 (t80) REVERT: B 487 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6856 (t80) REVERT: C 249 TYR cc_start: 0.8459 (t80) cc_final: 0.7742 (t80) REVERT: D 249 TYR cc_start: 0.8472 (t80) cc_final: 0.7796 (t80) outliers start: 33 outliers final: 19 residues processed: 301 average time/residue: 0.2621 time to fit residues: 115.4982 Evaluate side-chains 242 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 222 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain B residue 547 ASN Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain C residue 547 ASN Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 461 LYS Chi-restraints excluded: chain D residue 547 ASN Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 607 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 136 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 163 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 HIS A 578 ASN B 550 HIS B 578 ASN C 550 HIS D 542 GLN D 550 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 14876 Z= 0.311 Angle : 0.639 7.268 20260 Z= 0.344 Chirality : 0.043 0.158 2368 Planarity : 0.004 0.056 2484 Dihedral : 4.713 29.241 2220 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.42 % Favored : 97.36 % Rotamer: Outliers : 2.51 % Allowed : 12.84 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: 0.23 (0.18), residues: 1780 helix: 0.85 (0.16), residues: 992 sheet: 0.57 (0.34), residues: 176 loop : -1.05 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 380 HIS 0.001 0.000 HIS A 379 PHE 0.016 0.002 PHE D 436 TYR 0.025 0.002 TYR C 527 ARG 0.005 0.000 ARG C 464 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 234 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 TYR cc_start: 0.8648 (t80) cc_final: 0.7685 (t80) REVERT: B 249 TYR cc_start: 0.8616 (t80) cc_final: 0.7576 (t80) REVERT: C 249 TYR cc_start: 0.8630 (t80) cc_final: 0.7626 (t80) REVERT: D 249 TYR cc_start: 0.8647 (t80) cc_final: 0.7682 (t80) REVERT: D 570 TRP cc_start: 0.8458 (m100) cc_final: 0.8211 (m100) outliers start: 37 outliers final: 29 residues processed: 264 average time/residue: 0.2182 time to fit residues: 89.2365 Evaluate side-chains 233 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 204 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 537 GLN Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 537 GLN Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 607 ILE Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 640 ILE Chi-restraints excluded: chain D residue 659 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 5.9990 chunk 123 optimal weight: 0.0970 chunk 84 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 542 GLN D 578 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14876 Z= 0.157 Angle : 0.548 7.287 20260 Z= 0.297 Chirality : 0.040 0.133 2368 Planarity : 0.004 0.049 2484 Dihedral : 4.200 24.609 2220 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.58 % Favored : 97.19 % Rotamer: Outliers : 2.45 % Allowed : 14.20 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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 (0.19), residues: 1780 helix: 1.35 (0.16), residues: 972 sheet: -0.10 (0.35), residues: 184 loop : -0.94 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 570 HIS 0.001 0.000 HIS D 550 PHE 0.016 0.001 PHE D 670 TYR 0.018 0.001 TYR C 247 ARG 0.004 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 238 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 570 TRP cc_start: 0.8354 (m100) cc_final: 0.8132 (m100) outliers start: 36 outliers final: 31 residues processed: 261 average time/residue: 0.2496 time to fit residues: 100.3457 Evaluate side-chains 244 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 213 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 537 GLN Chi-restraints excluded: chain C residue 547 ASN Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 676 PHE Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 434 ASN Chi-restraints excluded: chain D residue 537 GLN Chi-restraints excluded: chain D residue 547 ASN Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 640 ILE Chi-restraints excluded: chain D residue 676 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 88 optimal weight: 0.6980 chunk 156 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 HIS B 550 HIS C 550 HIS D 550 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14876 Z= 0.223 Angle : 0.551 7.297 20260 Z= 0.297 Chirality : 0.040 0.124 2368 Planarity : 0.004 0.048 2484 Dihedral : 4.170 25.431 2220 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.60 % Favored : 96.18 % Rotamer: Outliers : 3.12 % Allowed : 15.08 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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 (0.19), residues: 1780 helix: 1.20 (0.16), residues: 996 sheet: -0.33 (0.35), residues: 184 loop : -0.92 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 570 HIS 0.001 0.000 HIS C 379 PHE 0.020 0.001 PHE C 670 TYR 0.024 0.001 TYR A 227 ARG 0.004 0.000 ARG B 581 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 227 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 570 TRP cc_start: 0.8375 (m100) cc_final: 0.8148 (m100) REVERT: D 675 MET cc_start: 0.7479 (mmm) cc_final: 0.7055 (mmp) outliers start: 46 outliers final: 31 residues processed: 266 average time/residue: 0.2415 time to fit residues: 97.9594 Evaluate side-chains 238 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 207 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 434 ASN Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 537 GLN Chi-restraints excluded: chain C residue 547 ASN Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 537 GLN Chi-restraints excluded: chain D residue 547 ASN Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 607 ILE Chi-restraints excluded: chain D residue 640 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 102 optimal weight: 0.0970 chunk 42 optimal weight: 3.9990 chunk 174 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 0.0270 chunk 91 optimal weight: 9.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14876 Z= 0.148 Angle : 0.525 8.053 20260 Z= 0.285 Chirality : 0.040 0.167 2368 Planarity : 0.004 0.046 2484 Dihedral : 3.938 21.775 2220 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.03 % Favored : 96.74 % Rotamer: Outliers : 2.24 % Allowed : 17.12 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: 0.68 (0.19), residues: 1780 helix: 1.42 (0.16), residues: 980 sheet: -0.37 (0.36), residues: 184 loop : -0.82 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 366 HIS 0.000 0.000 HIS B 550 PHE 0.017 0.001 PHE D 670 TYR 0.021 0.001 TYR C 527 ARG 0.003 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 243 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 26 residues processed: 264 average time/residue: 0.2280 time to fit residues: 92.2853 Evaluate side-chains 238 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 212 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 537 GLN Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 537 GLN Chi-restraints excluded: chain D residue 597 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 146 optimal weight: 0.0870 chunk 97 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 ASN A 550 HIS B 550 HIS C 550 HIS D 550 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14876 Z= 0.167 Angle : 0.529 8.541 20260 Z= 0.284 Chirality : 0.040 0.198 2368 Planarity : 0.004 0.045 2484 Dihedral : 3.921 22.642 2220 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.81 % Favored : 96.97 % Rotamer: Outliers : 2.11 % Allowed : 19.16 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: 0.67 (0.19), residues: 1780 helix: 1.38 (0.16), residues: 972 sheet: -0.10 (0.36), residues: 176 loop : -0.81 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 570 HIS 0.001 0.000 HIS D 550 PHE 0.022 0.001 PHE A 670 TYR 0.023 0.001 TYR A 227 ARG 0.003 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 235 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 413 VAL cc_start: 0.7161 (t) cc_final: 0.6914 (p) outliers start: 31 outliers final: 27 residues processed: 255 average time/residue: 0.2258 time to fit residues: 88.4919 Evaluate side-chains 242 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 215 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 537 GLN Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 537 GLN Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 640 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 85 optimal weight: 0.0970 chunk 16 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 HIS B 550 HIS C 550 HIS D 550 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14876 Z= 0.156 Angle : 0.530 9.195 20260 Z= 0.282 Chirality : 0.040 0.205 2368 Planarity : 0.004 0.044 2484 Dihedral : 3.847 22.017 2220 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.58 % Favored : 97.19 % Rotamer: Outliers : 1.90 % Allowed : 19.09 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: 0.68 (0.19), residues: 1780 helix: 1.26 (0.16), residues: 1000 sheet: -0.10 (0.37), residues: 176 loop : -0.66 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 366 HIS 0.001 0.000 HIS A 550 PHE 0.023 0.001 PHE D 670 TYR 0.024 0.001 TYR D 227 ARG 0.003 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 248 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 VAL cc_start: 0.7155 (t) cc_final: 0.6900 (p) REVERT: B 413 VAL cc_start: 0.7138 (t) cc_final: 0.6897 (p) REVERT: C 413 VAL cc_start: 0.7154 (t) cc_final: 0.6894 (p) REVERT: D 413 VAL cc_start: 0.7153 (t) cc_final: 0.6900 (p) REVERT: D 668 MET cc_start: 0.8239 (mmp) cc_final: 0.8039 (mmp) outliers start: 28 outliers final: 25 residues processed: 264 average time/residue: 0.2271 time to fit residues: 93.0142 Evaluate side-chains 258 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 233 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 537 GLN Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 537 GLN Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 640 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.6980 chunk 166 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 146 optimal weight: 0.3980 chunk 152 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 HIS B 550 HIS D 550 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14876 Z= 0.193 Angle : 0.541 8.302 20260 Z= 0.286 Chirality : 0.040 0.207 2368 Planarity : 0.004 0.045 2484 Dihedral : 3.895 23.026 2220 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.25 % Favored : 97.53 % Rotamer: Outliers : 2.17 % Allowed : 18.82 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: 0.70 (0.19), residues: 1780 helix: 1.27 (0.15), residues: 1000 sheet: -0.11 (0.37), residues: 176 loop : -0.61 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 570 HIS 0.001 0.000 HIS A 550 PHE 0.024 0.001 PHE A 670 TYR 0.023 0.001 TYR C 527 ARG 0.002 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 240 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 VAL cc_start: 0.7115 (t) cc_final: 0.6879 (p) REVERT: B 413 VAL cc_start: 0.7138 (t) cc_final: 0.6919 (p) REVERT: C 413 VAL cc_start: 0.7146 (t) cc_final: 0.6920 (p) REVERT: D 413 VAL cc_start: 0.7201 (t) cc_final: 0.6941 (p) REVERT: D 668 MET cc_start: 0.8210 (mmp) cc_final: 0.7999 (mmp) outliers start: 32 outliers final: 29 residues processed: 256 average time/residue: 0.2475 time to fit residues: 98.4227 Evaluate side-chains 257 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 228 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 537 GLN Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 537 GLN Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 640 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 40.0000 chunk 104 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 118 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 87 optimal weight: 0.0050 chunk 113 optimal weight: 0.0870 overall best weight: 0.9774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 547 ASN B 550 HIS C 550 HIS D 550 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14876 Z= 0.173 Angle : 0.537 8.767 20260 Z= 0.286 Chirality : 0.040 0.205 2368 Planarity : 0.004 0.047 2484 Dihedral : 3.853 22.795 2220 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.75 % Favored : 97.02 % Rotamer: Outliers : 2.24 % Allowed : 18.55 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: 0.73 (0.19), residues: 1780 helix: 1.30 (0.15), residues: 1000 sheet: -0.10 (0.37), residues: 176 loop : -0.62 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 570 HIS 0.001 0.000 HIS B 550 PHE 0.024 0.001 PHE D 576 TYR 0.023 0.001 TYR C 227 ARG 0.002 0.000 ARG B 464 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 244 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 VAL cc_start: 0.7189 (t) cc_final: 0.6946 (p) REVERT: B 413 VAL cc_start: 0.7209 (t) cc_final: 0.6959 (p) REVERT: C 413 VAL cc_start: 0.7183 (t) cc_final: 0.6927 (p) REVERT: D 413 VAL cc_start: 0.7107 (t) cc_final: 0.6868 (p) REVERT: D 668 MET cc_start: 0.8214 (mmp) cc_final: 0.7988 (mmp) outliers start: 33 outliers final: 28 residues processed: 261 average time/residue: 0.2217 time to fit residues: 89.2768 Evaluate side-chains 276 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 248 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 537 GLN Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 537 GLN Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 640 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 chunk 131 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 HIS B 550 HIS C 550 HIS D 550 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.132966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.101028 restraints weight = 24588.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.104875 restraints weight = 12246.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.107430 restraints weight = 8214.723| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14876 Z= 0.177 Angle : 0.540 8.270 20260 Z= 0.287 Chirality : 0.041 0.191 2368 Planarity : 0.004 0.047 2484 Dihedral : 3.862 22.869 2220 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.58 % Favored : 97.19 % Rotamer: Outliers : 1.97 % Allowed : 18.89 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: 0.76 (0.19), residues: 1780 helix: 1.34 (0.16), residues: 1008 sheet: -0.08 (0.38), residues: 176 loop : -0.68 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 570 HIS 0.001 0.000 HIS D 550 PHE 0.024 0.001 PHE D 670 TYR 0.024 0.001 TYR C 616 ARG 0.002 0.000 ARG B 464 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2779.46 seconds wall clock time: 51 minutes 7.46 seconds (3067.46 seconds total)