Starting phenix.real_space_refine on Fri Feb 16 21:00:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9o_10419/02_2024/6t9o_10419_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9o_10419/02_2024/6t9o_10419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9o_10419/02_2024/6t9o_10419.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9o_10419/02_2024/6t9o_10419.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9o_10419/02_2024/6t9o_10419_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9o_10419/02_2024/6t9o_10419_updated.pdb" } resolution = 3.39 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 76 5.16 5 C 10924 2.51 5 N 2472 2.21 5 O 3008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16481 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3903 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3903 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3903 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3903 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 190 Unusual residues: {' CA': 1, 'CLR': 1, 'NAG': 2, 'UMQ': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 17 Chain: "B" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 189 Unusual residues: {'CLR': 1, 'NAG': 2, 'UMQ': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 17 Chain: "C" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 189 Unusual residues: {'CLR': 1, 'NAG': 2, 'UMQ': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 17 Chain: "D" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 189 Unusual residues: {'CLR': 1, 'NAG': 2, 'UMQ': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 17 Time building chain proxies: 9.10, per 1000 atoms: 0.55 Number of scatterers: 16481 At special positions: 0 Unit cell: (115.056, 115.056, 111.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 76 16.00 O 3008 8.00 N 2472 7.00 C 10924 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=2.02 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 344 " distance=2.02 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 801 " - " ASN A 328 " " NAG A 802 " - " ASN A 362 " " NAG B 801 " - " ASN B 328 " " NAG B 802 " - " ASN B 362 " " NAG C 801 " - " ASN C 328 " " NAG C 802 " - " ASN C 362 " " NAG D 801 " - " ASN D 328 " " NAG D 802 " - " ASN D 362 " " NAG E 1 " - " ASN A 375 " " NAG F 1 " - " ASN B 375 " " NAG G 1 " - " ASN C 375 " " NAG H 1 " - " ASN D 375 " Time building additional restraints: 6.61 Conformation dependent library (CDL) restraints added in 2.9 seconds 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 8 sheets defined 54.7% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 216 through 240 removed outlier: 3.728A pdb=" N TYR A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 257 Processing helix chain 'A' and resid 276 through 284 Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 371 through 374 No H-bonds generated for 'chain 'A' and resid 371 through 374' Processing helix chain 'A' and resid 399 through 411 Processing helix chain 'A' and resid 468 through 497 removed outlier: 3.755A pdb=" N ILE A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 527 Processing helix chain 'A' and resid 533 through 540 removed outlier: 3.981A pdb=" N GLU A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 575 removed outlier: 3.623A pdb=" N LEU A 573 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N PHE A 574 " --> pdb=" O TRP A 570 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LYS A 575 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 592 Processing helix chain 'A' and resid 594 through 619 Processing helix chain 'A' and resid 624 through 626 No H-bonds generated for 'chain 'A' and resid 624 through 626' Processing helix chain 'A' and resid 629 through 641 Processing helix chain 'A' and resid 646 through 652 Processing helix chain 'A' and resid 656 through 666 Processing helix chain 'A' and resid 673 through 700 removed outlier: 4.015A pdb=" N LEU A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 240 removed outlier: 3.727A pdb=" N TYR B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 257 Processing helix chain 'B' and resid 276 through 284 Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 309 through 311 No H-bonds generated for 'chain 'B' and resid 309 through 311' Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 364 through 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 371 through 374 No H-bonds generated for 'chain 'B' and resid 371 through 374' Processing helix chain 'B' and resid 399 through 411 Processing helix chain 'B' and resid 468 through 497 removed outlier: 3.755A pdb=" N ILE B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 527 Processing helix chain 'B' and resid 533 through 540 removed outlier: 3.981A pdb=" N GLU B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 575 removed outlier: 3.624A pdb=" N LEU B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N PHE B 574 " --> pdb=" O TRP B 570 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LYS B 575 " --> pdb=" O ILE B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 592 Processing helix chain 'B' and resid 594 through 619 Processing helix chain 'B' and resid 624 through 626 No H-bonds generated for 'chain 'B' and resid 624 through 626' Processing helix chain 'B' and resid 629 through 641 Processing helix chain 'B' and resid 646 through 652 Processing helix chain 'B' and resid 656 through 666 Processing helix chain 'B' and resid 673 through 700 removed outlier: 4.015A pdb=" N LEU B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 240 removed outlier: 3.727A pdb=" N TYR C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 257 Processing helix chain 'C' and resid 276 through 284 Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 309 through 311 No H-bonds generated for 'chain 'C' and resid 309 through 311' Processing helix chain 'C' and resid 335 through 337 No H-bonds generated for 'chain 'C' and resid 335 through 337' Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 371 through 374 No H-bonds generated for 'chain 'C' and resid 371 through 374' Processing helix chain 'C' and resid 399 through 411 Processing helix chain 'C' and resid 468 through 497 removed outlier: 3.755A pdb=" N ILE C 497 " --> pdb=" O LEU C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 527 Processing helix chain 'C' and resid 533 through 540 removed outlier: 3.982A pdb=" N GLU C 540 " --> pdb=" O LEU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 575 removed outlier: 3.623A pdb=" N LEU C 573 " --> pdb=" O VAL C 569 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N PHE C 574 " --> pdb=" O TRP C 570 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LYS C 575 " --> pdb=" O ILE C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 592 Processing helix chain 'C' and resid 594 through 619 Processing helix chain 'C' and resid 624 through 626 No H-bonds generated for 'chain 'C' and resid 624 through 626' Processing helix chain 'C' and resid 629 through 641 Processing helix chain 'C' and resid 646 through 652 Processing helix chain 'C' and resid 656 through 666 Processing helix chain 'C' and resid 673 through 700 removed outlier: 4.014A pdb=" N LEU C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 240 removed outlier: 3.729A pdb=" N TYR D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 257 Processing helix chain 'D' and resid 276 through 284 Processing helix chain 'D' and resid 286 through 291 Processing helix chain 'D' and resid 309 through 311 No H-bonds generated for 'chain 'D' and resid 309 through 311' Processing helix chain 'D' and resid 335 through 337 No H-bonds generated for 'chain 'D' and resid 335 through 337' Processing helix chain 'D' and resid 364 through 366 No H-bonds generated for 'chain 'D' and resid 364 through 366' Processing helix chain 'D' and resid 371 through 374 No H-bonds generated for 'chain 'D' and resid 371 through 374' Processing helix chain 'D' and resid 399 through 411 Processing helix chain 'D' and resid 468 through 497 removed outlier: 3.754A pdb=" N ILE D 497 " --> pdb=" O LEU D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 527 Processing helix chain 'D' and resid 533 through 540 removed outlier: 3.981A pdb=" N GLU D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 575 removed outlier: 3.624A pdb=" N LEU D 573 " --> pdb=" O VAL D 569 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N PHE D 574 " --> pdb=" O TRP D 570 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LYS D 575 " --> pdb=" O ILE D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 592 Processing helix chain 'D' and resid 594 through 619 Processing helix chain 'D' and resid 624 through 626 No H-bonds generated for 'chain 'D' and resid 624 through 626' Processing helix chain 'D' and resid 629 through 641 Processing helix chain 'D' and resid 646 through 652 Processing helix chain 'D' and resid 656 through 666 Processing helix chain 'D' and resid 673 through 700 removed outlier: 4.015A pdb=" N LEU D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 313 through 315 Processing sheet with id= B, first strand: chain 'A' and resid 320 through 325 Processing sheet with id= C, first strand: chain 'B' and resid 313 through 315 Processing sheet with id= D, first strand: chain 'B' and resid 320 through 325 Processing sheet with id= E, first strand: chain 'C' and resid 313 through 315 Processing sheet with id= F, first strand: chain 'C' and resid 320 through 325 Processing sheet with id= G, first strand: chain 'D' and resid 313 through 315 Processing sheet with id= H, first strand: chain 'D' and resid 320 through 325 812 hydrogen bonds defined for protein. 2400 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: 4.67 Time building geometry restraints manager: 6.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4690 1.34 - 1.45: 3558 1.45 - 1.57: 8548 1.57 - 1.69: 0 1.69 - 1.81: 116 Bond restraints: 16912 Sorted by residual: bond pdb=" C2' UMQ A 809 " pdb=" C3' UMQ A 809 " ideal model delta sigma weight residual 1.521 1.564 -0.043 2.00e-02 2.50e+03 4.61e+00 bond pdb=" C2' UMQ C 809 " pdb=" C3' UMQ C 809 " ideal model delta sigma weight residual 1.521 1.564 -0.043 2.00e-02 2.50e+03 4.61e+00 bond pdb=" C2' UMQ D 809 " pdb=" C3' UMQ D 809 " ideal model delta sigma weight residual 1.521 1.563 -0.042 2.00e-02 2.50e+03 4.51e+00 bond pdb=" C2' UMQ B 809 " pdb=" C3' UMQ B 809 " ideal model delta sigma weight residual 1.521 1.563 -0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" C5 UMQ B 806 " pdb=" O5 UMQ B 806 " ideal model delta sigma weight residual 1.421 1.379 0.042 2.00e-02 2.50e+03 4.44e+00 ... (remaining 16907 not shown) Histogram of bond angle deviations from ideal: 97.18 - 104.58: 164 104.58 - 111.98: 8299 111.98 - 119.38: 5760 119.38 - 126.78: 8565 126.78 - 134.18: 168 Bond angle restraints: 22956 Sorted by residual: angle pdb=" C1 UMQ C 806 " pdb=" O1 UMQ C 806 " pdb=" C4' UMQ C 806 " ideal model delta sigma weight residual 119.70 110.26 9.44 3.00e+00 1.11e-01 9.90e+00 angle pdb=" C1 UMQ B 806 " pdb=" O1 UMQ B 806 " pdb=" C4' UMQ B 806 " ideal model delta sigma weight residual 119.70 110.31 9.39 3.00e+00 1.11e-01 9.80e+00 angle pdb=" C1 UMQ D 806 " pdb=" O1 UMQ D 806 " pdb=" C4' UMQ D 806 " ideal model delta sigma weight residual 119.70 110.32 9.38 3.00e+00 1.11e-01 9.79e+00 angle pdb=" C1 UMQ A 806 " pdb=" O1 UMQ A 806 " pdb=" C4' UMQ A 806 " ideal model delta sigma weight residual 119.70 110.35 9.35 3.00e+00 1.11e-01 9.72e+00 angle pdb=" CA LEU A 374 " pdb=" CB LEU A 374 " pdb=" CG LEU A 374 " ideal model delta sigma weight residual 116.30 126.82 -10.52 3.50e+00 8.16e-02 9.03e+00 ... (remaining 22951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.23: 9656 13.23 - 26.46: 732 26.46 - 39.69: 216 39.69 - 52.92: 80 52.92 - 66.15: 28 Dihedral angle restraints: 10712 sinusoidal: 5004 harmonic: 5708 Sorted by residual: dihedral pdb=" CB CYS A 331 " pdb=" SG CYS A 331 " pdb=" SG CYS A 344 " pdb=" CB CYS A 344 " ideal model delta sinusoidal sigma weight residual -86.00 -151.55 65.55 1 1.00e+01 1.00e-02 5.63e+01 dihedral pdb=" CB CYS B 331 " pdb=" SG CYS B 331 " pdb=" SG CYS B 344 " pdb=" CB CYS B 344 " ideal model delta sinusoidal sigma weight residual -86.00 -151.54 65.54 1 1.00e+01 1.00e-02 5.62e+01 dihedral pdb=" CB CYS C 331 " pdb=" SG CYS C 331 " pdb=" SG CYS C 344 " pdb=" CB CYS C 344 " ideal model delta sinusoidal sigma weight residual -86.00 -151.52 65.52 1 1.00e+01 1.00e-02 5.62e+01 ... (remaining 10709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2138 0.071 - 0.142: 443 0.142 - 0.213: 111 0.213 - 0.284: 16 0.284 - 0.355: 4 Chirality restraints: 2712 Sorted by residual: chirality pdb=" C1 NAG C 802 " pdb=" ND2 ASN C 362 " pdb=" C2 NAG C 802 " pdb=" O5 NAG C 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C1 NAG B 802 " pdb=" ND2 ASN B 362 " pdb=" C2 NAG B 802 " pdb=" O5 NAG B 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" C1 NAG D 802 " pdb=" ND2 ASN D 362 " pdb=" C2 NAG D 802 " pdb=" O5 NAG D 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 2709 not shown) Planarity restraints: 2740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 634 " -0.034 2.00e-02 2.50e+03 2.18e-02 8.33e+00 pdb=" CG PHE D 634 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE D 634 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 634 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE D 634 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE D 634 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE D 634 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 634 " 0.034 2.00e-02 2.50e+03 2.18e-02 8.32e+00 pdb=" CG PHE C 634 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 634 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 634 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE C 634 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 634 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 634 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 634 " 0.033 2.00e-02 2.50e+03 2.17e-02 8.23e+00 pdb=" CG PHE B 634 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B 634 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 634 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE B 634 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 634 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 634 " 0.025 2.00e-02 2.50e+03 ... (remaining 2737 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1739 2.74 - 3.28: 15426 3.28 - 3.82: 27123 3.82 - 4.36: 32959 4.36 - 4.90: 57346 Nonbonded interactions: 134593 Sorted by model distance: nonbonded pdb=" OH TYR C 227 " pdb=" O VAL C 569 " model vdw 2.200 2.440 nonbonded pdb=" OH TYR D 227 " pdb=" O VAL D 569 " model vdw 2.200 2.440 nonbonded pdb=" OH TYR B 227 " pdb=" O VAL B 569 " model vdw 2.200 2.440 nonbonded pdb=" OH TYR A 227 " pdb=" O VAL A 569 " model vdw 2.201 2.440 nonbonded pdb=" OE1 GLU D 491 " pdb=" OH TYR D 502 " model vdw 2.271 2.440 ... (remaining 134588 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' and (resid 214 through 702 or resid 801 through 810)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.530 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: 3.140 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 44.690 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.100 Set refine NCS operators: 0.010 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.064 16912 Z= 0.602 Angle : 1.007 10.515 22956 Z= 0.509 Chirality : 0.066 0.355 2712 Planarity : 0.006 0.054 2728 Dihedral : 11.321 66.146 7004 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.71 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.77 (0.15), residues: 1908 helix: -2.29 (0.11), residues: 1108 sheet: -2.34 (0.35), residues: 192 loop : -2.53 (0.20), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP A 507 HIS 0.005 0.002 HIS D 379 PHE 0.034 0.003 PHE C 634 TYR 0.039 0.003 TYR B 249 ARG 0.008 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 429 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 SER cc_start: 0.8764 (p) cc_final: 0.8254 (t) REVERT: A 367 ILE cc_start: 0.8961 (mt) cc_final: 0.8509 (pt) REVERT: A 398 THR cc_start: 0.8575 (p) cc_final: 0.8196 (t) REVERT: A 489 VAL cc_start: 0.8598 (t) cc_final: 0.8322 (p) REVERT: A 570 TRP cc_start: 0.8517 (m100) cc_final: 0.8089 (m100) REVERT: A 625 ASP cc_start: 0.7488 (m-30) cc_final: 0.7278 (m-30) REVERT: A 648 GLU cc_start: 0.8390 (pt0) cc_final: 0.8156 (pt0) REVERT: A 650 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7407 (tt0) REVERT: B 275 SER cc_start: 0.8804 (p) cc_final: 0.8269 (t) REVERT: B 367 ILE cc_start: 0.9004 (mt) cc_final: 0.8673 (pt) REVERT: B 398 THR cc_start: 0.8485 (p) cc_final: 0.7832 (p) REVERT: B 444 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7772 (mt-10) REVERT: B 570 TRP cc_start: 0.8436 (m100) cc_final: 0.7993 (m100) REVERT: B 650 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7645 (tt0) REVERT: C 223 GLU cc_start: 0.6938 (pt0) cc_final: 0.6696 (tp30) REVERT: C 367 ILE cc_start: 0.8970 (mt) cc_final: 0.8609 (pt) REVERT: C 398 THR cc_start: 0.8464 (p) cc_final: 0.8048 (p) REVERT: C 489 VAL cc_start: 0.8532 (t) cc_final: 0.8260 (p) REVERT: C 531 ASN cc_start: 0.7892 (t0) cc_final: 0.7678 (t0) REVERT: C 570 TRP cc_start: 0.8468 (m100) cc_final: 0.8052 (m100) REVERT: D 223 GLU cc_start: 0.6875 (pt0) cc_final: 0.6646 (tp30) REVERT: D 271 LYS cc_start: 0.8903 (mttt) cc_final: 0.8623 (mttm) REVERT: D 275 SER cc_start: 0.8755 (p) cc_final: 0.8251 (t) REVERT: D 398 THR cc_start: 0.8598 (p) cc_final: 0.8259 (t) REVERT: D 489 VAL cc_start: 0.8617 (t) cc_final: 0.8374 (p) REVERT: D 570 TRP cc_start: 0.8501 (m100) cc_final: 0.8138 (m100) REVERT: D 587 SER cc_start: 0.8468 (m) cc_final: 0.8260 (t) REVERT: D 650 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7175 (tm-30) outliers start: 0 outliers final: 0 residues processed: 429 average time/residue: 0.2869 time to fit residues: 183.0367 Evaluate side-chains 232 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 174 optimal weight: 8.9990 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 323 GLN ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 HIS A 636 GLN B 255 GLN B 323 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 HIS B 636 GLN C 255 GLN C 323 GLN ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS C 636 GLN D 323 GLN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 550 HIS D 636 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16912 Z= 0.238 Angle : 0.512 8.860 22956 Z= 0.274 Chirality : 0.041 0.290 2712 Planarity : 0.004 0.047 2728 Dihedral : 9.891 59.874 3564 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.20 % Favored : 96.59 % Rotamer: Outliers : 2.34 % Allowed : 6.18 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.72 (0.17), residues: 1908 helix: -0.38 (0.14), residues: 1092 sheet: -2.05 (0.35), residues: 200 loop : -2.01 (0.21), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 554 HIS 0.002 0.001 HIS C 379 PHE 0.022 0.002 PHE C 600 TYR 0.020 0.001 TYR D 486 ARG 0.004 0.001 ARG B 592 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 263 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 LYS cc_start: 0.8801 (mttt) cc_final: 0.8592 (mttm) REVERT: A 275 SER cc_start: 0.8780 (p) cc_final: 0.8241 (t) REVERT: A 333 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8296 (tp) REVERT: A 488 VAL cc_start: 0.8900 (t) cc_final: 0.8595 (m) REVERT: A 570 TRP cc_start: 0.8395 (m100) cc_final: 0.7902 (m100) REVERT: A 650 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7566 (tt0) REVERT: B 367 ILE cc_start: 0.8982 (mt) cc_final: 0.8619 (pt) REVERT: B 570 TRP cc_start: 0.8358 (m100) cc_final: 0.8006 (m100) REVERT: B 650 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7634 (tt0) REVERT: C 223 GLU cc_start: 0.6943 (pt0) cc_final: 0.6682 (tp30) REVERT: C 486 TYR cc_start: 0.8443 (t80) cc_final: 0.8153 (t80) REVERT: C 531 ASN cc_start: 0.7856 (t0) cc_final: 0.7549 (t0) REVERT: C 570 TRP cc_start: 0.8402 (m100) cc_final: 0.8054 (m100) REVERT: D 223 GLU cc_start: 0.6817 (pt0) cc_final: 0.6616 (tp30) REVERT: D 253 MET cc_start: 0.8305 (mmt) cc_final: 0.7948 (mmt) REVERT: D 271 LYS cc_start: 0.8765 (mttt) cc_final: 0.8535 (mttm) REVERT: D 275 SER cc_start: 0.8777 (p) cc_final: 0.8225 (t) REVERT: D 528 ARG cc_start: 0.8219 (mmt180) cc_final: 0.7608 (mmt-90) REVERT: D 570 TRP cc_start: 0.8404 (m100) cc_final: 0.7940 (m100) outliers start: 39 outliers final: 29 residues processed: 293 average time/residue: 0.2576 time to fit residues: 119.1708 Evaluate side-chains 254 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 224 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 492 ILE Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 584 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 30.0000 chunk 54 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 118 optimal weight: 0.0170 chunk 48 optimal weight: 30.0000 chunk 174 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 140 optimal weight: 0.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 525 ASN C 636 GLN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 525 ASN D 636 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16912 Z= 0.134 Angle : 0.426 8.535 22956 Z= 0.229 Chirality : 0.038 0.264 2712 Planarity : 0.003 0.039 2728 Dihedral : 8.361 59.890 3564 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.20 % Favored : 96.59 % Rotamer: Outliers : 2.10 % Allowed : 8.63 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.18), residues: 1908 helix: 0.63 (0.15), residues: 1084 sheet: -1.76 (0.35), residues: 200 loop : -1.64 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 507 HIS 0.002 0.001 HIS D 379 PHE 0.021 0.001 PHE A 600 TYR 0.018 0.001 TYR D 486 ARG 0.005 0.000 ARG D 592 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 248 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ASN cc_start: 0.6902 (m110) cc_final: 0.6461 (p0) REVERT: A 275 SER cc_start: 0.8730 (p) cc_final: 0.8211 (t) REVERT: A 488 VAL cc_start: 0.8929 (t) cc_final: 0.8609 (m) REVERT: A 570 TRP cc_start: 0.8353 (m100) cc_final: 0.7930 (m100) REVERT: A 650 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7527 (tt0) REVERT: B 245 ASN cc_start: 0.7189 (m-40) cc_final: 0.6673 (p0) REVERT: B 259 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: B 367 ILE cc_start: 0.8990 (mt) cc_final: 0.8787 (tp) REVERT: B 570 TRP cc_start: 0.8369 (m100) cc_final: 0.8090 (m100) REVERT: C 245 ASN cc_start: 0.7162 (m-40) cc_final: 0.6556 (p0) REVERT: C 531 ASN cc_start: 0.7746 (t0) cc_final: 0.7482 (t0) REVERT: C 570 TRP cc_start: 0.8380 (m100) cc_final: 0.8049 (m100) REVERT: C 673 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8525 (mp) REVERT: D 245 ASN cc_start: 0.7164 (m-40) cc_final: 0.6661 (p0) REVERT: D 271 LYS cc_start: 0.8735 (mttt) cc_final: 0.8484 (mttm) REVERT: D 275 SER cc_start: 0.8766 (p) cc_final: 0.8254 (t) REVERT: D 488 VAL cc_start: 0.8863 (t) cc_final: 0.8597 (m) REVERT: D 570 TRP cc_start: 0.8351 (m100) cc_final: 0.7955 (m100) outliers start: 35 outliers final: 25 residues processed: 269 average time/residue: 0.2437 time to fit residues: 105.2528 Evaluate side-chains 238 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 211 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 CYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 117 optimal weight: 0.7980 chunk 175 optimal weight: 8.9990 chunk 185 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16912 Z= 0.167 Angle : 0.425 9.165 22956 Z= 0.225 Chirality : 0.038 0.253 2712 Planarity : 0.003 0.039 2728 Dihedral : 7.721 59.449 3564 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.52 % Favored : 97.27 % Rotamer: Outliers : 2.10 % Allowed : 9.59 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.18), residues: 1908 helix: 1.07 (0.15), residues: 1084 sheet: -1.61 (0.35), residues: 200 loop : -1.50 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 554 HIS 0.002 0.001 HIS D 498 PHE 0.022 0.001 PHE B 600 TYR 0.022 0.001 TYR C 486 ARG 0.003 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 212 time to evaluate : 1.778 Fit side-chains revert: symmetry clash REVERT: A 245 ASN cc_start: 0.7123 (m-40) cc_final: 0.6535 (p0) REVERT: A 275 SER cc_start: 0.8781 (p) cc_final: 0.8240 (t) REVERT: A 570 TRP cc_start: 0.8384 (m100) cc_final: 0.7992 (m100) REVERT: A 650 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7606 (tt0) REVERT: B 245 ASN cc_start: 0.7114 (m-40) cc_final: 0.6716 (p0) REVERT: B 259 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8047 (m-30) REVERT: B 312 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7826 (mm-30) REVERT: B 367 ILE cc_start: 0.9013 (mt) cc_final: 0.8784 (tp) REVERT: B 570 TRP cc_start: 0.8385 (m100) cc_final: 0.8142 (m100) REVERT: C 245 ASN cc_start: 0.7204 (m-40) cc_final: 0.6659 (p0) REVERT: C 570 TRP cc_start: 0.8387 (m100) cc_final: 0.8091 (m100) REVERT: C 673 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8536 (mp) REVERT: D 245 ASN cc_start: 0.7267 (m-40) cc_final: 0.6600 (p0) REVERT: D 275 SER cc_start: 0.8794 (p) cc_final: 0.8225 (t) REVERT: D 570 TRP cc_start: 0.8356 (m100) cc_final: 0.7960 (m100) REVERT: D 596 ASP cc_start: 0.7367 (m-30) cc_final: 0.7141 (m-30) REVERT: D 673 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8502 (mp) outliers start: 35 outliers final: 25 residues processed: 237 average time/residue: 0.2287 time to fit residues: 89.1477 Evaluate side-chains 229 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 201 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 94 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 GLN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 653 ASN C 674 ASN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 GLN D 653 ASN ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 16912 Z= 0.462 Angle : 0.600 11.055 22956 Z= 0.305 Chirality : 0.044 0.240 2712 Planarity : 0.004 0.043 2728 Dihedral : 8.358 59.916 3564 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.56 % Favored : 96.23 % Rotamer: Outliers : 3.18 % Allowed : 9.71 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.40 (0.18), residues: 1908 helix: 0.76 (0.15), residues: 1096 sheet: -1.71 (0.35), residues: 200 loop : -1.54 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 414 HIS 0.006 0.001 HIS D 498 PHE 0.023 0.002 PHE A 230 TYR 0.021 0.002 TYR B 249 ARG 0.003 0.001 ARG D 654 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 210 time to evaluate : 1.946 Fit side-chains REVERT: A 275 SER cc_start: 0.8927 (p) cc_final: 0.8294 (t) REVERT: A 488 VAL cc_start: 0.8936 (t) cc_final: 0.8686 (m) REVERT: A 570 TRP cc_start: 0.8481 (m100) cc_final: 0.8062 (m100) REVERT: A 650 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7826 (tt0) REVERT: B 245 ASN cc_start: 0.7160 (m-40) cc_final: 0.6603 (p0) REVERT: B 259 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8082 (m-30) REVERT: B 570 TRP cc_start: 0.8484 (m100) cc_final: 0.8155 (m100) REVERT: B 650 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7810 (tt0) REVERT: C 312 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7855 (mm-30) REVERT: C 525 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8603 (t160) REVERT: C 570 TRP cc_start: 0.8478 (m100) cc_final: 0.8099 (m100) REVERT: C 673 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8759 (mp) REVERT: D 275 SER cc_start: 0.8929 (p) cc_final: 0.8290 (t) REVERT: D 570 TRP cc_start: 0.8443 (m100) cc_final: 0.8029 (m100) REVERT: D 596 ASP cc_start: 0.7637 (m-30) cc_final: 0.7387 (m-30) REVERT: D 673 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8622 (mp) outliers start: 53 outliers final: 45 residues processed: 254 average time/residue: 0.2335 time to fit residues: 95.8531 Evaluate side-chains 246 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 197 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 CYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 492 ILE Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 185 optimal weight: 0.7980 chunk 154 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 GLN C 653 ASN C 674 ASN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 GLN D 653 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16912 Z= 0.194 Angle : 0.454 8.238 22956 Z= 0.236 Chirality : 0.039 0.244 2712 Planarity : 0.003 0.039 2728 Dihedral : 7.825 59.992 3564 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.88 % Favored : 96.91 % Rotamer: Outliers : 2.46 % Allowed : 10.79 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.07 (0.19), residues: 1908 helix: 1.22 (0.15), residues: 1084 sheet: -1.60 (0.35), residues: 200 loop : -1.43 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 554 HIS 0.003 0.001 HIS D 498 PHE 0.023 0.001 PHE D 600 TYR 0.019 0.001 TYR A 486 ARG 0.002 0.000 ARG D 592 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 214 time to evaluate : 1.786 Fit side-chains REVERT: A 245 ASN cc_start: 0.7180 (m-40) cc_final: 0.6495 (p0) REVERT: A 275 SER cc_start: 0.8891 (p) cc_final: 0.8264 (t) REVERT: A 488 VAL cc_start: 0.8957 (t) cc_final: 0.8692 (m) REVERT: A 570 TRP cc_start: 0.8418 (m100) cc_final: 0.7994 (m100) REVERT: A 650 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7970 (tm-30) REVERT: B 245 ASN cc_start: 0.7158 (m-40) cc_final: 0.6704 (p0) REVERT: B 259 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8060 (m-30) REVERT: B 367 ILE cc_start: 0.9102 (mt) cc_final: 0.8761 (pt) REVERT: B 570 TRP cc_start: 0.8427 (m100) cc_final: 0.8100 (m100) REVERT: C 245 ASN cc_start: 0.7174 (m-40) cc_final: 0.6668 (p0) REVERT: C 312 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7852 (mm-30) REVERT: C 570 TRP cc_start: 0.8424 (m100) cc_final: 0.8031 (m100) REVERT: C 673 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8721 (mp) REVERT: D 275 SER cc_start: 0.8861 (p) cc_final: 0.8223 (t) REVERT: D 570 TRP cc_start: 0.8416 (m100) cc_final: 0.7962 (m100) REVERT: D 673 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8606 (mp) outliers start: 41 outliers final: 32 residues processed: 248 average time/residue: 0.2363 time to fit residues: 94.7421 Evaluate side-chains 235 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 200 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 105 optimal weight: 0.2980 chunk 135 optimal weight: 0.4980 chunk 156 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 185 optimal weight: 0.5980 chunk 115 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 525 ASN C 636 GLN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16912 Z= 0.144 Angle : 0.415 9.877 22956 Z= 0.219 Chirality : 0.038 0.236 2712 Planarity : 0.003 0.038 2728 Dihedral : 7.152 55.259 3564 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.67 % Favored : 97.12 % Rotamer: Outliers : 2.10 % Allowed : 11.99 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.19), residues: 1908 helix: 1.46 (0.15), residues: 1088 sheet: -1.34 (0.36), residues: 200 loop : -1.29 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 414 HIS 0.002 0.001 HIS C 501 PHE 0.019 0.001 PHE A 600 TYR 0.019 0.001 TYR A 486 ARG 0.002 0.000 ARG D 592 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 214 time to evaluate : 1.985 Fit side-chains revert: symmetry clash REVERT: A 245 ASN cc_start: 0.7100 (m-40) cc_final: 0.6606 (p0) REVERT: A 275 SER cc_start: 0.8841 (p) cc_final: 0.8242 (t) REVERT: A 312 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7717 (mm-30) REVERT: A 488 VAL cc_start: 0.8943 (t) cc_final: 0.8665 (m) REVERT: A 570 TRP cc_start: 0.8396 (m100) cc_final: 0.8113 (m100) REVERT: A 673 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8525 (mp) REVERT: B 224 LEU cc_start: 0.7838 (tt) cc_final: 0.7635 (tt) REVERT: B 245 ASN cc_start: 0.7098 (m-40) cc_final: 0.6747 (p0) REVERT: B 259 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.8018 (m-30) REVERT: B 367 ILE cc_start: 0.9121 (mt) cc_final: 0.8795 (pt) REVERT: B 570 TRP cc_start: 0.8421 (m100) cc_final: 0.8131 (m100) REVERT: C 245 ASN cc_start: 0.7127 (m-40) cc_final: 0.6780 (p0) REVERT: C 312 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7830 (mm-30) REVERT: C 570 TRP cc_start: 0.8394 (m100) cc_final: 0.8150 (m100) REVERT: C 673 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8700 (mp) REVERT: C 675 MET cc_start: 0.7605 (mmt) cc_final: 0.7241 (mmt) REVERT: D 245 ASN cc_start: 0.7008 (m-40) cc_final: 0.6622 (p0) REVERT: D 275 SER cc_start: 0.8849 (p) cc_final: 0.8245 (t) REVERT: D 312 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7737 (mm-30) REVERT: D 488 VAL cc_start: 0.8971 (t) cc_final: 0.8740 (m) REVERT: D 570 TRP cc_start: 0.8391 (m100) cc_final: 0.8095 (m100) REVERT: D 673 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8621 (mp) outliers start: 35 outliers final: 28 residues processed: 241 average time/residue: 0.2381 time to fit residues: 92.2521 Evaluate side-chains 228 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 196 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 168 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 GLN ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 674 ASN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16912 Z= 0.342 Angle : 0.528 10.779 22956 Z= 0.269 Chirality : 0.041 0.231 2712 Planarity : 0.003 0.039 2728 Dihedral : 7.592 56.568 3564 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.94 % Favored : 96.86 % Rotamer: Outliers : 2.88 % Allowed : 11.69 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.19), residues: 1908 helix: 1.28 (0.15), residues: 1092 sheet: -1.47 (0.36), residues: 200 loop : -1.41 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 554 HIS 0.005 0.001 HIS D 498 PHE 0.024 0.002 PHE D 423 TYR 0.016 0.002 TYR A 486 ARG 0.006 0.000 ARG C 397 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 203 time to evaluate : 1.759 Fit side-chains revert: symmetry clash REVERT: A 245 ASN cc_start: 0.7224 (m-40) cc_final: 0.6554 (p0) REVERT: A 275 SER cc_start: 0.8919 (p) cc_final: 0.8281 (t) REVERT: A 312 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7818 (mm-30) REVERT: A 488 VAL cc_start: 0.8942 (t) cc_final: 0.8663 (m) REVERT: A 570 TRP cc_start: 0.8463 (m100) cc_final: 0.8069 (m100) REVERT: A 650 GLU cc_start: 0.8311 (tm-30) cc_final: 0.8012 (tm-30) REVERT: A 673 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8633 (mp) REVERT: B 245 ASN cc_start: 0.7108 (m-40) cc_final: 0.6647 (p0) REVERT: B 259 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8076 (m-30) REVERT: B 570 TRP cc_start: 0.8480 (m100) cc_final: 0.8145 (m100) REVERT: B 650 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8036 (tm-30) REVERT: C 245 ASN cc_start: 0.7077 (m-40) cc_final: 0.6660 (p0) REVERT: C 275 SER cc_start: 0.8934 (p) cc_final: 0.8319 (t) REVERT: C 570 TRP cc_start: 0.8464 (m100) cc_final: 0.8122 (m100) REVERT: C 673 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8761 (mp) REVERT: D 245 ASN cc_start: 0.7100 (m-40) cc_final: 0.6592 (p0) REVERT: D 253 MET cc_start: 0.8243 (mmt) cc_final: 0.7910 (mmt) REVERT: D 275 SER cc_start: 0.8941 (p) cc_final: 0.8297 (t) REVERT: D 312 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7889 (mm-30) REVERT: D 488 VAL cc_start: 0.8892 (t) cc_final: 0.8612 (m) REVERT: D 570 TRP cc_start: 0.8446 (m100) cc_final: 0.8032 (m100) REVERT: D 673 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8658 (mp) outliers start: 48 outliers final: 36 residues processed: 243 average time/residue: 0.2428 time to fit residues: 94.4667 Evaluate side-chains 236 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 196 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 172 optimal weight: 9.9990 chunk 103 optimal weight: 0.5980 chunk 75 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 163 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 GLN C 636 GLN C 674 ASN D 430 ASN D 636 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16912 Z= 0.130 Angle : 0.426 10.467 22956 Z= 0.222 Chirality : 0.037 0.231 2712 Planarity : 0.003 0.037 2728 Dihedral : 6.943 54.450 3564 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.73 % Favored : 97.06 % Rotamer: Outliers : 2.04 % Allowed : 12.71 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.64 (0.19), residues: 1908 helix: 1.66 (0.15), residues: 1088 sheet: -1.21 (0.36), residues: 200 loop : -1.22 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 414 HIS 0.001 0.000 HIS C 379 PHE 0.019 0.001 PHE D 423 TYR 0.017 0.001 TYR A 486 ARG 0.005 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 196 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ASN cc_start: 0.7089 (m-40) cc_final: 0.6693 (p0) REVERT: A 275 SER cc_start: 0.8874 (p) cc_final: 0.8270 (t) REVERT: A 488 VAL cc_start: 0.8927 (t) cc_final: 0.8639 (m) REVERT: A 570 TRP cc_start: 0.8397 (m100) cc_final: 0.8162 (m100) REVERT: A 673 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8592 (mp) REVERT: B 245 ASN cc_start: 0.7037 (m-40) cc_final: 0.6795 (p0) REVERT: B 259 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: B 275 SER cc_start: 0.8888 (p) cc_final: 0.8290 (t) REVERT: B 367 ILE cc_start: 0.9147 (mt) cc_final: 0.8905 (pt) REVERT: B 570 TRP cc_start: 0.8410 (m100) cc_final: 0.8112 (m100) REVERT: B 675 MET cc_start: 0.7560 (mmt) cc_final: 0.7154 (mmt) REVERT: C 245 ASN cc_start: 0.7036 (m-40) cc_final: 0.6783 (p0) REVERT: C 275 SER cc_start: 0.8879 (p) cc_final: 0.8294 (t) REVERT: C 570 TRP cc_start: 0.8398 (m100) cc_final: 0.8122 (m100) REVERT: C 673 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8720 (mp) REVERT: C 675 MET cc_start: 0.7647 (mmt) cc_final: 0.7216 (mmt) REVERT: D 245 ASN cc_start: 0.7097 (m-40) cc_final: 0.6794 (p0) REVERT: D 275 SER cc_start: 0.8884 (p) cc_final: 0.8258 (t) REVERT: D 488 VAL cc_start: 0.8919 (t) cc_final: 0.8635 (m) REVERT: D 570 TRP cc_start: 0.8376 (m100) cc_final: 0.8136 (m100) REVERT: D 673 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8582 (mp) outliers start: 34 outliers final: 27 residues processed: 224 average time/residue: 0.2356 time to fit residues: 87.6844 Evaluate side-chains 219 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 188 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.6980 chunk 111 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 191 optimal weight: 20.0000 chunk 176 optimal weight: 0.1980 chunk 152 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 ASN C 430 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16912 Z= 0.142 Angle : 0.430 10.196 22956 Z= 0.221 Chirality : 0.038 0.226 2712 Planarity : 0.003 0.038 2728 Dihedral : 6.706 56.611 3564 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.04 % Favored : 97.75 % Rotamer: Outliers : 1.92 % Allowed : 13.07 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.77 (0.19), residues: 1908 helix: 1.77 (0.15), residues: 1088 sheet: -1.11 (0.36), residues: 200 loop : -1.20 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 554 HIS 0.002 0.001 HIS D 498 PHE 0.020 0.001 PHE D 423 TYR 0.017 0.001 TYR A 486 ARG 0.004 0.000 ARG B 464 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 196 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ASN cc_start: 0.7057 (m-40) cc_final: 0.6680 (p0) REVERT: A 275 SER cc_start: 0.8892 (p) cc_final: 0.8285 (t) REVERT: A 488 VAL cc_start: 0.8892 (t) cc_final: 0.8604 (m) REVERT: A 570 TRP cc_start: 0.8412 (m100) cc_final: 0.8160 (m100) REVERT: A 673 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8615 (mp) REVERT: B 259 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: B 367 ILE cc_start: 0.9156 (mt) cc_final: 0.8916 (pt) REVERT: B 488 VAL cc_start: 0.8886 (t) cc_final: 0.8621 (m) REVERT: B 570 TRP cc_start: 0.8418 (m100) cc_final: 0.8188 (m100) REVERT: B 590 MET cc_start: 0.8665 (tpp) cc_final: 0.8409 (mmm) REVERT: B 675 MET cc_start: 0.7602 (mmt) cc_final: 0.7229 (mmt) REVERT: C 275 SER cc_start: 0.8874 (p) cc_final: 0.8288 (t) REVERT: C 570 TRP cc_start: 0.8424 (m100) cc_final: 0.8075 (m100) REVERT: C 673 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8730 (mp) REVERT: C 675 MET cc_start: 0.7420 (mmt) cc_final: 0.7139 (mmt) REVERT: D 245 ASN cc_start: 0.7043 (m-40) cc_final: 0.6774 (p0) REVERT: D 275 SER cc_start: 0.8885 (p) cc_final: 0.8270 (t) REVERT: D 488 VAL cc_start: 0.8901 (t) cc_final: 0.8614 (m) REVERT: D 570 TRP cc_start: 0.8405 (m100) cc_final: 0.8172 (m100) REVERT: D 673 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8606 (mp) outliers start: 32 outliers final: 27 residues processed: 221 average time/residue: 0.2338 time to fit residues: 84.5252 Evaluate side-chains 217 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 186 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 22 optimal weight: 0.0670 chunk 42 optimal weight: 10.0000 chunk 152 optimal weight: 0.5980 chunk 63 optimal weight: 8.9990 chunk 156 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 overall best weight: 1.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.135953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.108351 restraints weight = 20748.967| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.95 r_work: 0.2887 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16912 Z= 0.185 Angle : 0.447 10.301 22956 Z= 0.228 Chirality : 0.038 0.224 2712 Planarity : 0.003 0.039 2728 Dihedral : 6.681 58.139 3564 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.57 % Favored : 97.22 % Rotamer: Outliers : 1.86 % Allowed : 13.25 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.19), residues: 1908 helix: 1.80 (0.15), residues: 1088 sheet: -1.11 (0.37), residues: 200 loop : -1.19 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 554 HIS 0.002 0.001 HIS D 498 PHE 0.021 0.001 PHE D 423 TYR 0.017 0.001 TYR A 486 ARG 0.004 0.000 ARG B 464 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3309.46 seconds wall clock time: 61 minutes 19.50 seconds (3679.50 seconds total)