Starting phenix.real_space_refine on Sat Feb 17 00:05:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9n_10418/02_2024/6t9n_10418_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9n_10418/02_2024/6t9n_10418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9n_10418/02_2024/6t9n_10418.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9n_10418/02_2024/6t9n_10418.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9n_10418/02_2024/6t9n_10418_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9n_10418/02_2024/6t9n_10418_updated.pdb" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 80 5.16 5 C 11232 2.51 5 N 2504 2.21 5 O 3100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 16917 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3917 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 469} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3917 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 469} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3917 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 469} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3917 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 469} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 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: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 319 Unusual residues: {' CA': 1, 'CLR': 1, 'NAG': 2, 'UMQ': 9} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 22 Chain: "B" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 250 Unusual residues: {'CLR': 1, 'NAG': 2, 'UMQ': 7} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 22 Chain: "C" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 284 Unusual residues: {'CLR': 1, 'NAG': 2, 'UMQ': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 22 Chain: "D" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 284 Unusual residues: {'CLR': 1, 'NAG': 2, 'UMQ': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 22 Time building chain proxies: 9.00, per 1000 atoms: 0.53 Number of scatterers: 16917 At special positions: 0 Unit cell: (112.614, 112.614, 108.504, 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 80 16.00 O 3100 8.00 N 2504 7.00 C 11232 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=2.04 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=2.04 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " distance=2.04 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 344 " distance=2.04 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 802 " - " ASN A 328 " " NAG A 803 " - " ASN A 362 " " NAG B 802 " - " ASN B 328 " " NAG B 803 " - " ASN B 362 " " NAG C 802 " - " ASN C 328 " " NAG C 803 " - " ASN C 362 " " NAG D 802 " - " ASN D 328 " " NAG D 803 " - " 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: 7.29 Conformation dependent library (CDL) restraints added in 2.8 seconds 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 8 sheets defined 53.1% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'A' and resid 214 through 241 Processing helix chain 'A' and resid 247 through 257 removed outlier: 4.181A pdb=" N MET A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET A 253 " --> pdb=" O TYR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 283 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 399 through 411 Processing helix chain 'A' and resid 468 through 495 Processing helix chain 'A' and resid 507 through 527 Processing helix chain 'A' and resid 533 through 540 removed outlier: 3.717A pdb=" N GLU A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 575 removed outlier: 3.707A pdb=" N LEU A 573 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N PHE A 574 " --> pdb=" O TRP A 570 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LYS A 575 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 619 removed outlier: 5.009A pdb=" N LYS A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASP A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) 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 667 Processing helix chain 'A' and resid 673 through 697 removed outlier: 4.067A pdb=" N LEU A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 241 Processing helix chain 'B' and resid 247 through 257 removed outlier: 4.181A pdb=" N MET B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 283 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 399 through 411 Processing helix chain 'B' and resid 468 through 495 Processing helix chain 'B' and resid 507 through 527 Processing helix chain 'B' and resid 533 through 540 removed outlier: 3.716A pdb=" N GLU B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 575 removed outlier: 3.707A pdb=" N LEU B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N PHE B 574 " --> pdb=" O TRP B 570 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LYS B 575 " --> pdb=" O ILE B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 619 removed outlier: 5.010A pdb=" N LYS B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASP B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) 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 667 Processing helix chain 'B' and resid 673 through 697 removed outlier: 4.068A pdb=" N LEU B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 241 Processing helix chain 'C' and resid 247 through 257 removed outlier: 4.182A pdb=" N MET C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET C 253 " --> pdb=" O TYR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 283 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 399 through 411 Processing helix chain 'C' and resid 468 through 495 Processing helix chain 'C' and resid 507 through 527 Processing helix chain 'C' and resid 533 through 540 removed outlier: 3.717A pdb=" N GLU C 540 " --> pdb=" O LEU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 575 removed outlier: 3.707A pdb=" N LEU C 573 " --> pdb=" O VAL C 569 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N PHE C 574 " --> pdb=" O TRP C 570 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LYS C 575 " --> pdb=" O ILE C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 619 removed outlier: 5.009A pdb=" N LYS C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASP C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) 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 667 Processing helix chain 'C' and resid 673 through 697 removed outlier: 4.067A pdb=" N LEU C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 241 Processing helix chain 'D' and resid 247 through 257 removed outlier: 4.181A pdb=" N MET D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET D 253 " --> pdb=" O TYR D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 283 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 399 through 411 Processing helix chain 'D' and resid 468 through 495 Processing helix chain 'D' and resid 507 through 527 Processing helix chain 'D' and resid 533 through 540 removed outlier: 3.717A pdb=" N GLU D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 575 removed outlier: 3.709A pdb=" N LEU D 573 " --> pdb=" O VAL D 569 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N PHE D 574 " --> pdb=" O TRP D 570 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LYS D 575 " --> pdb=" O ILE D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 619 removed outlier: 5.010A pdb=" N LYS D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASP D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) 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 667 Processing helix chain 'D' and resid 673 through 697 removed outlier: 4.067A 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 391 through 394 removed outlier: 3.562A pdb=" N ALA A 421 " --> pdb=" O LEU A 324 " (cutoff:3.500A) 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 391 through 394 removed outlier: 3.562A pdb=" N ALA B 421 " --> pdb=" O LEU B 324 " (cutoff:3.500A) 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 391 through 394 removed outlier: 3.562A pdb=" N ALA C 421 " --> pdb=" O LEU C 324 " (cutoff:3.500A) 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 391 through 394 removed outlier: 3.562A pdb=" N ALA D 421 " --> pdb=" O LEU D 324 " (cutoff:3.500A) 848 hydrogen bonds defined for protein. 2496 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: 4.56 Time building geometry restraints manager: 7.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3265 1.33 - 1.45: 4748 1.45 - 1.57: 9206 1.57 - 1.70: 13 1.70 - 1.82: 124 Bond restraints: 17356 Sorted by residual: bond pdb=" C1' UMQ B 809 " pdb=" O5' UMQ B 809 " ideal model delta sigma weight residual 1.405 1.491 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C1' UMQ D 809 " pdb=" O5' UMQ D 809 " ideal model delta sigma weight residual 1.405 1.491 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C1' UMQ C 809 " pdb=" O5' UMQ C 809 " ideal model delta sigma weight residual 1.405 1.490 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C1' UMQ A 809 " pdb=" O5' UMQ A 809 " ideal model delta sigma weight residual 1.405 1.490 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C1' UMQ A 809 " pdb=" C2' UMQ A 809 " ideal model delta sigma weight residual 1.525 1.599 -0.074 2.00e-02 2.50e+03 1.39e+01 ... (remaining 17351 not shown) Histogram of bond angle deviations from ideal: 96.10 - 103.72: 148 103.72 - 111.33: 7432 111.33 - 118.95: 6670 118.95 - 126.57: 9071 126.57 - 134.18: 191 Bond angle restraints: 23512 Sorted by residual: angle pdb=" CA LEU B 374 " pdb=" CB LEU B 374 " pdb=" CG LEU B 374 " ideal model delta sigma weight residual 116.30 129.61 -13.31 3.50e+00 8.16e-02 1.45e+01 angle pdb=" CA LEU A 374 " pdb=" CB LEU A 374 " pdb=" CG LEU A 374 " ideal model delta sigma weight residual 116.30 129.57 -13.27 3.50e+00 8.16e-02 1.44e+01 angle pdb=" CA LEU D 374 " pdb=" CB LEU D 374 " pdb=" CG LEU D 374 " ideal model delta sigma weight residual 116.30 129.56 -13.26 3.50e+00 8.16e-02 1.44e+01 angle pdb=" CA LEU C 374 " pdb=" CB LEU C 374 " pdb=" CG LEU C 374 " ideal model delta sigma weight residual 116.30 129.55 -13.25 3.50e+00 8.16e-02 1.43e+01 angle pdb=" C ARG C 361 " pdb=" N ASN C 362 " pdb=" CA ASN C 362 " ideal model delta sigma weight residual 122.79 117.02 5.77 1.63e+00 3.76e-01 1.25e+01 ... (remaining 23507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.32: 10924 27.32 - 54.65: 395 54.65 - 81.97: 45 81.97 - 109.29: 24 109.29 - 136.62: 8 Dihedral angle restraints: 11396 sinusoidal: 5700 harmonic: 5696 Sorted by residual: 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 93.00 164.60 -71.60 1 1.00e+01 1.00e-02 6.57e+01 dihedral pdb=" CB CYS D 331 " pdb=" SG CYS D 331 " pdb=" SG CYS D 344 " pdb=" CB CYS D 344 " ideal model delta sinusoidal sigma weight residual 93.00 164.55 -71.55 1 1.00e+01 1.00e-02 6.56e+01 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 93.00 164.53 -71.53 1 1.00e+01 1.00e-02 6.56e+01 ... (remaining 11393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2051 0.068 - 0.135: 530 0.135 - 0.203: 185 0.203 - 0.270: 38 0.270 - 0.338: 8 Chirality restraints: 2812 Sorted by residual: chirality pdb=" C4' UMQ A 811 " pdb=" C3' UMQ A 811 " pdb=" C5' UMQ A 811 " pdb=" O1 UMQ A 811 " both_signs ideal model delta sigma weight residual False -2.54 -2.88 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" C4' UMQ A 814 " pdb=" C3' UMQ A 814 " pdb=" C5' UMQ A 814 " pdb=" O1 UMQ A 814 " both_signs ideal model delta sigma weight residual False -2.54 -2.88 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C4' UMQ C 811 " pdb=" C3' UMQ C 811 " pdb=" C5' UMQ C 811 " pdb=" O1 UMQ C 811 " both_signs ideal model delta sigma weight residual False -2.54 -2.88 0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 2809 not shown) Planarity restraints: 2740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 362 " -0.023 2.00e-02 2.50e+03 2.45e-02 7.52e+00 pdb=" CG ASN B 362 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN B 362 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 362 " 0.038 2.00e-02 2.50e+03 pdb=" C1 NAG B 803 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 362 " -0.023 2.00e-02 2.50e+03 2.43e-02 7.40e+00 pdb=" CG ASN C 362 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN C 362 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 362 " 0.037 2.00e-02 2.50e+03 pdb=" C1 NAG C 803 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 362 " 0.023 2.00e-02 2.50e+03 2.43e-02 7.36e+00 pdb=" CG ASN D 362 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN D 362 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN D 362 " -0.037 2.00e-02 2.50e+03 pdb=" C1 NAG D 803 " 0.028 2.00e-02 2.50e+03 ... (remaining 2737 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2690 2.75 - 3.29: 15276 3.29 - 3.83: 28550 3.83 - 4.36: 35715 4.36 - 4.90: 60487 Nonbonded interactions: 142718 Sorted by model distance: nonbonded pdb=" OH TYR C 227 " pdb=" O VAL C 569 " model vdw 2.216 2.440 nonbonded pdb=" O GLU A 340 " pdb=" NH2 ARG D 306 " model vdw 2.217 2.520 nonbonded pdb=" OH TYR D 227 " pdb=" O VAL D 569 " model vdw 2.217 2.440 nonbonded pdb=" OH TYR A 227 " pdb=" O VAL A 569 " model vdw 2.217 2.440 nonbonded pdb=" OH TYR B 227 " pdb=" O VAL B 569 " model vdw 2.217 2.440 ... (remaining 142713 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 213 through 700 or resid 801 through 810 or (resid 811 thr \ ough 812 and (name CA or name CB or name CG or name CD or name CH or name C1' or \ name C2' or name C3' or name C4' or name C5' or name C6' or name CC or name CF \ or name CI or name CJ or name CK or name CL or name O1 or name O1' or name O2' o \ r name O3' or name O5' or name O6')))) selection = chain 'B' selection = (chain 'C' and (resid 213 through 700 or resid 801 through 810 or (resid 811 thr \ ough 812 and (name CA or name CB or name CG or name CD or name CH or name C1' or \ name C2' or name C3' or name C4' or name C5' or name C6' or name CC or name CF \ or name CI or name CJ or name CK or name CL or name O1 or name O1' or name O2' o \ r name O3' or name O5' or name O6')))) selection = (chain 'D' and (resid 213 through 700 or resid 801 through 810 or (resid 811 thr \ ough 812 and (name CA or name CB or name CG or name CD or name CH or name C1' or \ name C2' or name C3' or name C4' or name C5' or name C6' or name CC or name CF \ or name CI or name CJ or name CK or name CL or name O1 or name O1' or name O2' o \ r name O3' or name O5' or name O6')))) } 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: 0.580 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: 3.580 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 45.510 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.090 17356 Z= 0.738 Angle : 1.165 13.308 23512 Z= 0.577 Chirality : 0.074 0.338 2812 Planarity : 0.006 0.064 2728 Dihedral : 14.614 136.616 7696 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.15 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: -3.35 (0.15), residues: 1904 helix: -2.18 (0.11), residues: 1100 sheet: -1.74 (0.33), residues: 200 loop : -2.02 (0.19), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.005 TRP D 293 HIS 0.006 0.003 HIS C 501 PHE 0.028 0.004 PHE D 600 TYR 0.029 0.004 TYR D 249 ARG 0.009 0.001 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 1.878 Fit side-chains REVERT: A 575 LYS cc_start: 0.8603 (mtpt) cc_final: 0.8353 (mtpp) REVERT: B 499 LYS cc_start: 0.7715 (mmmt) cc_final: 0.7020 (mmtt) REVERT: B 575 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8427 (mtpp) REVERT: C 499 LYS cc_start: 0.7743 (mmmt) cc_final: 0.7052 (mmtt) REVERT: D 255 GLN cc_start: 0.8165 (mt0) cc_final: 0.7965 (mt0) REVERT: D 267 LYS cc_start: 0.8241 (mtmm) cc_final: 0.8026 (mtpt) REVERT: D 499 LYS cc_start: 0.7669 (mmmt) cc_final: 0.7012 (mmtt) REVERT: D 575 LYS cc_start: 0.8513 (mtpt) cc_final: 0.8239 (mtpp) outliers start: 0 outliers final: 4 residues processed: 326 average time/residue: 1.0347 time to fit residues: 385.4731 Evaluate side-chains 215 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 211 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 690 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 174 optimal weight: 8.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN A 580 ASN A 636 GLN B 313 ASN B 323 GLN B 555 GLN B 580 ASN B 636 GLN C 323 GLN C 580 ASN C 636 GLN D 323 GLN D 636 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 17356 Z= 0.154 Angle : 0.560 8.904 23512 Z= 0.274 Chirality : 0.041 0.293 2812 Planarity : 0.004 0.043 2728 Dihedral : 13.117 105.980 4208 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.16 % Favored : 98.63 % Rotamer: Outliers : 2.20 % Allowed : 8.04 % Favored : 89.76 % 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: -1.17 (0.17), residues: 1904 helix: -0.19 (0.14), residues: 1100 sheet: -1.46 (0.32), residues: 200 loop : -1.38 (0.21), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 554 HIS 0.002 0.001 HIS A 498 PHE 0.023 0.001 PHE D 600 TYR 0.010 0.001 TYR C 486 ARG 0.004 0.000 ARG D 581 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 258 time to evaluate : 1.765 Fit side-chains REVERT: A 559 ASN cc_start: 0.7933 (OUTLIER) cc_final: 0.7425 (m-40) REVERT: A 624 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7124 (p0) REVERT: A 690 ASP cc_start: 0.7324 (t0) cc_final: 0.7024 (m-30) REVERT: B 228 LEU cc_start: 0.8995 (mt) cc_final: 0.8792 (mt) REVERT: B 242 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7278 (mmt) REVERT: B 624 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.7104 (p0) REVERT: B 690 ASP cc_start: 0.7390 (t0) cc_final: 0.7055 (m-30) REVERT: C 559 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7417 (m-40) REVERT: C 575 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8436 (mtpp) REVERT: C 624 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.7064 (p0) REVERT: C 650 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: C 681 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7821 (m-40) REVERT: C 690 ASP cc_start: 0.7326 (t0) cc_final: 0.7039 (m-30) REVERT: D 267 LYS cc_start: 0.8180 (mtmm) cc_final: 0.7954 (mtpt) REVERT: D 559 ASN cc_start: 0.7799 (OUTLIER) cc_final: 0.7285 (m-40) REVERT: D 575 LYS cc_start: 0.8495 (mtpt) cc_final: 0.8246 (mtpp) REVERT: D 624 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.7070 (p0) REVERT: D 650 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7764 (tm-30) outliers start: 37 outliers final: 7 residues processed: 282 average time/residue: 0.9556 time to fit residues: 310.3518 Evaluate side-chains 221 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 202 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 547 ASN Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 650 GLU Chi-restraints excluded: chain C residue 681 ASN Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 650 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 174 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 chunk 140 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 GLN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN C 636 GLN ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 GLN ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17356 Z= 0.161 Angle : 0.532 8.526 23512 Z= 0.256 Chirality : 0.041 0.291 2812 Planarity : 0.003 0.040 2728 Dihedral : 11.706 91.543 4200 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.31 % Favored : 98.48 % Rotamer: Outliers : 2.98 % Allowed : 10.95 % Favored : 86.07 % 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: -0.02 (0.18), residues: 1904 helix: 0.84 (0.15), residues: 1084 sheet: -1.20 (0.32), residues: 200 loop : -1.00 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 554 HIS 0.002 0.000 HIS D 550 PHE 0.021 0.001 PHE D 600 TYR 0.009 0.001 TYR A 348 ARG 0.004 0.000 ARG C 361 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 234 time to evaluate : 1.743 Fit side-chains REVERT: A 559 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7409 (m-40) REVERT: A 624 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7179 (p0) REVERT: B 624 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7208 (p0) REVERT: B 681 ASN cc_start: 0.7927 (t0) cc_final: 0.7434 (m-40) REVERT: C 559 ASN cc_start: 0.7899 (OUTLIER) cc_final: 0.7401 (m-40) REVERT: C 575 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8418 (mtpp) REVERT: C 624 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.7136 (p0) REVERT: D 267 LYS cc_start: 0.8203 (mtmm) cc_final: 0.7904 (mtpt) REVERT: D 559 ASN cc_start: 0.7839 (OUTLIER) cc_final: 0.7359 (m-40) REVERT: D 624 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7138 (p0) REVERT: D 690 ASP cc_start: 0.7588 (m-30) cc_final: 0.7360 (t0) outliers start: 50 outliers final: 11 residues processed: 267 average time/residue: 0.9492 time to fit residues: 292.7197 Evaluate side-chains 228 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 209 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 547 ASN Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 624 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 20.0000 chunk 131 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 175 optimal weight: 20.0000 chunk 185 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 GLN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 GLN D 580 ASN D 636 GLN ** 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: 0.8488 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17356 Z= 0.336 Angle : 0.626 8.297 23512 Z= 0.296 Chirality : 0.045 0.342 2812 Planarity : 0.004 0.043 2728 Dihedral : 11.579 87.768 4200 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.31 % Favored : 98.48 % Rotamer: Outliers : 3.81 % Allowed : 11.13 % Favored : 85.06 % 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: 0.15 (0.18), residues: 1904 helix: 0.88 (0.15), residues: 1108 sheet: -1.17 (0.32), residues: 200 loop : -0.75 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 554 HIS 0.005 0.001 HIS D 550 PHE 0.022 0.002 PHE D 600 TYR 0.015 0.002 TYR C 249 ARG 0.003 0.000 ARG C 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 225 time to evaluate : 1.739 Fit side-chains revert: symmetry clash REVERT: A 559 ASN cc_start: 0.7960 (OUTLIER) cc_final: 0.7464 (m-40) REVERT: A 624 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7222 (p0) REVERT: A 681 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7644 (m-40) REVERT: B 344 CYS cc_start: 0.6970 (p) cc_final: 0.6657 (t) REVERT: B 624 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7242 (p0) REVERT: C 559 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.7461 (m-40) REVERT: C 575 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8471 (mtpp) REVERT: C 624 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7212 (p0) REVERT: C 681 ASN cc_start: 0.8117 (OUTLIER) cc_final: 0.7666 (m-40) REVERT: D 267 LYS cc_start: 0.8232 (mtmm) cc_final: 0.7956 (mtpt) REVERT: D 559 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7440 (m-40) REVERT: D 624 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7215 (p0) outliers start: 64 outliers final: 18 residues processed: 272 average time/residue: 0.9118 time to fit residues: 287.0208 Evaluate side-chains 236 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 208 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 681 ASN Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 681 ASN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 547 ASN Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 624 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 76 optimal weight: 20.0000 chunk 158 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 GLN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 GLN ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 ASN D 580 ASN D 636 GLN ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17356 Z= 0.164 Angle : 0.555 9.315 23512 Z= 0.260 Chirality : 0.042 0.361 2812 Planarity : 0.003 0.040 2728 Dihedral : 10.924 78.433 4200 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.58 % Favored : 98.21 % Rotamer: Outliers : 2.38 % Allowed : 12.86 % Favored : 84.76 % 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: 0.58 (0.18), residues: 1904 helix: 1.26 (0.15), residues: 1092 sheet: -0.99 (0.33), residues: 200 loop : -0.61 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 554 HIS 0.001 0.000 HIS B 550 PHE 0.021 0.001 PHE D 600 TYR 0.009 0.001 TYR C 348 ARG 0.004 0.000 ARG C 361 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 234 time to evaluate : 1.838 Fit side-chains REVERT: A 559 ASN cc_start: 0.7924 (OUTLIER) cc_final: 0.7422 (m-40) REVERT: A 624 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7181 (p0) REVERT: A 681 ASN cc_start: 0.7898 (OUTLIER) cc_final: 0.7430 (m-40) REVERT: B 624 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7211 (p0) REVERT: C 344 CYS cc_start: 0.6855 (p) cc_final: 0.6621 (t) REVERT: C 559 ASN cc_start: 0.7885 (OUTLIER) cc_final: 0.7381 (m-40) REVERT: C 575 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8445 (mtpp) REVERT: C 624 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7205 (p0) REVERT: D 267 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7898 (mtpt) REVERT: D 559 ASN cc_start: 0.7893 (OUTLIER) cc_final: 0.7409 (m-40) REVERT: D 624 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7218 (p0) REVERT: D 690 ASP cc_start: 0.7607 (m-30) cc_final: 0.7394 (t0) outliers start: 40 outliers final: 13 residues processed: 265 average time/residue: 0.9461 time to fit residues: 290.3182 Evaluate side-chains 242 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 220 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 681 ASN Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 547 ASN Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 547 ASN Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 624 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 108 optimal weight: 0.0980 chunk 45 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 GLN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 GLN ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 ASN D 636 GLN ** 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: 0.8458 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17356 Z= 0.224 Angle : 0.583 9.241 23512 Z= 0.271 Chirality : 0.043 0.386 2812 Planarity : 0.003 0.040 2728 Dihedral : 10.639 73.609 4200 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.63 % Favored : 98.16 % Rotamer: Outliers : 3.04 % Allowed : 12.98 % Favored : 83.99 % 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: 0.70 (0.19), residues: 1904 helix: 1.33 (0.15), residues: 1092 sheet: -0.93 (0.33), residues: 200 loop : -0.51 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 554 HIS 0.003 0.001 HIS B 550 PHE 0.020 0.001 PHE C 600 TYR 0.011 0.001 TYR D 348 ARG 0.004 0.000 ARG C 361 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 226 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7438 (m-40) REVERT: A 624 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7232 (p0) REVERT: A 681 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7466 (m-40) REVERT: B 583 MET cc_start: 0.8275 (mmt) cc_final: 0.8011 (mmt) REVERT: B 624 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7243 (p0) REVERT: C 559 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.7411 (m-40) REVERT: C 575 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8457 (mtpp) REVERT: C 583 MET cc_start: 0.8290 (mmt) cc_final: 0.8005 (mmt) REVERT: C 624 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7240 (p0) REVERT: D 267 LYS cc_start: 0.8204 (mtmm) cc_final: 0.7907 (mtpt) REVERT: D 559 ASN cc_start: 0.7928 (OUTLIER) cc_final: 0.7457 (m-40) REVERT: D 624 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7255 (p0) outliers start: 51 outliers final: 15 residues processed: 265 average time/residue: 0.9619 time to fit residues: 294.5552 Evaluate side-chains 239 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 215 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 681 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 547 ASN Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 336 ASP Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 547 ASN Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 624 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 185 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 GLN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 GLN ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 ASN D 636 GLN ** 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: 0.8446 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17356 Z= 0.190 Angle : 0.565 8.570 23512 Z= 0.263 Chirality : 0.043 0.396 2812 Planarity : 0.003 0.041 2728 Dihedral : 10.341 68.016 4200 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.58 % Favored : 98.21 % Rotamer: Outliers : 2.50 % Allowed : 13.63 % Favored : 83.87 % 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: 0.98 (0.19), residues: 1904 helix: 1.59 (0.15), residues: 1068 sheet: -0.81 (0.34), residues: 200 loop : -0.37 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 554 HIS 0.002 0.000 HIS B 550 PHE 0.020 0.001 PHE D 600 TYR 0.010 0.001 TYR C 348 ARG 0.001 0.000 ARG C 361 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 219 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 ASN cc_start: 0.7944 (OUTLIER) cc_final: 0.7449 (m-40) REVERT: A 624 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7217 (p0) REVERT: B 583 MET cc_start: 0.8274 (mmt) cc_final: 0.8005 (mmt) REVERT: B 624 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7252 (p0) REVERT: C 559 ASN cc_start: 0.7891 (OUTLIER) cc_final: 0.7404 (m-40) REVERT: C 575 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8456 (mtpp) REVERT: C 583 MET cc_start: 0.8280 (mmt) cc_final: 0.8047 (mmt) REVERT: C 624 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7251 (p0) REVERT: D 267 LYS cc_start: 0.8214 (mtmm) cc_final: 0.7921 (mtpt) REVERT: D 559 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7443 (m-40) REVERT: D 624 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7269 (p0) outliers start: 42 outliers final: 15 residues processed: 254 average time/residue: 0.9013 time to fit residues: 267.4044 Evaluate side-chains 236 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 213 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 336 ASP Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 547 ASN Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 624 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 GLN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 ASN C 636 GLN ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 ASN D 636 GLN ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17356 Z= 0.168 Angle : 0.557 8.720 23512 Z= 0.259 Chirality : 0.042 0.402 2812 Planarity : 0.003 0.040 2728 Dihedral : 10.042 62.283 4200 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.73 % Favored : 98.06 % Rotamer: Outliers : 2.32 % Allowed : 14.17 % Favored : 83.51 % 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: 1.10 (0.19), residues: 1904 helix: 1.69 (0.15), residues: 1068 sheet: -0.75 (0.34), residues: 200 loop : -0.32 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 554 HIS 0.002 0.000 HIS A 550 PHE 0.019 0.001 PHE D 600 TYR 0.021 0.001 TYR A 486 ARG 0.002 0.000 ARG C 361 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 224 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 ASN cc_start: 0.7940 (OUTLIER) cc_final: 0.7456 (m-40) REVERT: A 624 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7273 (p0) REVERT: B 583 MET cc_start: 0.8264 (mmt) cc_final: 0.7991 (mmt) REVERT: B 624 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7285 (p0) REVERT: C 559 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7429 (m-40) REVERT: C 575 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8457 (mtpp) REVERT: C 583 MET cc_start: 0.8280 (mmt) cc_final: 0.8056 (mmt) REVERT: C 624 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7305 (p0) REVERT: D 267 LYS cc_start: 0.8206 (mtmm) cc_final: 0.7907 (mtpt) REVERT: D 559 ASN cc_start: 0.7940 (OUTLIER) cc_final: 0.7454 (m-40) REVERT: D 624 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7335 (p0) outliers start: 39 outliers final: 17 residues processed: 254 average time/residue: 0.8990 time to fit residues: 266.1530 Evaluate side-chains 232 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 207 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 336 ASP Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 547 ASN Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 624 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 172 optimal weight: 0.1980 chunk 103 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 171 optimal weight: 0.3980 chunk 113 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 GLN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 GLN ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 GLN ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 681 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17356 Z= 0.130 Angle : 0.538 9.070 23512 Z= 0.251 Chirality : 0.041 0.398 2812 Planarity : 0.003 0.039 2728 Dihedral : 9.601 59.759 4200 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.52 % Favored : 98.27 % Rotamer: Outliers : 1.49 % Allowed : 15.24 % Favored : 83.27 % 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: 1.33 (0.19), residues: 1904 helix: 1.87 (0.15), residues: 1068 sheet: -0.61 (0.34), residues: 200 loop : -0.22 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 554 HIS 0.001 0.000 HIS C 498 PHE 0.019 0.001 PHE D 600 TYR 0.008 0.001 TYR C 348 ARG 0.003 0.000 ARG C 361 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 220 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7463 (m-40) REVERT: B 583 MET cc_start: 0.8263 (mmt) cc_final: 0.8060 (mmt) REVERT: C 559 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7445 (m-40) REVERT: C 575 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8400 (mtpp) REVERT: C 583 MET cc_start: 0.8279 (mmt) cc_final: 0.8060 (mmt) REVERT: D 267 LYS cc_start: 0.8167 (mtmm) cc_final: 0.7895 (mtpt) REVERT: D 559 ASN cc_start: 0.7892 (OUTLIER) cc_final: 0.7429 (m-40) outliers start: 25 outliers final: 7 residues processed: 240 average time/residue: 0.8657 time to fit residues: 243.6266 Evaluate side-chains 220 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 209 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain D residue 336 ASP Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 547 ASN Chi-restraints excluded: chain D residue 559 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 191 optimal weight: 9.9990 chunk 176 optimal weight: 7.9990 chunk 152 optimal weight: 0.0470 chunk 15 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN A 636 GLN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 GLN ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 GLN ** 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: 0.8407 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17356 Z= 0.152 Angle : 0.556 13.201 23512 Z= 0.256 Chirality : 0.042 0.398 2812 Planarity : 0.003 0.039 2728 Dihedral : 9.452 59.595 4200 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.79 % Favored : 98.00 % Rotamer: Outliers : 1.37 % Allowed : 15.24 % Favored : 83.39 % 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: 1.42 (0.19), residues: 1904 helix: 1.92 (0.15), residues: 1068 sheet: -0.56 (0.34), residues: 200 loop : -0.16 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 554 HIS 0.001 0.000 HIS C 550 PHE 0.019 0.001 PHE D 600 TYR 0.021 0.001 TYR D 486 ARG 0.002 0.000 ARG C 361 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 208 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7484 (m-40) REVERT: A 624 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7370 (p0) REVERT: B 583 MET cc_start: 0.8231 (mmt) cc_final: 0.7992 (mmt) REVERT: C 559 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7451 (m-40) REVERT: C 583 MET cc_start: 0.8275 (mmt) cc_final: 0.8014 (mmt) REVERT: D 267 LYS cc_start: 0.8204 (mtmm) cc_final: 0.7944 (mtpt) REVERT: D 559 ASN cc_start: 0.7924 (OUTLIER) cc_final: 0.7467 (m-40) REVERT: D 690 ASP cc_start: 0.7624 (m-30) cc_final: 0.7364 (t0) outliers start: 23 outliers final: 6 residues processed: 226 average time/residue: 0.8325 time to fit residues: 221.7318 Evaluate side-chains 208 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 198 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain D residue 336 ASP Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 559 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 152 optimal weight: 0.0040 chunk 63 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 GLN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 GLN ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 GLN ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.139661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.108665 restraints weight = 19292.394| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.62 r_work: 0.2946 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17356 Z= 0.166 Angle : 0.553 9.214 23512 Z= 0.257 Chirality : 0.042 0.398 2812 Planarity : 0.003 0.039 2728 Dihedral : 9.356 57.973 4200 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.73 % Favored : 98.06 % Rotamer: Outliers : 1.31 % Allowed : 15.30 % Favored : 83.39 % 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: 1.44 (0.19), residues: 1904 helix: 1.93 (0.15), residues: 1068 sheet: -0.53 (0.34), residues: 200 loop : -0.13 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 554 HIS 0.002 0.000 HIS C 550 PHE 0.019 0.001 PHE D 600 TYR 0.009 0.001 TYR B 348 ARG 0.001 0.000 ARG C 361 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5245.76 seconds wall clock time: 94 minutes 51.85 seconds (5691.85 seconds total)