Starting phenix.real_space_refine on Thu Feb 5 08:11:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q9s_52966/02_2026/9q9s_52966.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q9s_52966/02_2026/9q9s_52966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q9s_52966/02_2026/9q9s_52966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q9s_52966/02_2026/9q9s_52966.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q9s_52966/02_2026/9q9s_52966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q9s_52966/02_2026/9q9s_52966.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 9873 2.51 5 N 2748 2.21 5 O 3030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15738 Number of models: 1 Model: "" Number of chains: 18 Chain: "d" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 870 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "e" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 870 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "f" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 870 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "A" Number of atoms: 4264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4264 Classifications: {'peptide': 530} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 503} Chain breaks: 3 Chain: "B" Number of atoms: 4264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4264 Classifications: {'peptide': 530} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 503} Chain breaks: 3 Chain: "C" Number of atoms: 4264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4264 Classifications: {'peptide': 530} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 503} Chain breaks: 3 Chain: "D" 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: "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: "I" 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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 Time building chain proxies: 3.39, per 1000 atoms: 0.22 Number of scatterers: 15738 At special positions: 0 Unit cell: (141.1, 135.29, 107.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 3030 8.00 N 2748 7.00 C 9873 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS d 22 " - pdb=" SG CYS d 97 " distance=2.06 Simple disulfide: pdb=" SG CYS e 22 " - pdb=" SG CYS e 97 " distance=2.06 Simple disulfide: pdb=" SG CYS f 22 " - pdb=" SG CYS f 97 " distance=2.06 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 570 " distance=2.07 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 526 " distance=2.04 Simple disulfide: pdb=" SG CYS A 202 " - pdb=" SG CYS A 266 " distance=2.04 Simple disulfide: pdb=" SG CYS A 359 " - pdb=" SG CYS A 407 " distance=2.06 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS A 630 " distance=2.05 Simple disulfide: pdb=" SG CYS B 111 " - pdb=" SG CYS B 570 " distance=2.05 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 526 " distance=2.02 Simple disulfide: pdb=" SG CYS B 202 " - pdb=" SG CYS B 266 " distance=2.05 Simple disulfide: pdb=" SG CYS B 359 " - pdb=" SG CYS B 407 " distance=2.05 Simple disulfide: pdb=" SG CYS B 593 " - pdb=" SG CYS B 630 " distance=2.05 Simple disulfide: pdb=" SG CYS C 111 " - pdb=" SG CYS C 570 " distance=2.05 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 526 " distance=2.05 Simple disulfide: pdb=" SG CYS C 202 " - pdb=" SG CYS C 266 " distance=2.05 Simple disulfide: pdb=" SG CYS C 359 " - pdb=" SG CYS C 407 " distance=2.06 Simple disulfide: pdb=" SG CYS C 593 " - pdb=" SG CYS C 630 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 D 1 " - " NAG D 2 " " 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG D 1 " - " ASN A 136 " " NAG E 1 " - " ASN B 136 " " NAG F 1 " - " ASN C 136 " " NAG G 1 " - " ASN A 393 " " NAG H 1 " - " ASN B 393 " " NAG I 1 " - " ASN C 393 " " NAG J 1 " - " ASN A 425 " " NAG K 1 " - " ASN B 425 " " NAG L 1 " - " ASN C 425 " " NAG M 1 " - " ASN A 671 " " NAG N 1 " - " ASN B 671 " " NAG O 1 " - " ASN C 671 " Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 723.2 milliseconds 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 39 sheets defined 22.8% alpha, 43.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'd' and resid 29 through 33 Processing helix chain 'd' and resid 88 through 92 Processing helix chain 'e' and resid 29 through 33 Processing helix chain 'e' and resid 88 through 92 Processing helix chain 'f' and resid 29 through 33 Processing helix chain 'f' and resid 88 through 92 Processing helix chain 'A' and resid 91 through 100 Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 406 through 423 removed outlier: 4.148A pdb=" N ASP A 411 " --> pdb=" O CYS A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 453 through 464 removed outlier: 4.068A pdb=" N LEU A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 506 removed outlier: 4.989A pdb=" N PHE A 505 " --> pdb=" O ARG A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 543 removed outlier: 4.142A pdb=" N HIS A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE A 521 " --> pdb=" O MET A 517 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 541 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 542 " --> pdb=" O GLU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 657 through 661 removed outlier: 3.826A pdb=" N VAL A 661 " --> pdb=" O ARG A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 672 removed outlier: 3.620A pdb=" N LEU A 670 " --> pdb=" O THR A 666 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A 672 " --> pdb=" O ILE A 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 100 Processing helix chain 'B' and resid 188 through 195 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 310 through 312 No H-bonds generated for 'chain 'B' and resid 310 through 312' Processing helix chain 'B' and resid 398 through 402 Processing helix chain 'B' and resid 406 through 423 removed outlier: 3.970A pdb=" N ASP B 411 " --> pdb=" O CYS B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 453 through 464 removed outlier: 4.446A pdb=" N LEU B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 504 Processing helix chain 'B' and resid 507 through 543 removed outlier: 3.584A pdb=" N HIS B 513 " --> pdb=" O HIS B 509 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE B 521 " --> pdb=" O MET B 517 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS B 541 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU B 542 " --> pdb=" O GLU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 574 through 576 No H-bonds generated for 'chain 'B' and resid 574 through 576' Processing helix chain 'B' and resid 659 through 661 No H-bonds generated for 'chain 'B' and resid 659 through 661' Processing helix chain 'B' and resid 666 through 672 removed outlier: 3.829A pdb=" N ILE B 672 " --> pdb=" O ILE B 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 100 Processing helix chain 'C' and resid 188 through 195 Processing helix chain 'C' and resid 195 through 200 Processing helix chain 'C' and resid 218 through 222 Processing helix chain 'C' and resid 310 through 312 No H-bonds generated for 'chain 'C' and resid 310 through 312' Processing helix chain 'C' and resid 398 through 402 Processing helix chain 'C' and resid 406 through 423 removed outlier: 4.254A pdb=" N ASP C 411 " --> pdb=" O CYS C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 426 No H-bonds generated for 'chain 'C' and resid 424 through 426' Processing helix chain 'C' and resid 453 through 464 removed outlier: 4.065A pdb=" N LEU C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 504 Processing helix chain 'C' and resid 507 through 543 removed outlier: 3.701A pdb=" N HIS C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE C 521 " --> pdb=" O MET C 517 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS C 541 " --> pdb=" O ASN C 537 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU C 542 " --> pdb=" O GLU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 574 through 576 No H-bonds generated for 'chain 'C' and resid 574 through 576' Processing helix chain 'C' and resid 659 through 661 No H-bonds generated for 'chain 'C' and resid 659 through 661' Processing helix chain 'C' and resid 666 through 672 removed outlier: 3.601A pdb=" N LEU C 670 " --> pdb=" O THR C 666 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 672 " --> pdb=" O ILE C 668 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'd' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'd' and resid 10 through 11 removed outlier: 6.557A pdb=" N LEU d 36 " --> pdb=" O THR d 52 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR d 52 " --> pdb=" O LEU d 36 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP d 38 " --> pdb=" O VAL d 50 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL d 42 " --> pdb=" O SER d 46 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N SER d 46 " --> pdb=" O VAL d 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 10 through 11 Processing sheet with id=AA4, first strand: chain 'e' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'e' and resid 10 through 11 removed outlier: 6.537A pdb=" N LEU e 36 " --> pdb=" O THR e 52 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR e 52 " --> pdb=" O LEU e 36 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TRP e 38 " --> pdb=" O VAL e 50 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL e 42 " --> pdb=" O SER e 46 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N SER e 46 " --> pdb=" O VAL e 42 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER e 58 " --> pdb=" O THR e 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'e' and resid 10 through 11 Processing sheet with id=AA7, first strand: chain 'f' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'f' and resid 10 through 11 removed outlier: 6.531A pdb=" N LEU f 36 " --> pdb=" O THR f 52 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR f 52 " --> pdb=" O LEU f 36 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP f 38 " --> pdb=" O VAL f 50 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL f 42 " --> pdb=" O SER f 46 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N SER f 46 " --> pdb=" O VAL f 42 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N SER f 58 " --> pdb=" O THR f 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'f' and resid 10 through 11 Processing sheet with id=AB1, first strand: chain 'A' and resid 571 through 573 removed outlier: 6.431A pdb=" N TYR A 109 " --> pdb=" O LEU A 620 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 556 through 559 removed outlier: 3.785A pdb=" N THR B 662 " --> pdb=" O VAL A 119 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 390 through 392 removed outlier: 5.386A pdb=" N THR A 362 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLU A 147 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TRP A 364 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N PHE A 145 " --> pdb=" O TRP A 364 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU A 366 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL A 143 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ASP A 368 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE A 141 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET A 370 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU A 139 " --> pdb=" O MET A 370 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG A 372 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR A 137 " --> pdb=" O ARG A 372 " (cutoff:3.500A) removed outlier: 14.465A pdb=" N TYR A 137 " --> pdb=" O SER A 452 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N SER A 452 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU A 139 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 390 through 392 removed outlier: 5.386A pdb=" N THR A 362 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLU A 147 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TRP A 364 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N PHE A 145 " --> pdb=" O TRP A 364 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU A 366 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL A 143 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ASP A 368 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE A 141 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET A 370 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU A 139 " --> pdb=" O MET A 370 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG A 372 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR A 137 " --> pdb=" O ARG A 372 " (cutoff:3.500A) removed outlier: 14.465A pdb=" N TYR A 137 " --> pdb=" O SER A 452 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N SER A 452 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU A 139 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 183 through 186 Processing sheet with id=AB6, first strand: chain 'A' and resid 230 through 231 removed outlier: 7.321A pdb=" N LYS A 155 " --> pdb=" O ASP A 350 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP A 350 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR A 335 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AB8, first strand: chain 'A' and resid 206 through 210 Processing sheet with id=AB9, first strand: chain 'A' and resid 592 through 594 Processing sheet with id=AC1, first strand: chain 'A' and resid 635 through 640 removed outlier: 3.567A pdb=" N GLY A 643 " --> pdb=" O PHE A 640 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS A 654 " --> pdb=" O TYR A 646 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLU A 648 " --> pdb=" O TYR A 652 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N TYR A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 662 through 663 removed outlier: 6.991A pdb=" N THR A 662 " --> pdb=" O GLN C 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 571 through 573 removed outlier: 6.396A pdb=" N TYR B 109 " --> pdb=" O LEU B 620 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 556 through 559 removed outlier: 3.896A pdb=" N THR C 662 " --> pdb=" O VAL B 119 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 391 through 392 removed outlier: 5.498A pdb=" N THR B 362 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLU B 147 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N TRP B 364 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE B 145 " --> pdb=" O TRP B 364 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU B 366 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL B 143 " --> pdb=" O GLU B 366 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ASP B 368 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILE B 141 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET B 370 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU B 139 " --> pdb=" O MET B 370 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG B 372 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TYR B 137 " --> pdb=" O ARG B 372 " (cutoff:3.500A) removed outlier: 14.607A pdb=" N TYR B 137 " --> pdb=" O SER B 452 " (cutoff:3.500A) removed outlier: 10.224A pdb=" N SER B 452 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU B 139 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 removed outlier: 5.498A pdb=" N THR B 362 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLU B 147 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N TRP B 364 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE B 145 " --> pdb=" O TRP B 364 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU B 366 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL B 143 " --> pdb=" O GLU B 366 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ASP B 368 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILE B 141 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET B 370 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU B 139 " --> pdb=" O MET B 370 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG B 372 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TYR B 137 " --> pdb=" O ARG B 372 " (cutoff:3.500A) removed outlier: 14.607A pdb=" N TYR B 137 " --> pdb=" O SER B 452 " (cutoff:3.500A) removed outlier: 10.224A pdb=" N SER B 452 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU B 139 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 183 through 186 Processing sheet with id=AC8, first strand: chain 'B' and resid 230 through 231 removed outlier: 7.342A pdb=" N LYS B 155 " --> pdb=" O ASP B 350 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASP B 350 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG B 337 " --> pdb=" O ASP B 318 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP B 318 " --> pdb=" O ARG B 337 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU B 339 " --> pdb=" O GLN B 316 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLN B 316 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N THR B 341 " --> pdb=" O PHE B 314 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE B 314 " --> pdb=" O THR B 341 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AD1, first strand: chain 'B' and resid 206 through 210 Processing sheet with id=AD2, first strand: chain 'B' and resid 592 through 594 Processing sheet with id=AD3, first strand: chain 'B' and resid 635 through 640 removed outlier: 3.690A pdb=" N HIS B 654 " --> pdb=" O TYR B 646 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLU B 648 " --> pdb=" O TYR B 652 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYR B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 571 through 573 removed outlier: 6.394A pdb=" N TYR C 109 " --> pdb=" O LEU C 620 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 391 through 392 removed outlier: 5.394A pdb=" N THR C 362 " --> pdb=" O GLU C 147 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLU C 147 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TRP C 364 " --> pdb=" O PHE C 145 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N PHE C 145 " --> pdb=" O TRP C 364 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU C 366 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C 143 " --> pdb=" O GLU C 366 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP C 368 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE C 141 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N MET C 370 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU C 139 " --> pdb=" O MET C 370 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG C 372 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR C 137 " --> pdb=" O ARG C 372 " (cutoff:3.500A) removed outlier: 14.417A pdb=" N TYR C 137 " --> pdb=" O SER C 452 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N SER C 452 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU C 139 " --> pdb=" O LEU C 450 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 391 through 392 removed outlier: 5.394A pdb=" N THR C 362 " --> pdb=" O GLU C 147 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLU C 147 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TRP C 364 " --> pdb=" O PHE C 145 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N PHE C 145 " --> pdb=" O TRP C 364 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU C 366 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C 143 " --> pdb=" O GLU C 366 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP C 368 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE C 141 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N MET C 370 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU C 139 " --> pdb=" O MET C 370 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG C 372 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR C 137 " --> pdb=" O ARG C 372 " (cutoff:3.500A) removed outlier: 14.417A pdb=" N TYR C 137 " --> pdb=" O SER C 452 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N SER C 452 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU C 139 " --> pdb=" O LEU C 450 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 183 through 186 Processing sheet with id=AD8, first strand: chain 'C' and resid 230 through 231 removed outlier: 7.314A pdb=" N LYS C 155 " --> pdb=" O ASP C 350 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASP C 350 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N THR C 335 " --> pdb=" O GLY C 319 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 201 through 203 Processing sheet with id=AE1, first strand: chain 'C' and resid 206 through 210 Processing sheet with id=AE2, first strand: chain 'C' and resid 592 through 594 Processing sheet with id=AE3, first strand: chain 'C' and resid 635 through 639 removed outlier: 3.700A pdb=" N HIS C 654 " --> pdb=" O TYR C 646 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU C 648 " --> pdb=" O TYR C 652 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N TYR C 652 " --> pdb=" O GLU C 648 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 1914 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: 2.57 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5187 1.34 - 1.46: 3916 1.46 - 1.58: 6842 1.58 - 1.69: 0 1.69 - 1.81: 138 Bond restraints: 16083 Sorted by residual: bond pdb=" C4 NAG M 1 " pdb=" O4 NAG M 1 " ideal model delta sigma weight residual 1.409 1.496 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C4 NAG I 1 " pdb=" O4 NAG I 1 " ideal model delta sigma weight residual 1.409 1.493 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C4 NAG N 1 " pdb=" O4 NAG N 1 " ideal model delta sigma weight residual 1.409 1.493 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C4 NAG H 1 " pdb=" O4 NAG H 1 " ideal model delta sigma weight residual 1.409 1.493 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C4 NAG D 1 " pdb=" O4 NAG D 1 " ideal model delta sigma weight residual 1.409 1.493 -0.084 2.00e-02 2.50e+03 1.77e+01 ... (remaining 16078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 18317 2.74 - 5.49: 3320 5.49 - 8.23: 178 8.23 - 10.97: 3 10.97 - 13.72: 1 Bond angle restraints: 21819 Sorted by residual: angle pdb=" CA ASP C 669 " pdb=" CB ASP C 669 " pdb=" CG ASP C 669 " ideal model delta sigma weight residual 112.60 120.75 -8.15 1.00e+00 1.00e+00 6.64e+01 angle pdb=" CA ASP A 669 " pdb=" CB ASP A 669 " pdb=" CG ASP A 669 " ideal model delta sigma weight residual 112.60 120.34 -7.74 1.00e+00 1.00e+00 5.99e+01 angle pdb=" CA CYS A 570 " pdb=" CB CYS A 570 " pdb=" SG CYS A 570 " ideal model delta sigma weight residual 114.40 128.12 -13.72 2.30e+00 1.89e-01 3.56e+01 angle pdb=" CA ASN e 60 " pdb=" CB ASN e 60 " pdb=" CG ASN e 60 " ideal model delta sigma weight residual 112.60 118.29 -5.69 1.00e+00 1.00e+00 3.24e+01 angle pdb=" CA PHE e 69 " pdb=" CB PHE e 69 " pdb=" CG PHE e 69 " ideal model delta sigma weight residual 113.80 119.48 -5.68 1.00e+00 1.00e+00 3.23e+01 ... (remaining 21814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 9256 17.83 - 35.67: 514 35.67 - 53.50: 132 53.50 - 71.34: 42 71.34 - 89.17: 4 Dihedral angle restraints: 9948 sinusoidal: 4302 harmonic: 5646 Sorted by residual: dihedral pdb=" CB CYS C 128 " pdb=" SG CYS C 128 " pdb=" SG CYS C 526 " pdb=" CB CYS C 526 " ideal model delta sinusoidal sigma weight residual 93.00 170.80 -77.80 1 1.00e+01 1.00e-02 7.57e+01 dihedral pdb=" CB CYS A 128 " pdb=" SG CYS A 128 " pdb=" SG CYS A 526 " pdb=" CB CYS A 526 " ideal model delta sinusoidal sigma weight residual 93.00 162.31 -69.31 1 1.00e+01 1.00e-02 6.21e+01 dihedral pdb=" C CYS A 570 " pdb=" N CYS A 570 " pdb=" CA CYS A 570 " pdb=" CB CYS A 570 " ideal model delta harmonic sigma weight residual -122.60 -139.80 17.20 0 2.50e+00 1.60e-01 4.73e+01 ... (remaining 9945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 1924 0.144 - 0.288: 464 0.288 - 0.432: 53 0.432 - 0.576: 15 0.576 - 0.720: 1 Chirality restraints: 2457 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.07e+01 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.12e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.82e+01 ... (remaining 2454 not shown) Planarity restraints: 2814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 671 " -0.096 2.00e-02 2.50e+03 1.08e-01 1.45e+02 pdb=" CG ASN C 671 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN C 671 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN C 671 " 0.174 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 424 " 0.110 2.00e-02 2.50e+03 6.29e-02 7.91e+01 pdb=" CG TYR B 424 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 424 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 TYR B 424 " -0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR B 424 " -0.043 2.00e-02 2.50e+03 pdb=" CE2 TYR B 424 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR B 424 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 424 " 0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 424 " -0.108 2.00e-02 2.50e+03 6.22e-02 7.74e+01 pdb=" CG TYR A 424 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR A 424 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR A 424 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR A 424 " 0.043 2.00e-02 2.50e+03 pdb=" CE2 TYR A 424 " 0.036 2.00e-02 2.50e+03 pdb=" CZ TYR A 424 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 424 " -0.100 2.00e-02 2.50e+03 ... (remaining 2811 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 7552 2.99 - 3.47: 14481 3.47 - 3.95: 25026 3.95 - 4.42: 27528 4.42 - 4.90: 48786 Nonbonded interactions: 123373 Sorted by model distance: nonbonded pdb=" N ASP f 55 " pdb=" O ASP f 55 " model vdw 2.513 2.496 nonbonded pdb=" N ASP e 55 " pdb=" O ASP e 55 " model vdw 2.514 2.496 nonbonded pdb=" N ASP d 55 " pdb=" O ASP d 55 " model vdw 2.519 2.496 nonbonded pdb=" OG SER C 665 " pdb=" OD2 ASP C 669 " model vdw 2.536 3.040 nonbonded pdb=" OG SER A 665 " pdb=" OD2 ASP A 669 " model vdw 2.549 3.040 ... (remaining 123368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'd' selection = chain 'e' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.470 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 : 0.011 0.087 16125 Z= 0.634 Angle : 1.990 13.718 21927 Z= 1.291 Chirality : 0.125 0.720 2457 Planarity : 0.015 0.151 2802 Dihedral : 12.252 89.172 6270 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.94 % Favored : 96.90 % Rotamer: Outliers : 1.09 % Allowed : 2.66 % Favored : 96.25 % Cbeta Deviations : 0.94 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.17), residues: 1905 helix: -0.94 (0.25), residues: 297 sheet: -0.83 (0.20), residues: 507 loop : -0.85 (0.16), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 624 TYR 0.110 0.019 TYR B 424 PHE 0.065 0.012 PHE B 282 TRP 0.082 0.018 TRP B 525 HIS 0.013 0.004 HIS B 95 Details of bonding type rmsd covalent geometry : bond 0.01133 (16083) covalent geometry : angle 1.96341 (21819) SS BOND : bond 0.02193 ( 18) SS BOND : angle 2.79848 ( 36) hydrogen bonds : bond 0.16240 ( 649) hydrogen bonds : angle 7.78026 ( 1914) link_BETA1-4 : bond 0.04007 ( 12) link_BETA1-4 : angle 5.81598 ( 36) link_NAG-ASN : bond 0.01671 ( 12) link_NAG-ASN : angle 5.79384 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 239 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 3 residues processed: 253 average time/residue: 0.7604 time to fit residues: 206.6541 Evaluate side-chains 162 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 159 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 63 ASP Chi-restraints excluded: chain f residue 18 LEU Chi-restraints excluded: chain A residue 99 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 60 ASN A 243 HIS B 95 HIS C 365 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.107166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.068059 restraints weight = 29820.743| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.57 r_work: 0.2879 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 16125 Z= 0.154 Angle : 0.719 14.029 21927 Z= 0.373 Chirality : 0.047 0.218 2457 Planarity : 0.004 0.036 2802 Dihedral : 5.912 103.711 2688 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.30 % Allowed : 10.41 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.18), residues: 1905 helix: 1.05 (0.30), residues: 279 sheet: -0.28 (0.19), residues: 594 loop : -0.40 (0.17), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 313 TYR 0.016 0.001 TYR C 603 PHE 0.016 0.002 PHE B 282 TRP 0.012 0.002 TRP A 525 HIS 0.007 0.001 HIS C 509 Details of bonding type rmsd covalent geometry : bond 0.00344 (16083) covalent geometry : angle 0.68970 (21819) SS BOND : bond 0.00816 ( 18) SS BOND : angle 1.85735 ( 36) hydrogen bonds : bond 0.04824 ( 649) hydrogen bonds : angle 6.06705 ( 1914) link_BETA1-4 : bond 0.00373 ( 12) link_BETA1-4 : angle 2.62008 ( 36) link_NAG-ASN : bond 0.00571 ( 12) link_NAG-ASN : angle 4.02041 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.626 Fit side-chains REVERT: d 41 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7363 (tp-100) REVERT: d 74 ASP cc_start: 0.8157 (t70) cc_final: 0.7755 (t0) REVERT: e 74 ASP cc_start: 0.8019 (t0) cc_final: 0.7655 (t0) REVERT: e 104 MET cc_start: 0.8549 (ttp) cc_final: 0.8346 (ttp) REVERT: f 3 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8591 (mp10) REVERT: f 41 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7321 (tp40) REVERT: f 74 ASP cc_start: 0.8124 (t70) cc_final: 0.7669 (t0) REVERT: f 90 GLU cc_start: 0.9098 (mp0) cc_final: 0.8888 (pm20) REVERT: A 123 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7865 (mp0) REVERT: A 272 ASP cc_start: 0.8553 (m-30) cc_final: 0.8101 (m-30) REVERT: A 512 ARG cc_start: 0.8486 (mmm160) cc_final: 0.8005 (tpm-80) REVERT: B 127 ARG cc_start: 0.8491 (ttp80) cc_final: 0.8139 (tpm170) REVERT: B 616 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8305 (mt-10) REVERT: C 228 GLU cc_start: 0.8823 (pt0) cc_final: 0.8538 (pp20) outliers start: 38 outliers final: 17 residues processed: 198 average time/residue: 0.8138 time to fit residues: 174.7453 Evaluate side-chains 175 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 56 ARG Chi-restraints excluded: chain d residue 63 ASP Chi-restraints excluded: chain d residue 94 VAL Chi-restraints excluded: chain e residue 5 VAL Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain f residue 41 GLN Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 359 CYS Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 564 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 38 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 152 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 182 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS B 219 HIS C 95 HIS C 219 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.105077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.065655 restraints weight = 30545.722| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.63 r_work: 0.2821 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 16125 Z= 0.278 Angle : 0.712 14.647 21927 Z= 0.367 Chirality : 0.049 0.211 2457 Planarity : 0.005 0.060 2802 Dihedral : 5.582 42.736 2684 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.84 % Allowed : 12.52 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.18), residues: 1905 helix: 1.43 (0.30), residues: 282 sheet: 0.01 (0.20), residues: 600 loop : -0.33 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 131 TYR 0.021 0.002 TYR B 603 PHE 0.019 0.002 PHE A 282 TRP 0.015 0.002 TRP d 101 HIS 0.006 0.001 HIS C 509 Details of bonding type rmsd covalent geometry : bond 0.00672 (16083) covalent geometry : angle 0.68755 (21819) SS BOND : bond 0.01016 ( 18) SS BOND : angle 1.93035 ( 36) hydrogen bonds : bond 0.04637 ( 649) hydrogen bonds : angle 5.82461 ( 1914) link_BETA1-4 : bond 0.00409 ( 12) link_BETA1-4 : angle 2.26498 ( 36) link_NAG-ASN : bond 0.00323 ( 12) link_NAG-ASN : angle 3.64021 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 0.518 Fit side-chains REVERT: d 41 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7345 (tp-100) REVERT: d 74 ASP cc_start: 0.8117 (t70) cc_final: 0.7717 (t0) REVERT: e 5 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8556 (m) REVERT: e 74 ASP cc_start: 0.8149 (t0) cc_final: 0.7659 (t0) REVERT: e 112 ARG cc_start: 0.8761 (ttm110) cc_final: 0.8506 (ttm-80) REVERT: f 3 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8660 (mp10) REVERT: f 74 ASP cc_start: 0.8167 (t70) cc_final: 0.7747 (t0) REVERT: f 90 GLU cc_start: 0.9198 (mp0) cc_final: 0.8908 (pm20) REVERT: A 272 ASP cc_start: 0.8529 (m-30) cc_final: 0.8111 (m-30) REVERT: A 512 ARG cc_start: 0.8517 (mmm160) cc_final: 0.7922 (tpm-80) REVERT: B 616 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8482 (mt-10) REVERT: C 92 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8771 (tt) REVERT: C 228 GLU cc_start: 0.8858 (pt0) cc_final: 0.8575 (pp20) REVERT: C 272 ASP cc_start: 0.8573 (m-30) cc_final: 0.8193 (m-30) REVERT: C 361 MET cc_start: 0.8278 (mmt) cc_final: 0.8023 (mmt) outliers start: 47 outliers final: 24 residues processed: 188 average time/residue: 0.7917 time to fit residues: 159.4570 Evaluate side-chains 172 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 65 VAL Chi-restraints excluded: chain d residue 94 VAL Chi-restraints excluded: chain e residue 5 VAL Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 94 VAL Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 359 CYS Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 564 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 183 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS A 243 HIS B 504 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.106754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.067612 restraints weight = 29818.229| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.63 r_work: 0.2840 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 : 0.003 0.041 16125 Z= 0.145 Angle : 0.625 14.086 21927 Z= 0.316 Chirality : 0.044 0.209 2457 Planarity : 0.004 0.065 2802 Dihedral : 5.117 40.061 2682 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.09 % Allowed : 12.89 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.18), residues: 1905 helix: 1.67 (0.30), residues: 282 sheet: 0.23 (0.20), residues: 591 loop : -0.24 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 131 TYR 0.028 0.001 TYR B 424 PHE 0.038 0.001 PHE B 505 TRP 0.011 0.001 TRP d 101 HIS 0.005 0.001 HIS C 509 Details of bonding type rmsd covalent geometry : bond 0.00333 (16083) covalent geometry : angle 0.60302 (21819) SS BOND : bond 0.00559 ( 18) SS BOND : angle 1.39747 ( 36) hydrogen bonds : bond 0.03936 ( 649) hydrogen bonds : angle 5.47896 ( 1914) link_BETA1-4 : bond 0.00333 ( 12) link_BETA1-4 : angle 1.98999 ( 36) link_NAG-ASN : bond 0.00407 ( 12) link_NAG-ASN : angle 3.39457 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 159 time to evaluate : 0.394 Fit side-chains REVERT: d 41 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7253 (tp-100) REVERT: d 74 ASP cc_start: 0.8107 (t70) cc_final: 0.7645 (t0) REVERT: d 79 THR cc_start: 0.9043 (m) cc_final: 0.8789 (t) REVERT: d 88 LYS cc_start: 0.8353 (mtpt) cc_final: 0.8040 (mtpm) REVERT: d 90 GLU cc_start: 0.8950 (pm20) cc_final: 0.8514 (pm20) REVERT: e 74 ASP cc_start: 0.8182 (t0) cc_final: 0.7672 (t0) REVERT: e 90 GLU cc_start: 0.9059 (pm20) cc_final: 0.8843 (pm20) REVERT: f 3 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8633 (mp10) REVERT: f 41 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7209 (tp-100) REVERT: f 74 ASP cc_start: 0.8149 (t70) cc_final: 0.7716 (t0) REVERT: f 90 GLU cc_start: 0.9217 (mp0) cc_final: 0.8969 (pm20) REVERT: A 272 ASP cc_start: 0.8448 (m-30) cc_final: 0.8081 (m-30) REVERT: A 512 ARG cc_start: 0.8481 (mmm160) cc_final: 0.8008 (tpm-80) REVERT: A 560 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7690 (mmm) REVERT: B 126 ARG cc_start: 0.7878 (ptt-90) cc_final: 0.7095 (pmt170) REVERT: B 135 GLN cc_start: 0.7434 (mm-40) cc_final: 0.7212 (mp10) REVERT: B 616 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8492 (mt-10) REVERT: C 97 ARG cc_start: 0.8938 (mmp-170) cc_final: 0.8732 (mmm160) REVERT: C 126 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7652 (pmt170) REVERT: C 228 GLU cc_start: 0.8876 (pt0) cc_final: 0.8596 (pp20) REVERT: C 272 ASP cc_start: 0.8509 (m-30) cc_final: 0.8186 (m-30) outliers start: 51 outliers final: 24 residues processed: 199 average time/residue: 0.8018 time to fit residues: 172.0876 Evaluate side-chains 176 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 49 LEU Chi-restraints excluded: chain d residue 94 VAL Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain f residue 41 GLN Chi-restraints excluded: chain f residue 94 VAL Chi-restraints excluded: chain f residue 114 THR Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 564 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 44 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 186 optimal weight: 0.4980 chunk 161 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 189 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS A 243 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.106574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.067343 restraints weight = 30274.547| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.62 r_work: 0.2852 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16125 Z= 0.156 Angle : 0.620 13.842 21927 Z= 0.312 Chirality : 0.044 0.226 2457 Planarity : 0.004 0.049 2802 Dihedral : 4.971 37.843 2682 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.15 % Allowed : 13.55 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.18), residues: 1905 helix: 1.82 (0.30), residues: 282 sheet: 0.28 (0.20), residues: 612 loop : -0.29 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 131 TYR 0.021 0.001 TYR B 424 PHE 0.014 0.001 PHE B 505 TRP 0.011 0.001 TRP d 101 HIS 0.014 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00366 (16083) covalent geometry : angle 0.59952 (21819) SS BOND : bond 0.00578 ( 18) SS BOND : angle 1.42158 ( 36) hydrogen bonds : bond 0.03790 ( 649) hydrogen bonds : angle 5.31566 ( 1914) link_BETA1-4 : bond 0.00311 ( 12) link_BETA1-4 : angle 1.89473 ( 36) link_NAG-ASN : bond 0.00365 ( 12) link_NAG-ASN : angle 3.29932 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 0.718 Fit side-chains REVERT: d 74 ASP cc_start: 0.8133 (t70) cc_final: 0.7703 (t0) REVERT: d 88 LYS cc_start: 0.8318 (mtpt) cc_final: 0.8012 (mtpm) REVERT: d 90 GLU cc_start: 0.8939 (pm20) cc_final: 0.8558 (pm20) REVERT: e 74 ASP cc_start: 0.8246 (t0) cc_final: 0.7722 (t0) REVERT: e 90 GLU cc_start: 0.9093 (pm20) cc_final: 0.8857 (pm20) REVERT: f 3 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8615 (mp10) REVERT: f 41 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7270 (tp-100) REVERT: f 74 ASP cc_start: 0.8209 (t70) cc_final: 0.7746 (t0) REVERT: f 90 GLU cc_start: 0.9235 (mp0) cc_final: 0.8919 (pm20) REVERT: A 272 ASP cc_start: 0.8444 (m-30) cc_final: 0.8096 (m-30) REVERT: A 512 ARG cc_start: 0.8489 (mmm160) cc_final: 0.8018 (tpm-80) REVERT: A 560 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7772 (mmm) REVERT: B 126 ARG cc_start: 0.7890 (ptt-90) cc_final: 0.7366 (pmt170) REVERT: B 127 ARG cc_start: 0.8496 (ttp80) cc_final: 0.8151 (tpm170) REVERT: B 135 GLN cc_start: 0.7440 (mm-40) cc_final: 0.7201 (mp10) REVERT: B 281 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8658 (mp0) REVERT: B 616 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8446 (mt-10) REVERT: C 97 ARG cc_start: 0.8901 (mmp-170) cc_final: 0.8693 (mmm160) REVERT: C 126 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7720 (pmt170) REVERT: C 228 GLU cc_start: 0.8901 (pt0) cc_final: 0.8576 (pp20) REVERT: C 272 ASP cc_start: 0.8494 (m-30) cc_final: 0.8197 (m-30) outliers start: 52 outliers final: 28 residues processed: 194 average time/residue: 0.8667 time to fit residues: 181.2458 Evaluate side-chains 181 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 94 VAL Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 41 GLN Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 94 VAL Chi-restraints excluded: chain f residue 114 THR Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 564 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 155 optimal weight: 1.9990 chunk 174 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 167 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 61 optimal weight: 0.0970 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS A 243 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.105249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.066120 restraints weight = 30233.097| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.59 r_work: 0.2776 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 16125 Z= 0.231 Angle : 0.656 15.267 21927 Z= 0.332 Chirality : 0.046 0.237 2457 Planarity : 0.004 0.037 2802 Dihedral : 5.048 36.676 2682 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.27 % Allowed : 13.73 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.18), residues: 1905 helix: 1.94 (0.30), residues: 282 sheet: 0.25 (0.20), residues: 615 loop : -0.35 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 131 TYR 0.020 0.001 TYR B 424 PHE 0.016 0.002 PHE C 282 TRP 0.010 0.001 TRP d 101 HIS 0.004 0.001 HIS C 509 Details of bonding type rmsd covalent geometry : bond 0.00554 (16083) covalent geometry : angle 0.63591 (21819) SS BOND : bond 0.00619 ( 18) SS BOND : angle 1.63012 ( 36) hydrogen bonds : bond 0.04039 ( 649) hydrogen bonds : angle 5.31850 ( 1914) link_BETA1-4 : bond 0.00302 ( 12) link_BETA1-4 : angle 1.81771 ( 36) link_NAG-ASN : bond 0.00320 ( 12) link_NAG-ASN : angle 3.30281 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 142 time to evaluate : 0.633 Fit side-chains REVERT: d 41 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7355 (tp-100) REVERT: d 74 ASP cc_start: 0.8037 (t70) cc_final: 0.7604 (t0) REVERT: d 88 LYS cc_start: 0.8282 (mtpt) cc_final: 0.8000 (mtpm) REVERT: d 90 GLU cc_start: 0.8975 (pm20) cc_final: 0.8598 (pm20) REVERT: e 41 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7187 (tp-100) REVERT: e 74 ASP cc_start: 0.8242 (t0) cc_final: 0.7723 (t0) REVERT: e 90 GLU cc_start: 0.9297 (pm20) cc_final: 0.9092 (pm20) REVERT: f 3 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8592 (mp10) REVERT: f 41 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7190 (mm-40) REVERT: f 74 ASP cc_start: 0.8156 (t70) cc_final: 0.7621 (t0) REVERT: f 90 GLU cc_start: 0.9260 (mp0) cc_final: 0.8908 (pm20) REVERT: A 272 ASP cc_start: 0.8449 (m-30) cc_final: 0.8084 (m-30) REVERT: A 560 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7792 (tpp) REVERT: B 126 ARG cc_start: 0.7913 (ptt-90) cc_final: 0.7412 (pmt170) REVERT: B 127 ARG cc_start: 0.8510 (ttp80) cc_final: 0.8150 (ttp80) REVERT: B 135 GLN cc_start: 0.7398 (mm-40) cc_final: 0.6968 (mp10) REVERT: B 238 THR cc_start: 0.8785 (m) cc_final: 0.8572 (p) REVERT: B 616 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8452 (mt-10) REVERT: C 126 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7680 (pmt170) REVERT: C 228 GLU cc_start: 0.8920 (pt0) cc_final: 0.8567 (pp20) REVERT: C 272 ASP cc_start: 0.8493 (m-30) cc_final: 0.8194 (m-30) outliers start: 54 outliers final: 29 residues processed: 182 average time/residue: 0.7914 time to fit residues: 155.3244 Evaluate side-chains 176 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 94 VAL Chi-restraints excluded: chain e residue 41 GLN Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 41 GLN Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 94 VAL Chi-restraints excluded: chain f residue 114 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 564 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 178 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 177 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS A 243 HIS B 95 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.106540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.067583 restraints weight = 29993.449| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.59 r_work: 0.2805 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16125 Z= 0.141 Angle : 0.610 16.299 21927 Z= 0.307 Chirality : 0.043 0.244 2457 Planarity : 0.004 0.054 2802 Dihedral : 4.829 35.629 2682 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.42 % Allowed : 15.25 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.19), residues: 1905 helix: 2.03 (0.30), residues: 282 sheet: 0.35 (0.20), residues: 615 loop : -0.27 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG A 512 TYR 0.017 0.001 TYR B 424 PHE 0.013 0.001 PHE B 282 TRP 0.011 0.001 TRP d 101 HIS 0.004 0.001 HIS C 509 Details of bonding type rmsd covalent geometry : bond 0.00333 (16083) covalent geometry : angle 0.59021 (21819) SS BOND : bond 0.00571 ( 18) SS BOND : angle 1.49548 ( 36) hydrogen bonds : bond 0.03641 ( 649) hydrogen bonds : angle 5.15858 ( 1914) link_BETA1-4 : bond 0.00335 ( 12) link_BETA1-4 : angle 1.72453 ( 36) link_NAG-ASN : bond 0.00403 ( 12) link_NAG-ASN : angle 3.18042 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.641 Fit side-chains REVERT: d 41 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7307 (tp-100) REVERT: d 56 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7457 (mpp-170) REVERT: d 74 ASP cc_start: 0.8072 (t70) cc_final: 0.7656 (t0) REVERT: d 88 LYS cc_start: 0.8257 (mtpt) cc_final: 0.7978 (mtpm) REVERT: d 90 GLU cc_start: 0.8991 (pm20) cc_final: 0.8626 (pm20) REVERT: e 41 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7182 (tp-100) REVERT: e 74 ASP cc_start: 0.8246 (t0) cc_final: 0.7730 (t0) REVERT: f 3 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8599 (mp10) REVERT: f 41 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7158 (mm-40) REVERT: f 74 ASP cc_start: 0.8159 (t70) cc_final: 0.7640 (t0) REVERT: f 90 GLU cc_start: 0.9263 (mp0) cc_final: 0.8891 (pm20) REVERT: A 127 ARG cc_start: 0.8831 (ptm-80) cc_final: 0.8528 (ttp80) REVERT: A 272 ASP cc_start: 0.8389 (m-30) cc_final: 0.8084 (m-30) REVERT: A 512 ARG cc_start: 0.8383 (mmm160) cc_final: 0.7818 (tpm-80) REVERT: A 560 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7703 (mmm) REVERT: B 126 ARG cc_start: 0.7967 (ptt-90) cc_final: 0.7450 (pmt170) REVERT: B 127 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8084 (tpm170) REVERT: B 135 GLN cc_start: 0.7389 (mm-40) cc_final: 0.6958 (mp10) REVERT: B 616 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8454 (mt-10) REVERT: B 670 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8027 (tp) REVERT: C 126 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7613 (pmt170) REVERT: C 228 GLU cc_start: 0.8983 (pt0) cc_final: 0.8593 (pp20) REVERT: C 272 ASP cc_start: 0.8432 (m-30) cc_final: 0.8170 (m-30) outliers start: 40 outliers final: 22 residues processed: 180 average time/residue: 0.7941 time to fit residues: 154.1958 Evaluate side-chains 173 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 56 ARG Chi-restraints excluded: chain d residue 94 VAL Chi-restraints excluded: chain e residue 41 GLN Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 41 GLN Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 94 VAL Chi-restraints excluded: chain f residue 114 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 664 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 27 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 1 GLN A 243 HIS B 95 HIS B 513 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.104711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.065755 restraints weight = 30414.131| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.58 r_work: 0.2826 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 16125 Z= 0.263 Angle : 0.684 19.173 21927 Z= 0.344 Chirality : 0.046 0.247 2457 Planarity : 0.004 0.046 2802 Dihedral : 5.056 35.907 2682 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.27 % Allowed : 14.46 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.19), residues: 1905 helix: 2.03 (0.30), residues: 282 sheet: 0.28 (0.20), residues: 615 loop : -0.37 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 512 TYR 0.018 0.001 TYR B 424 PHE 0.017 0.002 PHE C 282 TRP 0.009 0.001 TRP d 101 HIS 0.005 0.001 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.00630 (16083) covalent geometry : angle 0.66402 (21819) SS BOND : bond 0.00637 ( 18) SS BOND : angle 1.96475 ( 36) hydrogen bonds : bond 0.04122 ( 649) hydrogen bonds : angle 5.30455 ( 1914) link_BETA1-4 : bond 0.00307 ( 12) link_BETA1-4 : angle 1.69778 ( 36) link_NAG-ASN : bond 0.00330 ( 12) link_NAG-ASN : angle 3.26942 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 141 time to evaluate : 0.521 Fit side-chains REVERT: d 41 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7310 (tp-100) REVERT: d 56 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7612 (mpp-170) REVERT: d 74 ASP cc_start: 0.8093 (t70) cc_final: 0.7656 (t0) REVERT: e 41 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7213 (tp-100) REVERT: e 74 ASP cc_start: 0.8311 (t0) cc_final: 0.7801 (t0) REVERT: f 3 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8607 (mp10) REVERT: f 41 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7206 (mm-40) REVERT: f 74 ASP cc_start: 0.8207 (t70) cc_final: 0.7670 (t0) REVERT: f 90 GLU cc_start: 0.9229 (mp0) cc_final: 0.8890 (pm20) REVERT: A 127 ARG cc_start: 0.8762 (ptm-80) cc_final: 0.8441 (ttp80) REVERT: A 272 ASP cc_start: 0.8461 (m-30) cc_final: 0.8094 (m-30) REVERT: A 512 ARG cc_start: 0.8399 (mmm160) cc_final: 0.7922 (tpm-80) REVERT: A 560 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7851 (tpp) REVERT: B 127 ARG cc_start: 0.8529 (ttp80) cc_final: 0.8324 (ttp80) REVERT: B 135 GLN cc_start: 0.7504 (mm-40) cc_final: 0.7034 (mp10) REVERT: B 238 THR cc_start: 0.8828 (m) cc_final: 0.8602 (p) REVERT: B 616 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8451 (mt-10) REVERT: B 670 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8120 (tp) REVERT: C 126 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7648 (pmt170) REVERT: C 228 GLU cc_start: 0.8931 (pt0) cc_final: 0.8559 (pp20) REVERT: C 272 ASP cc_start: 0.8504 (m-30) cc_final: 0.8204 (m-30) outliers start: 54 outliers final: 30 residues processed: 184 average time/residue: 0.7683 time to fit residues: 152.8041 Evaluate side-chains 174 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 56 ARG Chi-restraints excluded: chain d residue 94 VAL Chi-restraints excluded: chain e residue 41 GLN Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 41 GLN Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 94 VAL Chi-restraints excluded: chain f residue 114 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 664 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 75 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 127 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 chunk 189 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 60 ASN A 219 HIS A 243 HIS B 95 HIS C 509 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.106308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.067540 restraints weight = 30297.184| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.59 r_work: 0.2809 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16125 Z= 0.137 Angle : 0.629 18.530 21927 Z= 0.313 Chirality : 0.043 0.254 2457 Planarity : 0.004 0.040 2802 Dihedral : 4.789 35.683 2682 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.36 % Allowed : 15.43 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.19), residues: 1905 helix: 2.11 (0.30), residues: 282 sheet: 0.40 (0.21), residues: 615 loop : -0.29 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 512 TYR 0.017 0.001 TYR C 375 PHE 0.013 0.001 PHE A 282 TRP 0.011 0.001 TRP e 101 HIS 0.005 0.001 HIS B 513 Details of bonding type rmsd covalent geometry : bond 0.00321 (16083) covalent geometry : angle 0.61249 (21819) SS BOND : bond 0.00513 ( 18) SS BOND : angle 1.27543 ( 36) hydrogen bonds : bond 0.03603 ( 649) hydrogen bonds : angle 5.12403 ( 1914) link_BETA1-4 : bond 0.00328 ( 12) link_BETA1-4 : angle 1.62761 ( 36) link_NAG-ASN : bond 0.00403 ( 12) link_NAG-ASN : angle 3.11112 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.694 Fit side-chains REVERT: d 41 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7305 (tp-100) REVERT: d 74 ASP cc_start: 0.8118 (t70) cc_final: 0.7696 (t0) REVERT: e 13 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7907 (pm20) REVERT: e 41 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7250 (tp-100) REVERT: e 74 ASP cc_start: 0.8307 (t0) cc_final: 0.7814 (t0) REVERT: f 3 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8596 (mp10) REVERT: f 41 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7197 (mm-40) REVERT: f 74 ASP cc_start: 0.8229 (t70) cc_final: 0.7697 (t0) REVERT: f 90 GLU cc_start: 0.9266 (mp0) cc_final: 0.8891 (pm20) REVERT: f 109 LYS cc_start: 0.8408 (mmmt) cc_final: 0.8182 (mppt) REVERT: A 127 ARG cc_start: 0.8747 (ptm-80) cc_final: 0.8409 (tpp80) REVERT: A 272 ASP cc_start: 0.8438 (m-30) cc_final: 0.8138 (m-30) REVERT: A 512 ARG cc_start: 0.8424 (mmm160) cc_final: 0.7991 (tpm-80) REVERT: A 560 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7827 (tpp) REVERT: B 127 ARG cc_start: 0.8476 (ttp80) cc_final: 0.8266 (ttp80) REVERT: B 135 GLN cc_start: 0.7433 (mm-40) cc_final: 0.6982 (mp10) REVERT: B 238 THR cc_start: 0.8814 (m) cc_final: 0.8602 (p) REVERT: B 616 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8482 (mt-10) REVERT: B 670 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8118 (tp) REVERT: C 126 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7683 (pmt170) REVERT: C 228 GLU cc_start: 0.8950 (pt0) cc_final: 0.8570 (pp20) REVERT: C 272 ASP cc_start: 0.8444 (m-30) cc_final: 0.8186 (m-30) outliers start: 39 outliers final: 26 residues processed: 180 average time/residue: 0.6946 time to fit residues: 135.6878 Evaluate side-chains 174 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 63 ASP Chi-restraints excluded: chain d residue 94 VAL Chi-restraints excluded: chain e residue 41 GLN Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 41 GLN Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 94 VAL Chi-restraints excluded: chain f residue 114 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 48 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 110 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 1 GLN f 1 GLN A 219 HIS A 243 HIS B 95 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.106471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.067749 restraints weight = 30133.567| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.58 r_work: 0.2815 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16125 Z= 0.133 Angle : 0.624 19.185 21927 Z= 0.312 Chirality : 0.043 0.254 2457 Planarity : 0.004 0.061 2802 Dihedral : 4.718 35.368 2682 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.18 % Allowed : 15.79 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.19), residues: 1905 helix: 2.15 (0.30), residues: 282 sheet: 0.50 (0.21), residues: 612 loop : -0.25 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG e 112 TYR 0.015 0.001 TYR B 375 PHE 0.013 0.001 PHE A 282 TRP 0.009 0.001 TRP d 101 HIS 0.007 0.001 HIS C 509 Details of bonding type rmsd covalent geometry : bond 0.00312 (16083) covalent geometry : angle 0.60697 (21819) SS BOND : bond 0.00480 ( 18) SS BOND : angle 1.27510 ( 36) hydrogen bonds : bond 0.03533 ( 649) hydrogen bonds : angle 5.08479 ( 1914) link_BETA1-4 : bond 0.00341 ( 12) link_BETA1-4 : angle 1.61457 ( 36) link_NAG-ASN : bond 0.00395 ( 12) link_NAG-ASN : angle 3.08839 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.765 Fit side-chains REVERT: d 41 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7333 (tp-100) REVERT: d 74 ASP cc_start: 0.8117 (t70) cc_final: 0.7665 (t0) REVERT: d 79 THR cc_start: 0.9018 (m) cc_final: 0.8513 (p) REVERT: e 41 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7265 (tp-100) REVERT: e 74 ASP cc_start: 0.8323 (t0) cc_final: 0.7790 (t0) REVERT: e 79 THR cc_start: 0.8951 (m) cc_final: 0.8373 (p) REVERT: e 109 LYS cc_start: 0.8448 (mmmt) cc_final: 0.8080 (mmtm) REVERT: e 112 ARG cc_start: 0.8772 (mtp-110) cc_final: 0.8570 (ttm110) REVERT: f 3 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8594 (mp10) REVERT: f 41 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7165 (mm-40) REVERT: f 74 ASP cc_start: 0.8234 (t70) cc_final: 0.7704 (t0) REVERT: f 90 GLU cc_start: 0.9267 (mp0) cc_final: 0.8894 (pm20) REVERT: f 109 LYS cc_start: 0.8500 (mmmt) cc_final: 0.8199 (mppt) REVERT: A 127 ARG cc_start: 0.8743 (ptm-80) cc_final: 0.8415 (tpp80) REVERT: A 272 ASP cc_start: 0.8420 (m-30) cc_final: 0.8137 (m-30) REVERT: A 512 ARG cc_start: 0.8415 (mmm160) cc_final: 0.7972 (tpm-80) REVERT: A 560 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7860 (tpp) REVERT: B 126 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7712 (pmt170) REVERT: B 127 ARG cc_start: 0.8482 (ttp80) cc_final: 0.8271 (ttp80) REVERT: B 135 GLN cc_start: 0.7442 (mm-40) cc_final: 0.6992 (mp10) REVERT: B 616 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8472 (mt-10) REVERT: B 670 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8083 (tp) REVERT: C 126 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7721 (pmt170) REVERT: C 228 GLU cc_start: 0.8953 (pt0) cc_final: 0.8563 (pp20) REVERT: C 272 ASP cc_start: 0.8402 (m-30) cc_final: 0.8179 (m-30) outliers start: 36 outliers final: 26 residues processed: 175 average time/residue: 0.7978 time to fit residues: 151.0610 Evaluate side-chains 177 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 94 VAL Chi-restraints excluded: chain e residue 41 GLN Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 41 GLN Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 94 VAL Chi-restraints excluded: chain f residue 114 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 76 optimal weight: 0.0980 chunk 143 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS B 95 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.105595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.066835 restraints weight = 30118.876| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.58 r_work: 0.2791 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16125 Z= 0.194 Angle : 0.648 19.120 21927 Z= 0.325 Chirality : 0.044 0.259 2457 Planarity : 0.004 0.059 2802 Dihedral : 4.801 35.431 2682 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.54 % Allowed : 15.79 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.19), residues: 1905 helix: 2.15 (0.30), residues: 282 sheet: 0.46 (0.21), residues: 612 loop : -0.29 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG e 112 TYR 0.016 0.001 TYR C 375 PHE 0.015 0.001 PHE C 282 TRP 0.010 0.001 TRP d 101 HIS 0.007 0.001 HIS C 509 Details of bonding type rmsd covalent geometry : bond 0.00465 (16083) covalent geometry : angle 0.63109 (21819) SS BOND : bond 0.00535 ( 18) SS BOND : angle 1.47431 ( 36) hydrogen bonds : bond 0.03744 ( 649) hydrogen bonds : angle 5.14251 ( 1914) link_BETA1-4 : bond 0.00314 ( 12) link_BETA1-4 : angle 1.58801 ( 36) link_NAG-ASN : bond 0.00336 ( 12) link_NAG-ASN : angle 3.11675 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5853.81 seconds wall clock time: 100 minutes 21.14 seconds (6021.14 seconds total)