Starting phenix.real_space_refine on Thu Feb 5 03:53:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ih8_52863/02_2026/9ih8_52863.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ih8_52863/02_2026/9ih8_52863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ih8_52863/02_2026/9ih8_52863.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ih8_52863/02_2026/9ih8_52863.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ih8_52863/02_2026/9ih8_52863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ih8_52863/02_2026/9ih8_52863.map" } resolution = 2.21 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= 0.016 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 69 5.16 5 C 9129 2.51 5 N 2517 2.21 5 O 2772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 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: 14487 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4745 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 560} Chain breaks: 1 Chain: "B" Number of atoms: 4745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4745 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 560} Chain breaks: 1 Chain: "C" Number of atoms: 4745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4745 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 560} Chain breaks: 1 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 Time building chain proxies: 3.50, per 1000 atoms: 0.24 Number of scatterers: 14487 At special positions: 0 Unit cell: (93.79, 97.94, 179.28, 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 69 16.00 O 2772 8.00 N 2517 7.00 C 9129 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 570 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 526 " distance=2.07 Simple disulfide: pdb=" SG CYS A 202 " - pdb=" SG CYS A 266 " distance=2.05 Simple disulfide: pdb=" SG CYS A 359 " - pdb=" SG CYS A 407 " distance=2.04 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=2.06 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 526 " distance=2.06 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=2.04 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-ASN " NAG D 1 " - " ASN B 671 " " NAG E 1 " - " ASN C 671 " " NAG F 1 " - " ASN A 671 " " NAG G 1 " - " ASN B 393 " " NAG H 1 " - " ASN C 393 " " NAG I 1 " - " ASN A 393 " " NAG J 1 " - " ASN A 136 " " NAG K 1 " - " ASN B 136 " " NAG L 1 " - " ASN C 136 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 512.5 milliseconds 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3342 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 32 sheets defined 25.0% alpha, 40.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 301 through 305 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 353 through 358 removed outlier: 3.739A pdb=" N ALA A 357 " --> pdb=" O PRO A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 405 through 424 removed outlier: 4.323A pdb=" N GLY A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 498 through 543 removed outlier: 3.577A pdb=" N LEU A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR A 534 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU A 535 " --> pdb=" O HIS A 531 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A 538 " --> pdb=" O THR A 534 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LYS A 541 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 3.899A 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 659 through 661 No H-bonds generated for 'chain 'A' and resid 659 through 661' Processing helix chain 'A' and resid 687 through 694 Processing helix chain 'A' and resid 698 through 708 Processing helix chain 'A' and resid 708 through 714 Processing helix chain 'B' and resid 188 through 195 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 220 through 222 No H-bonds generated for 'chain 'B' and resid 220 through 222' Processing helix chain 'B' and resid 301 through 305 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 353 through 358 removed outlier: 3.729A pdb=" N ALA B 357 " --> pdb=" O PRO B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 402 Processing helix chain 'B' and resid 405 through 424 removed outlier: 4.256A pdb=" N GLY B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 456 No H-bonds generated for 'chain 'B' and resid 454 through 456' Processing helix chain 'B' and resid 498 through 543 removed outlier: 3.583A pdb=" N LEU B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR B 534 " --> pdb=" O ASN B 530 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU B 535 " --> pdb=" O HIS B 531 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU B 538 " --> pdb=" O THR B 534 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS B 541 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 3.877A 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 687 through 694 Processing helix chain 'B' and resid 698 through 708 Processing helix chain 'B' and resid 708 through 714 Processing helix chain 'C' and resid 188 through 195 Processing helix chain 'C' and resid 195 through 200 Processing helix chain 'C' and resid 220 through 222 No H-bonds generated for 'chain 'C' and resid 220 through 222' Processing helix chain 'C' and resid 301 through 305 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 353 through 358 removed outlier: 3.745A pdb=" N ALA C 357 " --> pdb=" O PRO C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 402 Processing helix chain 'C' and resid 405 through 424 removed outlier: 4.334A pdb=" N GLY C 409 " --> pdb=" O GLY C 405 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 543 removed outlier: 3.519A pdb=" N LEU C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR C 534 " --> pdb=" O ASN C 530 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU C 535 " --> pdb=" O HIS C 531 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU C 538 " --> pdb=" O THR C 534 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LYS C 541 " --> pdb=" O ASN C 537 " (cutoff:3.500A) removed outlier: 3.923A 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 687 through 694 Processing helix chain 'C' and resid 698 through 708 removed outlier: 3.506A pdb=" N LEU C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 714 Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 110 Processing sheet with id=AA2, first strand: chain 'A' and resid 556 through 560 removed outlier: 6.865A pdb=" N VAL A 119 " --> pdb=" O THR C 662 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL C 664 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLN A 121 " --> pdb=" O VAL C 664 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 367 removed outlier: 5.427A pdb=" N LYS A 363 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LYS A 146 " --> pdb=" O LYS A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 361 through 367 removed outlier: 5.427A pdb=" N LYS A 363 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LYS A 146 " --> pdb=" O LYS A 363 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 174 through 186 removed outlier: 3.554A pdb=" N TYR A 174 " --> pdb=" O GLY A 171 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN A 167 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE A 180 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL A 165 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU A 182 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A 163 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG A 184 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LYS A 161 " --> pdb=" O ARG A 184 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N TYR A 159 " --> pdb=" O PRO A 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 230 through 231 removed outlier: 7.326A pdb=" N LYS A 155 " --> pdb=" O ASP A 350 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP A 350 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N THR A 335 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AA8, first strand: chain 'A' and resid 205 through 210 Processing sheet with id=AA9, first strand: chain 'A' and resid 370 through 375 Processing sheet with id=AB1, first strand: chain 'A' and resid 578 through 580 Processing sheet with id=AB2, first strand: chain 'A' and resid 592 through 594 Processing sheet with id=AB3, first strand: chain 'A' and resid 635 through 640 removed outlier: 3.535A pdb=" N HIS A 654 " --> pdb=" O TYR A 646 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLU A 648 " --> pdb=" O TYR A 652 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 662 through 664 removed outlier: 3.817A pdb=" N THR A 662 " --> pdb=" O VAL B 119 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 571 through 573 removed outlier: 6.549A pdb=" N TYR B 109 " --> pdb=" O LEU B 620 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 388 through 392 removed outlier: 5.414A pdb=" N LYS B 363 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LYS B 146 " --> pdb=" O LYS B 363 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU B 369 " --> pdb=" O GLY B 140 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY B 140 " --> pdb=" O GLU B 369 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU B 371 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR B 138 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU B 139 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 388 through 392 removed outlier: 5.414A pdb=" N LYS B 363 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LYS B 146 " --> pdb=" O LYS B 363 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU B 369 " --> pdb=" O GLY B 140 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY B 140 " --> pdb=" O GLU B 369 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU B 371 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR B 138 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU B 139 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 174 through 186 removed outlier: 5.168A pdb=" N SER B 175 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY B 171 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N PHE B 177 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TRP B 169 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY B 179 " --> pdb=" O GLN B 167 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 230 through 231 removed outlier: 7.372A pdb=" N LYS B 155 " --> pdb=" O ASP B 350 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ASP B 350 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THR B 335 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AC2, first strand: chain 'B' and resid 205 through 210 Processing sheet with id=AC3, first strand: chain 'B' and resid 592 through 594 Processing sheet with id=AC4, first strand: chain 'B' and resid 635 through 640 removed outlier: 3.566A pdb=" N HIS B 654 " --> pdb=" O TYR B 646 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLU B 648 " --> pdb=" O TYR B 652 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TYR B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 662 through 664 removed outlier: 3.725A pdb=" N THR B 662 " --> pdb=" O VAL C 119 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 108 through 110 Processing sheet with id=AC7, first strand: chain 'C' and resid 428 through 430 removed outlier: 6.298A pdb=" N LEU C 438 " --> pdb=" O ASN C 393 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASN C 393 " --> pdb=" O LEU C 438 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LYS C 363 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LYS C 146 " --> pdb=" O LYS C 363 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU C 369 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLY C 140 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU C 371 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR C 138 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLU C 139 " --> pdb=" O LEU C 450 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 174 through 186 removed outlier: 5.208A pdb=" N SER C 175 " --> pdb=" O GLY C 171 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY C 171 " --> pdb=" O SER C 175 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N PHE C 177 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N TRP C 169 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY C 179 " --> pdb=" O GLN C 167 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 230 through 231 removed outlier: 7.371A pdb=" N LYS C 155 " --> pdb=" O ASP C 350 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ASP C 350 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N THR C 335 " --> pdb=" O GLY C 319 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 201 through 203 Processing sheet with id=AD2, first strand: chain 'C' and resid 205 through 210 Processing sheet with id=AD3, first strand: chain 'C' and resid 578 through 580 Processing sheet with id=AD4, first strand: chain 'C' and resid 592 through 594 Processing sheet with id=AD5, first strand: chain 'C' and resid 635 through 640 removed outlier: 3.571A pdb=" N HIS C 654 " --> pdb=" O TYR C 646 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU C 648 " --> pdb=" O TYR C 652 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR C 652 " --> pdb=" O GLU C 648 " (cutoff:3.500A) 674 hydrogen bonds defined for protein. 1845 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: 2.45 Time building geometry restraints manager: 1.71 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: 4778 1.34 - 1.46: 3690 1.46 - 1.58: 6262 1.58 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 14838 Sorted by residual: bond pdb=" C4 NAG J 1 " pdb=" O4 NAG J 1 " ideal model delta sigma weight residual 1.409 1.495 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C4 NAG K 1 " pdb=" O4 NAG K 1 " ideal model delta sigma weight residual 1.409 1.494 -0.085 2.00e-02 2.50e+03 1.79e+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 1.78e+01 bond pdb=" C4 NAG E 1 " pdb=" O4 NAG E 1 " ideal model delta sigma weight residual 1.409 1.492 -0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C5 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.413 1.496 -0.083 2.00e-02 2.50e+03 1.73e+01 ... (remaining 14833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 16344 2.32 - 4.65: 3607 4.65 - 6.97: 198 6.97 - 9.29: 7 9.29 - 11.61: 1 Bond angle restraints: 20157 Sorted by residual: angle pdb=" CA VAL C 290 " pdb=" CB VAL C 290 " pdb=" CG2 VAL C 290 " ideal model delta sigma weight residual 110.40 98.79 11.61 1.70e+00 3.46e-01 4.67e+01 angle pdb=" N VAL C 290 " pdb=" CA VAL C 290 " pdb=" CB VAL C 290 " ideal model delta sigma weight residual 111.90 119.66 -7.76 1.26e+00 6.30e-01 3.79e+01 angle pdb=" OE1 GLN A 581 " pdb=" CD GLN A 581 " pdb=" NE2 GLN A 581 " ideal model delta sigma weight residual 122.60 117.55 5.05 1.00e+00 1.00e+00 2.55e+01 angle pdb=" OE1 GLN B 581 " pdb=" CD GLN B 581 " pdb=" NE2 GLN B 581 " ideal model delta sigma weight residual 122.60 117.71 4.89 1.00e+00 1.00e+00 2.39e+01 angle pdb=" C ALA B 456 " pdb=" N GLU B 457 " pdb=" CA GLU B 457 " ideal model delta sigma weight residual 121.70 130.36 -8.66 1.80e+00 3.09e-01 2.31e+01 ... (remaining 20152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.12: 8565 18.12 - 36.23: 391 36.23 - 54.35: 89 54.35 - 72.47: 37 72.47 - 90.58: 20 Dihedral angle restraints: 9102 sinusoidal: 3906 harmonic: 5196 Sorted by residual: dihedral pdb=" C ASN B 537 " pdb=" N ASN B 537 " pdb=" CA ASN B 537 " pdb=" CB ASN B 537 " ideal model delta harmonic sigma weight residual -122.60 -137.97 15.37 0 2.50e+00 1.60e-01 3.78e+01 dihedral pdb=" C ASN A 537 " pdb=" N ASN A 537 " pdb=" CA ASN A 537 " pdb=" CB ASN A 537 " ideal model delta harmonic sigma weight residual -122.60 -137.89 15.29 0 2.50e+00 1.60e-01 3.74e+01 dihedral pdb=" C ASN C 537 " pdb=" N ASN C 537 " pdb=" CA ASN C 537 " pdb=" CB ASN C 537 " ideal model delta harmonic sigma weight residual -122.60 -137.50 14.90 0 2.50e+00 1.60e-01 3.55e+01 ... (remaining 9099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1659 0.120 - 0.241: 500 0.241 - 0.361: 56 0.361 - 0.482: 25 0.482 - 0.602: 4 Chirality restraints: 2244 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.38e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.67e+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 8.32e+01 ... (remaining 2241 not shown) Planarity restraints: 2613 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 351 " 0.090 2.00e-02 2.50e+03 4.65e-02 5.40e+01 pdb=" CG TRP C 351 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP C 351 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP C 351 " -0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP C 351 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TRP C 351 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP C 351 " -0.062 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 351 " 0.041 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 351 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 351 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 351 " 0.088 2.00e-02 2.50e+03 4.41e-02 4.86e+01 pdb=" CG TRP B 351 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP B 351 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP B 351 " -0.053 2.00e-02 2.50e+03 pdb=" NE1 TRP B 351 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TRP B 351 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP B 351 " -0.053 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 351 " 0.043 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 351 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 351 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 536 " 0.078 2.00e-02 2.50e+03 4.30e-02 4.62e+01 pdb=" CG TRP C 536 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP C 536 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP C 536 " -0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP C 536 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TRP C 536 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP C 536 " -0.041 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 536 " 0.069 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 536 " -0.040 2.00e-02 2.50e+03 pdb=" CH2 TRP C 536 " 0.030 2.00e-02 2.50e+03 ... (remaining 2610 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 8586 3.05 - 3.51: 13259 3.51 - 3.98: 24425 3.98 - 4.44: 27305 4.44 - 4.90: 45227 Nonbonded interactions: 118802 Sorted by model distance: nonbonded pdb=" OG SER C 239 " pdb=" O GLU C 270 " model vdw 2.588 3.040 nonbonded pdb=" OG SER A 239 " pdb=" O GLU A 270 " model vdw 2.590 3.040 nonbonded pdb=" OG SER A 600 " pdb=" OE2 GLU A 611 " model vdw 2.592 3.040 nonbonded pdb=" OG SER B 239 " pdb=" O GLU B 270 " model vdw 2.600 3.040 nonbonded pdb=" O ARG B 299 " pdb=" OG SER B 302 " model vdw 2.601 3.040 ... (remaining 118797 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: 0.02 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' } 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: 6.260 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: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.990 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 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 0.086 14871 Z= 0.629 Angle : 1.802 11.614 20241 Z= 1.181 Chirality : 0.115 0.602 2244 Planarity : 0.016 0.197 2604 Dihedral : 12.593 90.583 5715 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 0.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.20 % Allowed : 1.63 % Favored : 98.18 % Cbeta Deviations : 0.66 % Peptide Plane: Cis-proline : 3.70 % 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: -0.98 (0.17), residues: 1752 helix: 0.11 (0.30), residues: 291 sheet: -0.97 (0.18), residues: 507 loop : -0.60 (0.17), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG B 502 TYR 0.088 0.014 TYR C 277 PHE 0.074 0.013 PHE B 282 TRP 0.090 0.018 TRP C 351 HIS 0.014 0.003 HIS B 634 Details of bonding type rmsd covalent geometry : bond 0.01110 (14838) covalent geometry : angle 1.78050 (20157) SS BOND : bond 0.01998 ( 15) SS BOND : angle 2.61336 ( 30) hydrogen bonds : bond 0.14816 ( 587) hydrogen bonds : angle 7.67957 ( 1845) link_BETA1-4 : bond 0.04139 ( 9) link_BETA1-4 : angle 5.81400 ( 27) link_NAG-ASN : bond 0.01651 ( 9) link_NAG-ASN : angle 5.00156 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 593 CYS cc_start: 0.6292 (m) cc_final: 0.6069 (m) outliers start: 3 outliers final: 0 residues processed: 151 average time/residue: 0.6717 time to fit residues: 109.6002 Evaluate side-chains 103 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 ASN B 577 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.084101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.053790 restraints weight = 22554.464| |-----------------------------------------------------------------------------| r_work (start): 0.2589 rms_B_bonded: 2.48 r_work: 0.2436 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2311 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14871 Z= 0.137 Angle : 0.546 5.125 20241 Z= 0.301 Chirality : 0.043 0.140 2244 Planarity : 0.004 0.050 2604 Dihedral : 4.531 20.800 2373 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.72 % Allowed : 5.60 % Favored : 93.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.03 (0.18), residues: 1752 helix: 1.49 (0.30), residues: 300 sheet: -0.45 (0.20), residues: 525 loop : -0.07 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 173 TYR 0.018 0.001 TYR A 594 PHE 0.017 0.002 PHE B 295 TRP 0.011 0.001 TRP B 536 HIS 0.009 0.002 HIS C 531 Details of bonding type rmsd covalent geometry : bond 0.00303 (14838) covalent geometry : angle 0.53770 (20157) SS BOND : bond 0.00290 ( 15) SS BOND : angle 0.79446 ( 30) hydrogen bonds : bond 0.04557 ( 587) hydrogen bonds : angle 6.10508 ( 1845) link_BETA1-4 : bond 0.00199 ( 9) link_BETA1-4 : angle 2.21963 ( 27) link_NAG-ASN : bond 0.00270 ( 9) link_NAG-ASN : angle 1.36868 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 HIS cc_start: 0.8750 (t70) cc_final: 0.8399 (t70) REVERT: A 173 ARG cc_start: 0.8427 (mtm-85) cc_final: 0.7918 (mtm-85) REVERT: A 593 CYS cc_start: 0.7097 (m) cc_final: 0.6688 (m) REVERT: A 611 GLU cc_start: 0.8072 (pp20) cc_final: 0.7734 (pp20) REVERT: B 611 GLU cc_start: 0.7983 (pp20) cc_final: 0.7742 (pp20) REVERT: C 107 GLN cc_start: 0.8773 (tp40) cc_final: 0.8332 (mm-40) REVERT: C 172 HIS cc_start: 0.8651 (t70) cc_final: 0.8192 (t70) REVERT: C 173 ARG cc_start: 0.8412 (mtm-85) cc_final: 0.7780 (mtm-85) REVERT: C 576 ASP cc_start: 0.8475 (p0) cc_final: 0.8191 (p0) REVERT: C 627 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9117 (mm) outliers start: 11 outliers final: 3 residues processed: 116 average time/residue: 0.5931 time to fit residues: 75.2378 Evaluate side-chains 105 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 627 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 161 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 HIS A 582 ASN A 703 GLN B 582 ASN C 577 ASN C 582 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.082321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.051700 restraints weight = 22734.763| |-----------------------------------------------------------------------------| r_work (start): 0.2531 rms_B_bonded: 2.50 r_work: 0.2379 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2254 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9142 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 14871 Z= 0.277 Angle : 0.559 4.691 20241 Z= 0.306 Chirality : 0.045 0.153 2244 Planarity : 0.005 0.046 2604 Dihedral : 4.472 15.008 2373 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 0.72 % Allowed : 6.38 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.32 (0.19), residues: 1752 helix: 1.64 (0.30), residues: 300 sheet: -0.11 (0.22), residues: 477 loop : 0.04 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 173 TYR 0.016 0.002 TYR A 291 PHE 0.020 0.002 PHE C 282 TRP 0.011 0.002 TRP C 349 HIS 0.007 0.002 HIS C 689 Details of bonding type rmsd covalent geometry : bond 0.00652 (14838) covalent geometry : angle 0.55350 (20157) SS BOND : bond 0.00426 ( 15) SS BOND : angle 0.81917 ( 30) hydrogen bonds : bond 0.04922 ( 587) hydrogen bonds : angle 5.97604 ( 1845) link_BETA1-4 : bond 0.00367 ( 9) link_BETA1-4 : angle 1.91064 ( 27) link_NAG-ASN : bond 0.00138 ( 9) link_NAG-ASN : angle 1.19575 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7887 (ttp80) REVERT: A 173 ARG cc_start: 0.8487 (mtm-85) cc_final: 0.8101 (mtm-85) REVERT: A 593 CYS cc_start: 0.7059 (m) cc_final: 0.6712 (m) REVERT: A 611 GLU cc_start: 0.8210 (pp20) cc_final: 0.7791 (pp20) REVERT: C 173 ARG cc_start: 0.8409 (mtm-85) cc_final: 0.7881 (mtm-85) REVERT: C 579 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8809 (tp) REVERT: C 581 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8632 (mm-40) REVERT: C 611 GLU cc_start: 0.8076 (pp20) cc_final: 0.7829 (pp20) REVERT: C 627 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9200 (mm) outliers start: 11 outliers final: 5 residues processed: 118 average time/residue: 0.5928 time to fit residues: 75.8288 Evaluate side-chains 108 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 635 ARG Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 627 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 71 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 152 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 634 HIS C 258 HIS C 577 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.083770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.053373 restraints weight = 22678.078| |-----------------------------------------------------------------------------| r_work (start): 0.2569 rms_B_bonded: 2.50 r_work: 0.2416 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2291 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14871 Z= 0.139 Angle : 0.481 4.220 20241 Z= 0.265 Chirality : 0.041 0.140 2244 Planarity : 0.004 0.042 2604 Dihedral : 4.182 14.698 2373 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.78 % Allowed : 7.42 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.46 (0.19), residues: 1752 helix: 1.87 (0.30), residues: 303 sheet: -0.04 (0.20), residues: 564 loop : 0.10 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 624 TYR 0.011 0.001 TYR C 291 PHE 0.014 0.001 PHE C 282 TRP 0.009 0.001 TRP A 536 HIS 0.006 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00314 (14838) covalent geometry : angle 0.47671 (20157) SS BOND : bond 0.00290 ( 15) SS BOND : angle 0.65908 ( 30) hydrogen bonds : bond 0.04095 ( 587) hydrogen bonds : angle 5.71021 ( 1845) link_BETA1-4 : bond 0.00292 ( 9) link_BETA1-4 : angle 1.54122 ( 27) link_NAG-ASN : bond 0.00183 ( 9) link_NAG-ASN : angle 0.96982 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7892 (ttp80) REVERT: A 173 ARG cc_start: 0.8464 (mtm-85) cc_final: 0.8064 (mtm-85) REVERT: A 517 MET cc_start: 0.9305 (mmp) cc_final: 0.9083 (mmp) REVERT: A 582 ASN cc_start: 0.8740 (t0) cc_final: 0.8340 (t0) REVERT: A 593 CYS cc_start: 0.7063 (m) cc_final: 0.6619 (m) REVERT: A 611 GLU cc_start: 0.8276 (pp20) cc_final: 0.7929 (pp20) REVERT: B 581 GLN cc_start: 0.8757 (mm110) cc_final: 0.8446 (mm110) REVERT: C 107 GLN cc_start: 0.8814 (tp40) cc_final: 0.8240 (mm-40) REVERT: C 127 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7953 (ttp80) REVERT: C 173 ARG cc_start: 0.8443 (mtm-85) cc_final: 0.8065 (mtm-85) REVERT: C 579 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8782 (tp) REVERT: C 581 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8652 (mm-40) REVERT: C 611 GLU cc_start: 0.8163 (pp20) cc_final: 0.7950 (pp20) outliers start: 12 outliers final: 6 residues processed: 115 average time/residue: 0.6821 time to fit residues: 85.3320 Evaluate side-chains 114 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 622 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 9 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.083159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.052680 restraints weight = 22626.257| |-----------------------------------------------------------------------------| r_work (start): 0.2555 rms_B_bonded: 2.49 r_work: 0.2402 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2277 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9136 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14871 Z= 0.194 Angle : 0.492 4.816 20241 Z= 0.270 Chirality : 0.042 0.136 2244 Planarity : 0.004 0.042 2604 Dihedral : 4.185 14.770 2373 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.11 % Allowed : 7.94 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.51 (0.19), residues: 1752 helix: 1.89 (0.30), residues: 303 sheet: 0.03 (0.20), residues: 564 loop : 0.13 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 624 TYR 0.012 0.001 TYR A 291 PHE 0.016 0.002 PHE C 282 TRP 0.009 0.001 TRP A 349 HIS 0.005 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00450 (14838) covalent geometry : angle 0.48829 (20157) SS BOND : bond 0.00334 ( 15) SS BOND : angle 0.64379 ( 30) hydrogen bonds : bond 0.04298 ( 587) hydrogen bonds : angle 5.67611 ( 1845) link_BETA1-4 : bond 0.00263 ( 9) link_BETA1-4 : angle 1.45533 ( 27) link_NAG-ASN : bond 0.00079 ( 9) link_NAG-ASN : angle 1.01276 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7862 (ttp80) REVERT: A 173 ARG cc_start: 0.8501 (mtm-85) cc_final: 0.8072 (mtm-85) REVERT: A 517 MET cc_start: 0.9317 (mmp) cc_final: 0.9024 (mmp) REVERT: A 593 CYS cc_start: 0.7012 (m) cc_final: 0.6535 (m) REVERT: A 611 GLU cc_start: 0.8381 (pp20) cc_final: 0.7987 (pp20) REVERT: B 107 GLN cc_start: 0.8888 (tp40) cc_final: 0.8671 (mm-40) REVERT: B 581 GLN cc_start: 0.8812 (mm110) cc_final: 0.8505 (mm110) REVERT: B 611 GLU cc_start: 0.7904 (pp20) cc_final: 0.7608 (pp20) REVERT: B 619 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8151 (tp30) REVERT: B 624 ARG cc_start: 0.9033 (mtt180) cc_final: 0.8791 (mtt180) REVERT: C 127 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7985 (ttp80) REVERT: C 173 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.8018 (mtm-85) REVERT: C 579 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8669 (tp) REVERT: C 581 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8598 (mm-40) REVERT: C 611 GLU cc_start: 0.8197 (pp20) cc_final: 0.7972 (pp20) outliers start: 17 outliers final: 11 residues processed: 124 average time/residue: 0.7385 time to fit residues: 98.9201 Evaluate side-chains 123 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 622 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 48 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.084128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.053891 restraints weight = 22684.893| |-----------------------------------------------------------------------------| r_work (start): 0.2581 rms_B_bonded: 2.49 r_work: 0.2430 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2307 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14871 Z= 0.132 Angle : 0.457 4.877 20241 Z= 0.251 Chirality : 0.041 0.138 2244 Planarity : 0.004 0.070 2604 Dihedral : 3.995 14.125 2373 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 1.30 % Allowed : 7.94 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.63 (0.19), residues: 1752 helix: 2.05 (0.30), residues: 303 sheet: 0.10 (0.21), residues: 564 loop : 0.18 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 173 TYR 0.010 0.001 TYR A 291 PHE 0.013 0.001 PHE B 282 TRP 0.008 0.001 TRP A 536 HIS 0.005 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00302 (14838) covalent geometry : angle 0.45348 (20157) SS BOND : bond 0.00271 ( 15) SS BOND : angle 0.55988 ( 30) hydrogen bonds : bond 0.03829 ( 587) hydrogen bonds : angle 5.52366 ( 1845) link_BETA1-4 : bond 0.00295 ( 9) link_BETA1-4 : angle 1.29959 ( 27) link_NAG-ASN : bond 0.00130 ( 9) link_NAG-ASN : angle 0.87636 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7829 (ttp80) REVERT: A 173 ARG cc_start: 0.8491 (mtm-85) cc_final: 0.8054 (mtm-85) REVERT: A 581 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8549 (mm-40) REVERT: A 593 CYS cc_start: 0.6911 (m) cc_final: 0.6504 (m) REVERT: A 611 GLU cc_start: 0.8340 (pp20) cc_final: 0.7914 (pp20) REVERT: B 581 GLN cc_start: 0.8819 (mm110) cc_final: 0.8528 (mm110) REVERT: B 619 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8226 (tp30) REVERT: C 107 GLN cc_start: 0.8797 (tp40) cc_final: 0.8321 (mm-40) REVERT: C 127 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7947 (ttp80) REVERT: C 173 ARG cc_start: 0.8409 (mtm-85) cc_final: 0.7997 (mtm-85) REVERT: C 581 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8655 (mm-40) REVERT: C 611 GLU cc_start: 0.8219 (pp20) cc_final: 0.7957 (pp20) REVERT: C 623 THR cc_start: 0.9163 (m) cc_final: 0.8553 (t) outliers start: 20 outliers final: 11 residues processed: 131 average time/residue: 0.6890 time to fit residues: 98.5234 Evaluate side-chains 126 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain C residue 236 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 144 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.082114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.051708 restraints weight = 22613.026| |-----------------------------------------------------------------------------| r_work (start): 0.2561 rms_B_bonded: 2.47 r_work: 0.2407 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2281 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9146 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 14871 Z= 0.307 Angle : 0.540 4.810 20241 Z= 0.294 Chirality : 0.045 0.173 2244 Planarity : 0.005 0.073 2604 Dihedral : 4.363 15.593 2373 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 1.17 % Allowed : 8.66 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.58 (0.19), residues: 1752 helix: 1.91 (0.30), residues: 300 sheet: 0.14 (0.21), residues: 531 loop : 0.13 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 173 TYR 0.015 0.002 TYR A 291 PHE 0.020 0.002 PHE B 282 TRP 0.010 0.002 TRP C 349 HIS 0.006 0.001 HIS C 689 Details of bonding type rmsd covalent geometry : bond 0.00718 (14838) covalent geometry : angle 0.53660 (20157) SS BOND : bond 0.00389 ( 15) SS BOND : angle 0.72694 ( 30) hydrogen bonds : bond 0.04772 ( 587) hydrogen bonds : angle 5.73429 ( 1845) link_BETA1-4 : bond 0.00209 ( 9) link_BETA1-4 : angle 1.37088 ( 27) link_NAG-ASN : bond 0.00214 ( 9) link_NAG-ASN : angle 1.11499 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7835 (ttp80) REVERT: A 173 ARG cc_start: 0.8510 (mtm-85) cc_final: 0.8058 (mtm-85) REVERT: A 581 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8506 (mm110) REVERT: A 611 GLU cc_start: 0.8431 (pp20) cc_final: 0.8094 (pp20) REVERT: B 581 GLN cc_start: 0.8863 (mm110) cc_final: 0.8488 (mm110) REVERT: B 619 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8119 (tp30) REVERT: B 623 THR cc_start: 0.9129 (m) cc_final: 0.8622 (t) REVERT: B 635 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8459 (mtp180) REVERT: C 127 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7956 (ttp80) REVERT: C 173 ARG cc_start: 0.8402 (mtm-85) cc_final: 0.7970 (mtm-85) REVERT: C 581 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8562 (mm-40) REVERT: C 611 GLU cc_start: 0.8218 (pp20) cc_final: 0.7996 (pp20) outliers start: 18 outliers final: 10 residues processed: 122 average time/residue: 0.7281 time to fit residues: 96.7570 Evaluate side-chains 122 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 635 ARG Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 622 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 chunk 166 optimal weight: 0.9990 chunk 91 optimal weight: 0.0570 chunk 102 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.084063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.053825 restraints weight = 22556.176| |-----------------------------------------------------------------------------| r_work (start): 0.2581 rms_B_bonded: 2.48 r_work: 0.2432 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2308 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9122 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14871 Z= 0.127 Angle : 0.460 5.485 20241 Z= 0.253 Chirality : 0.041 0.139 2244 Planarity : 0.004 0.065 2604 Dihedral : 4.027 14.440 2373 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 0.91 % Allowed : 9.51 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.66 (0.19), residues: 1752 helix: 2.07 (0.30), residues: 303 sheet: 0.16 (0.21), residues: 564 loop : 0.17 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 173 TYR 0.009 0.001 TYR A 291 PHE 0.013 0.001 PHE B 282 TRP 0.008 0.001 TRP C 349 HIS 0.005 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00286 (14838) covalent geometry : angle 0.45723 (20157) SS BOND : bond 0.00284 ( 15) SS BOND : angle 0.73222 ( 30) hydrogen bonds : bond 0.03803 ( 587) hydrogen bonds : angle 5.52645 ( 1845) link_BETA1-4 : bond 0.00265 ( 9) link_BETA1-4 : angle 1.20707 ( 27) link_NAG-ASN : bond 0.00148 ( 9) link_NAG-ASN : angle 0.84576 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7781 (ttp80) REVERT: A 173 ARG cc_start: 0.8486 (mtm-85) cc_final: 0.8049 (mtm-85) REVERT: A 581 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8585 (mm-40) REVERT: A 611 GLU cc_start: 0.8369 (pp20) cc_final: 0.8039 (pp20) REVERT: B 581 GLN cc_start: 0.8849 (mm110) cc_final: 0.8490 (mm110) REVERT: B 611 GLU cc_start: 0.7883 (pp20) cc_final: 0.7683 (pp20) REVERT: B 619 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8198 (tp30) REVERT: B 623 THR cc_start: 0.9218 (m) cc_final: 0.8719 (t) REVERT: C 107 GLN cc_start: 0.8818 (tp40) cc_final: 0.8340 (mm-40) REVERT: C 127 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7933 (ttp80) REVERT: C 173 ARG cc_start: 0.8402 (mtm-85) cc_final: 0.7950 (mtm-85) REVERT: C 581 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8606 (mm-40) REVERT: C 611 GLU cc_start: 0.8234 (pp20) cc_final: 0.7997 (pp20) REVERT: C 623 THR cc_start: 0.9154 (m) cc_final: 0.8487 (t) outliers start: 14 outliers final: 10 residues processed: 120 average time/residue: 0.6706 time to fit residues: 87.6419 Evaluate side-chains 123 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 622 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 102 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 161 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.083589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.053284 restraints weight = 22738.194| |-----------------------------------------------------------------------------| r_work (start): 0.2568 rms_B_bonded: 2.49 r_work: 0.2416 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2293 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9133 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14871 Z= 0.170 Angle : 0.480 6.150 20241 Z= 0.261 Chirality : 0.042 0.145 2244 Planarity : 0.004 0.058 2604 Dihedral : 4.068 14.503 2373 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 1.11 % Allowed : 9.64 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.68 (0.19), residues: 1752 helix: 2.11 (0.30), residues: 300 sheet: 0.17 (0.21), residues: 564 loop : 0.18 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 173 TYR 0.012 0.001 TYR A 291 PHE 0.015 0.001 PHE B 282 TRP 0.008 0.001 TRP B 349 HIS 0.004 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00392 (14838) covalent geometry : angle 0.47591 (20157) SS BOND : bond 0.00315 ( 15) SS BOND : angle 1.04031 ( 30) hydrogen bonds : bond 0.04046 ( 587) hydrogen bonds : angle 5.52545 ( 1845) link_BETA1-4 : bond 0.00234 ( 9) link_BETA1-4 : angle 1.23492 ( 27) link_NAG-ASN : bond 0.00075 ( 9) link_NAG-ASN : angle 0.95600 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7798 (ttp80) REVERT: A 173 ARG cc_start: 0.8500 (mtm-85) cc_final: 0.8057 (mtm-85) REVERT: A 581 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8531 (mm110) REVERT: A 598 LEU cc_start: 0.9137 (mt) cc_final: 0.8928 (mt) REVERT: A 611 GLU cc_start: 0.8471 (pp20) cc_final: 0.8060 (pp20) REVERT: B 581 GLN cc_start: 0.8850 (mm110) cc_final: 0.8504 (mm110) REVERT: B 598 LEU cc_start: 0.9036 (mt) cc_final: 0.8797 (mt) REVERT: B 611 GLU cc_start: 0.7857 (pp20) cc_final: 0.7643 (pp20) REVERT: B 619 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8189 (tp30) REVERT: B 623 THR cc_start: 0.9211 (m) cc_final: 0.8232 (t) REVERT: C 107 GLN cc_start: 0.8807 (tp40) cc_final: 0.8300 (mm-40) REVERT: C 127 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7948 (ttp80) REVERT: C 173 ARG cc_start: 0.8443 (mtm-85) cc_final: 0.7990 (mtm-85) REVERT: C 581 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8581 (mm-40) REVERT: C 611 GLU cc_start: 0.8266 (pp20) cc_final: 0.7946 (pp20) REVERT: C 623 THR cc_start: 0.9131 (m) cc_final: 0.8464 (t) outliers start: 17 outliers final: 13 residues processed: 123 average time/residue: 0.6503 time to fit residues: 86.8631 Evaluate side-chains 127 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 622 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 136 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 167 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.082756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.052402 restraints weight = 22502.048| |-----------------------------------------------------------------------------| r_work (start): 0.2552 rms_B_bonded: 2.47 r_work: 0.2401 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2277 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14871 Z= 0.227 Angle : 0.509 7.608 20241 Z= 0.277 Chirality : 0.043 0.163 2244 Planarity : 0.005 0.060 2604 Dihedral : 4.211 14.995 2373 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 1.04 % Allowed : 9.70 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.64 (0.19), residues: 1752 helix: 2.04 (0.30), residues: 300 sheet: 0.15 (0.21), residues: 564 loop : 0.16 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 173 TYR 0.014 0.001 TYR A 291 PHE 0.017 0.002 PHE B 282 TRP 0.008 0.001 TRP A 349 HIS 0.005 0.001 HIS C 689 Details of bonding type rmsd covalent geometry : bond 0.00528 (14838) covalent geometry : angle 0.50448 (20157) SS BOND : bond 0.00349 ( 15) SS BOND : angle 1.26039 ( 30) hydrogen bonds : bond 0.04370 ( 587) hydrogen bonds : angle 5.61637 ( 1845) link_BETA1-4 : bond 0.00210 ( 9) link_BETA1-4 : angle 1.23489 ( 27) link_NAG-ASN : bond 0.00140 ( 9) link_NAG-ASN : angle 1.02583 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7832 (ttp80) REVERT: A 173 ARG cc_start: 0.8484 (mtm-85) cc_final: 0.8033 (mtm-85) REVERT: A 581 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8528 (mm110) REVERT: B 581 GLN cc_start: 0.8878 (mm110) cc_final: 0.8524 (mm110) REVERT: B 598 LEU cc_start: 0.9085 (mt) cc_final: 0.8835 (mt) REVERT: B 619 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8119 (tp30) REVERT: B 623 THR cc_start: 0.9063 (m) cc_final: 0.8748 (t) REVERT: C 107 GLN cc_start: 0.8807 (tp40) cc_final: 0.8280 (mm-40) REVERT: C 127 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7960 (ttp80) REVERT: C 173 ARG cc_start: 0.8440 (mtm-85) cc_final: 0.7987 (mtm-85) REVERT: C 581 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8563 (mm-40) REVERT: C 611 GLU cc_start: 0.8240 (pp20) cc_final: 0.7906 (pp20) outliers start: 16 outliers final: 13 residues processed: 122 average time/residue: 0.6096 time to fit residues: 81.1973 Evaluate side-chains 126 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 622 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 129 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 163 optimal weight: 8.9990 chunk 144 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.083243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.052897 restraints weight = 22635.549| |-----------------------------------------------------------------------------| r_work (start): 0.2563 rms_B_bonded: 2.49 r_work: 0.2412 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2287 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9128 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14871 Z= 0.182 Angle : 0.489 7.399 20241 Z= 0.267 Chirality : 0.042 0.151 2244 Planarity : 0.004 0.056 2604 Dihedral : 4.136 14.851 2373 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.24 % Allowed : 9.64 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.66 (0.19), residues: 1752 helix: 2.07 (0.30), residues: 300 sheet: 0.18 (0.21), residues: 564 loop : 0.16 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 173 TYR 0.012 0.001 TYR A 291 PHE 0.015 0.001 PHE B 282 TRP 0.008 0.001 TRP A 349 HIS 0.004 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00420 (14838) covalent geometry : angle 0.48493 (20157) SS BOND : bond 0.00304 ( 15) SS BOND : angle 1.21186 ( 30) hydrogen bonds : bond 0.04119 ( 587) hydrogen bonds : angle 5.55332 ( 1845) link_BETA1-4 : bond 0.00229 ( 9) link_BETA1-4 : angle 1.19417 ( 27) link_NAG-ASN : bond 0.00079 ( 9) link_NAG-ASN : angle 0.96145 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5702.91 seconds wall clock time: 97 minutes 39.75 seconds (5859.75 seconds total)