Starting phenix.real_space_refine on Sat Jul 4 14:37:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yfh_33790/07_2026/7yfh_33790_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yfh_33790/07_2026/7yfh_33790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yfh_33790/07_2026/7yfh_33790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yfh_33790/07_2026/7yfh_33790.map" model { file = "/net/cci-nas-00/data/ceres_data/7yfh_33790/07_2026/7yfh_33790_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yfh_33790/07_2026/7yfh_33790_neut.cif" } resolution = 3.0 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= 0.003 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 98 5.16 5 C 13462 2.51 5 N 3658 2.21 5 O 4072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21290 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5185 Classifications: {'peptide': 653} Link IDs: {'PTRANS': 29, 'TRANS': 623} Chain breaks: 1 Chain: "B" Number of atoms: 5045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5045 Classifications: {'peptide': 652} Link IDs: {'PTRANS': 37, 'TRANS': 614} Chain breaks: 1 Chain: "C" Number of atoms: 5238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5238 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 30, 'TRANS': 628} Chain breaks: 1 Chain: "D" Number of atoms: 5047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5047 Classifications: {'peptide': 652} Link IDs: {'PTRANS': 37, 'TRANS': 614} Chain breaks: 1 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" 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: "T" 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: "W" 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: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "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: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" 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: "t" 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: "v" 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: "y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "3" 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: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'NAG': 4} Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'IWB': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'NAG': 5} Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.77, per 1000 atoms: 0.22 Number of scatterers: 21290 At special positions: 0 Unit cell: (125.307, 143.514, 137.088, 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 98 16.00 O 4072 8.00 N 3658 7.00 C 13462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.02 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 82 " - pdb=" SG CYS B 317 " distance=2.03 Simple disulfide: pdb=" SG CYS B 426 " - pdb=" SG CYS B 453 " distance=2.03 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.04 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 82 " - pdb=" SG CYS D 317 " distance=2.03 Simple disulfide: pdb=" SG CYS D 426 " - pdb=" SG CYS D 453 " distance=2.03 Simple disulfide: pdb=" SG CYS D 433 " - pdb=" SG CYS D 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 798 " distance=2.04 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 ALPHA1-4 " NAG E 2 " - " MAN E 3 " " NAG H 2 " - " MAN H 3 " " NAG K 2 " - " MAN K 3 " " NAG b 2 " - " MAN b 3 " " NAG y 2 " - " MAN y 3 " BETA1-4 " NAG 3 1 " - " NAG 3 2 " " NAG 5 1 " - " NAG 5 2 " " NAG E 1 " - " NAG E 2 " " NAG H 1 " - " NAG H 2 " " NAG K 1 " - " NAG K 2 " " NAG N 1 " - " NAG N 2 " " NAG P 1 " - " NAG P 2 " " NAG T 1 " - " NAG T 2 " " NAG W 1 " - " NAG W 2 " " NAG b 1 " - " NAG b 2 " " NAG e 1 " - " NAG e 2 " " NAG k 1 " - " NAG k 2 " " NAG m 1 " - " NAG m 2 " " NAG r 1 " - " NAG r 2 " " NAG t 1 " - " NAG t 2 " " NAG v 1 " - " NAG v 2 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG 3 1 " - " ASN D 685 " " NAG 5 1 " - " ASN D 337 " " NAG A 901 " - " ASN A 239 " " NAG A 902 " - " ASN A 300 " " NAG A 903 " - " ASN A 491 " " NAG A 904 " - " ASN A 440 " " NAG B 901 " - " ASN B 438 " " NAG B 902 " - " ASN B 70 " " NAG C 901 " - " ASN C 491 " " NAG C 902 " - " ASN C 350 " " NAG C 903 " - " ASN C 300 " " NAG C 904 " - " ASN C 239 " " NAG C 905 " - " ASN C 440 " " NAG D 901 " - " ASN D 438 " " NAG D 902 " - " ASN D 70 " " NAG E 1 " - " ASN A 771 " " NAG H 1 " - " ASN A 276 " " NAG K 1 " - " ASN A 368 " " NAG N 1 " - " ASN A 61 " " NAG P 1 " - " ASN A 203 " " NAG T 1 " - " ASN A 350 " " NAG W 1 " - " ASN A 471 " " NAG b 1 " - " ASN B 685 " " NAG e 1 " - " ASN B 337 " " NAG k 1 " - " ASN C 471 " " NAG m 1 " - " ASN C 368 " " NAG r 1 " - " ASN C 203 " " NAG t 1 " - " ASN C 61 " " NAG v 1 " - " ASN C 771 " " NAG y 1 " - " ASN C 276 " Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 895.1 milliseconds 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4848 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 32 sheets defined 38.8% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 37 through 53 Processing helix chain 'A' and resid 70 through 82 Processing helix chain 'A' and resid 99 through 103 removed outlier: 3.932A pdb=" N THR A 103 " --> pdb=" O ASP A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 4.136A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.856A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.775A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 188 removed outlier: 3.565A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.099A pdb=" N SER A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.760A pdb=" N ARG A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 297 Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 665 through 668 removed outlier: 3.765A pdb=" N ASN A 668 " --> pdb=" O THR A 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 668' Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 699 through 708 Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 744 Processing helix chain 'A' and resid 768 through 782 Processing helix chain 'A' and resid 783 through 792 Processing helix chain 'B' and resid 43 through 50 removed outlier: 3.903A pdb=" N ARG B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 55 removed outlier: 4.186A pdb=" N ASN B 54 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N PHE B 55 " --> pdb=" O SER B 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 51 through 55' Processing helix chain 'B' and resid 73 through 88 Processing helix chain 'B' and resid 103 through 116 removed outlier: 3.547A pdb=" N LEU B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 161 Processing helix chain 'B' and resid 174 through 188 Processing helix chain 'B' and resid 211 through 217 removed outlier: 3.590A pdb=" N LEU B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 243 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 284 through 308 Processing helix chain 'B' and resid 325 through 337 removed outlier: 3.962A pdb=" N ASN B 337 " --> pdb=" O ARG B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 687 through 696 Processing helix chain 'B' and resid 696 through 706 removed outlier: 3.920A pdb=" N LYS B 705 " --> pdb=" O THR B 701 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE B 706 " --> pdb=" O HIS B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 721 Processing helix chain 'B' and resid 730 through 739 removed outlier: 3.530A pdb=" N TYR B 735 " --> pdb=" O ALA B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 783 removed outlier: 4.604A pdb=" N ALA B 772 " --> pdb=" O HIS B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 794 removed outlier: 3.813A pdb=" N LYS B 788 " --> pdb=" O GLY B 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 54 Processing helix chain 'C' and resid 70 through 82 Processing helix chain 'C' and resid 104 through 114 removed outlier: 3.964A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 159 removed outlier: 4.080A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 removed outlier: 3.645A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 removed outlier: 3.521A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 Processing helix chain 'C' and resid 256 through 262 Processing helix chain 'C' and resid 276 through 297 removed outlier: 3.586A pdb=" N HIS C 280 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 327 Processing helix chain 'C' and resid 457 through 471 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 Processing helix chain 'C' and resid 699 through 709 removed outlier: 3.655A pdb=" N HIS C 709 " --> pdb=" O HIS C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 744 Processing helix chain 'C' and resid 768 through 782 Processing helix chain 'C' and resid 783 through 792 Processing helix chain 'D' and resid 41 through 49 removed outlier: 3.743A pdb=" N ARG D 49 " --> pdb=" O GLN D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 89 removed outlier: 3.681A pdb=" N ALA D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 116 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 145 through 160 Processing helix chain 'D' and resid 174 through 188 Processing helix chain 'D' and resid 209 through 217 removed outlier: 3.584A pdb=" N LEU D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'D' and resid 280 through 283 Processing helix chain 'D' and resid 284 through 308 Processing helix chain 'D' and resid 325 through 337 removed outlier: 3.838A pdb=" N GLU D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN D 337 " --> pdb=" O ARG D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 470 Processing helix chain 'D' and resid 492 through 500 Processing helix chain 'D' and resid 513 through 520 removed outlier: 3.859A pdb=" N ILE D 519 " --> pdb=" O GLU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 696 through 704 Processing helix chain 'D' and resid 710 through 721 Processing helix chain 'D' and resid 730 through 739 removed outlier: 3.525A pdb=" N TYR D 735 " --> pdb=" O ALA D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 753 removed outlier: 3.990A pdb=" N VAL D 753 " --> pdb=" O SER D 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 783 Processing helix chain 'D' and resid 784 through 794 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 6.491A pdb=" N VAL A 27 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N THR A 63 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE A 29 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL A 65 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASN A 28 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE A 90 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLY A 30 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N VAL A 92 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL A 32 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 7.156A pdb=" N ILE A 163 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N LEU A 195 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 3.810A pdb=" N GLY A 365 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLN A 357 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 330 through 333 removed outlier: 4.887A pdb=" N ASP A 332 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY A 336 " --> pdb=" O ASP A 332 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU A 339 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 410 through 413 removed outlier: 6.290A pdb=" N ILE A 435 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU A 478 " --> pdb=" O ILE A 435 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR A 437 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET A 512 " --> pdb=" O LYS A 399 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 487 through 488 removed outlier: 3.748A pdb=" N GLU A 488 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 497 " --> pdb=" O GLU A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 534 through 536 removed outlier: 3.851A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 681 through 682 removed outlier: 3.851A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 63 through 67 removed outlier: 3.686A pdb=" N GLY B 92 " --> pdb=" O THR B 31 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 200 removed outlier: 7.942A pdb=" N PHE B 165 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL B 198 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 167 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N THR B 200 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR B 169 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA B 164 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL B 225 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA B 166 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N TYR B 227 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE B 168 " --> pdb=" O TYR B 227 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 274 through 278 removed outlier: 6.688A pdb=" N MET B 358 " --> pdb=" O ARG B 374 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ARG B 374 " --> pdb=" O MET B 358 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL B 360 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B 376 " --> pdb=" O VAL B 379 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 415 through 417 removed outlier: 3.804A pdb=" N THR B 450 " --> pdb=" O ARG B 435 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU B 475 " --> pdb=" O PRO B 432 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 486 through 487 Processing sheet with id=AB5, first strand: chain 'B' and resid 680 through 681 removed outlier: 6.136A pdb=" N GLY B 681 " --> pdb=" O ILE B 727 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ASP B 729 " --> pdb=" O GLY B 681 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 680 through 681 removed outlier: 6.136A pdb=" N GLY B 681 " --> pdb=" O ILE B 727 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ASP B 729 " --> pdb=" O GLY B 681 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL B 527 " --> pdb=" O GLY B 758 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLY B 758 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR B 529 " --> pdb=" O THR B 756 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N THR B 756 " --> pdb=" O THR B 529 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 59 through 66 removed outlier: 8.126A pdb=" N VAL C 87 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 193 through 197 removed outlier: 3.796A pdb=" N LYS C 193 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 267 through 271 removed outlier: 3.940A pdb=" N GLY C 365 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 339 through 340 removed outlier: 4.745A pdb=" N GLU C 339 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 410 through 412 removed outlier: 6.367A pdb=" N ILE C 435 " --> pdb=" O VAL C 476 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU C 478 " --> pdb=" O ILE C 435 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR C 437 " --> pdb=" O LEU C 478 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ALA C 515 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLY C 759 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU C 517 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY C 757 " --> pdb=" O LEU C 517 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 410 through 412 removed outlier: 6.367A pdb=" N ILE C 435 " --> pdb=" O VAL C 476 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU C 478 " --> pdb=" O ILE C 435 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR C 437 " --> pdb=" O LEU C 478 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ALA C 515 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLY C 759 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU C 517 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY C 757 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS C 534 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 487 through 489 Processing sheet with id=AC5, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.868A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 63 through 66 removed outlier: 3.635A pdb=" N GLY D 92 " --> pdb=" O THR D 31 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 198 through 201 removed outlier: 9.320A pdb=" N LEU D 199 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL D 167 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LEU D 201 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR D 169 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA D 166 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N TYR D 227 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE D 168 " --> pdb=" O TYR D 227 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 274 through 278 removed outlier: 6.808A pdb=" N MET D 358 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ARG D 374 " --> pdb=" O MET D 358 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL D 360 " --> pdb=" O VAL D 372 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 339 through 340 Processing sheet with id=AD1, first strand: chain 'D' and resid 472 through 477 removed outlier: 3.589A pdb=" N VAL D 405 " --> pdb=" O ASP D 474 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 415 through 417 Processing sheet with id=AD3, first strand: chain 'D' and resid 486 through 487 Processing sheet with id=AD4, first strand: chain 'D' and resid 680 through 681 removed outlier: 6.539A pdb=" N GLY D 681 " --> pdb=" O ILE D 727 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N ASP D 729 " --> pdb=" O GLY D 681 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 745 " --> pdb=" O VAL D 535 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 680 through 681 removed outlier: 6.539A pdb=" N GLY D 681 " --> pdb=" O ILE D 727 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N ASP D 729 " --> pdb=" O GLY D 681 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL D 527 " --> pdb=" O GLY D 758 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLY D 758 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR D 529 " --> pdb=" O THR D 756 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR D 756 " --> pdb=" O THR D 529 " (cutoff:3.500A) 861 hydrogen bonds defined for protein. 2448 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.29 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.06: 1 1.06 - 1.25: 3032 1.25 - 1.44: 6301 1.44 - 1.63: 12257 1.63 - 1.82: 160 Bond restraints: 21751 Sorted by residual: bond pdb=" CB PRO D 323 " pdb=" CG PRO D 323 " ideal model delta sigma weight residual 1.492 0.865 0.627 5.00e-02 4.00e+02 1.57e+02 bond pdb=" CG PRO D 323 " pdb=" CD PRO D 323 " ideal model delta sigma weight residual 1.503 1.290 0.213 3.40e-02 8.65e+02 3.94e+01 bond pdb=" N PRO D 323 " pdb=" CA PRO D 323 " ideal model delta sigma weight residual 1.466 1.509 -0.043 1.19e-02 7.06e+03 1.31e+01 bond pdb=" C4 NAG K 1 " pdb=" O4 NAG K 1 " ideal model delta sigma weight residual 1.409 1.466 -0.057 2.00e-02 2.50e+03 8.25e+00 bond pdb=" C1 MAN E 3 " pdb=" C2 MAN E 3 " ideal model delta sigma weight residual 1.526 1.572 -0.046 2.00e-02 2.50e+03 5.36e+00 ... (remaining 21746 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.64: 29512 14.64 - 29.29: 2 29.29 - 43.93: 0 43.93 - 58.58: 0 58.58 - 73.22: 1 Bond angle restraints: 29515 Sorted by residual: angle pdb=" CB PRO D 323 " pdb=" CG PRO D 323 " pdb=" CD PRO D 323 " ideal model delta sigma weight residual 106.10 179.32 -73.22 3.20e+00 9.77e-02 5.24e+02 angle pdb=" N PRO D 323 " pdb=" CD PRO D 323 " pdb=" CG PRO D 323 " ideal model delta sigma weight residual 103.20 79.84 23.36 1.50e+00 4.44e-01 2.42e+02 angle pdb=" CA PRO D 323 " pdb=" CB PRO D 323 " pdb=" CG PRO D 323 " ideal model delta sigma weight residual 104.50 75.43 29.07 1.90e+00 2.77e-01 2.34e+02 angle pdb=" CA PRO D 323 " pdb=" N PRO D 323 " pdb=" CD PRO D 323 " ideal model delta sigma weight residual 112.00 101.99 10.01 1.40e+00 5.10e-01 5.11e+01 angle pdb=" N VAL D 246 " pdb=" CA VAL D 246 " pdb=" C VAL D 246 " ideal model delta sigma weight residual 113.47 109.29 4.18 1.01e+00 9.80e-01 1.71e+01 ... (remaining 29510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 13222 35.75 - 71.51: 477 71.51 - 107.26: 42 107.26 - 143.01: 0 143.01 - 178.77: 4 Dihedral angle restraints: 13745 sinusoidal: 6204 harmonic: 7541 Sorted by residual: dihedral pdb=" CB CYS D 743 " pdb=" SG CYS D 743 " pdb=" SG CYS D 798 " pdb=" CB CYS D 798 " ideal model delta sinusoidal sigma weight residual -86.00 -147.80 61.80 1 1.00e+01 1.00e-02 5.06e+01 dihedral pdb=" CA LYS D 133 " pdb=" C LYS D 133 " pdb=" N GLU D 134 " pdb=" CA GLU D 134 " ideal model delta harmonic sigma weight residual 180.00 153.49 26.51 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" N PRO D 323 " pdb=" CG PRO D 323 " pdb=" CD PRO D 323 " pdb=" CB PRO D 323 " ideal model delta sinusoidal sigma weight residual 30.00 96.86 -66.86 1 1.50e+01 4.44e-03 2.59e+01 ... (remaining 13742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 3420 0.139 - 0.277: 27 0.277 - 0.416: 2 0.416 - 0.554: 0 0.554 - 0.693: 1 Chirality restraints: 3450 Sorted by residual: chirality pdb=" C1 MAN K 3 " pdb=" O4 NAG K 2 " pdb=" C2 MAN K 3 " pdb=" O5 MAN K 3 " both_signs ideal model delta sigma weight residual False 2.40 2.10 0.30 2.00e-02 2.50e+03 2.25e+02 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 368 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.09 0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.13e+01 ... (remaining 3447 not shown) Planarity restraints: 3759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " 0.322 2.00e-02 2.50e+03 2.74e-01 9.41e+02 pdb=" C7 NAG K 1 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " 0.008 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " -0.470 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " 0.215 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.080 2.00e-02 2.50e+03 6.59e-02 5.43e+01 pdb=" C7 NAG H 2 " -0.021 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.061 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.105 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " 0.070 2.00e-02 2.50e+03 5.84e-02 4.27e+01 pdb=" C7 NAG K 2 " -0.016 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " -0.020 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " -0.091 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " 0.057 2.00e-02 2.50e+03 ... (remaining 3756 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 43 2.40 - 3.02: 12753 3.02 - 3.65: 30609 3.65 - 4.27: 46991 4.27 - 4.90: 80292 Nonbonded interactions: 170688 Sorted by model distance: nonbonded pdb=" O SER D 509 " pdb=" N GLU D 903 " model vdw 1.773 3.120 nonbonded pdb=" OD2 ASP D 729 " pdb=" OH TYR D 759 " model vdw 2.046 3.040 nonbonded pdb=" O SER B 509 " pdb=" N GLU B 903 " model vdw 2.071 3.120 nonbonded pdb=" ND2 ASN B 256 " pdb=" O VAL B 276 " model vdw 2.084 3.120 nonbonded pdb=" NH1 ARG D 516 " pdb=" OXT GLU D 903 " model vdw 2.092 3.120 ... (remaining 170683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '3' selection = chain '5' selection = chain 'N' selection = chain 'P' selection = chain 'T' selection = chain 'W' selection = chain 'e' selection = chain 'k' selection = chain 'm' selection = chain 'r' selection = chain 't' selection = chain 'v' } ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 25 through 545 or resid 663 through 794 or resid 902 throu \ gh 906)) } ncs_group { reference = (chain 'B' and (resid 29 through 537 or resid 658 through 799 or resid 902)) selection = (chain 'D' and (resid 29 through 799 or resid 901)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'b' selection = chain 'y' } 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.680 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.627 21815 Z= 0.279 Angle : 0.862 73.224 29695 Z= 0.405 Chirality : 0.050 0.693 3450 Planarity : 0.007 0.274 3729 Dihedral : 17.100 178.767 8861 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.35 % Favored : 94.42 % Rotamer: Outliers : 0.13 % Allowed : 22.66 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.16), residues: 2600 helix: 1.31 (0.17), residues: 947 sheet: -1.00 (0.24), residues: 455 loop : -1.63 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 318 TYR 0.017 0.001 TYR D 476 PHE 0.017 0.002 PHE C 533 TRP 0.015 0.001 TRP A 768 HIS 0.008 0.001 HIS A 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00714 / 0.27 (21751) covalent geometry : angle 0.84854 / 0.40 (29515) SS BOND : bond 0.00334 / 0.19 ( 12) SS BOND : angle 1.06822 / 0.72 ( 24) hydrogen bonds : bond 0.15054 / 10.81 ( 838) hydrogen bonds : angle 6.53001 / 4.55 ( 2448) link_ALPHA1-4 : bond 0.01022 / 0.54 ( 5) link_ALPHA1-4 : angle 2.39767 / 1.40 ( 15) link_BETA1-4 : bond 0.00618 / 0.36 ( 17) link_BETA1-4 : angle 1.52477 / 1.02 ( 51) link_NAG-ASN : bond 0.04277 / 1.63 ( 30) link_NAG-ASN : angle 2.51969 / 1.58 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 0.729 Fit side-chains REVERT: C 101 HIS cc_start: 0.6562 (m90) cc_final: 0.6113 (t70) outliers start: 3 outliers final: 0 residues processed: 100 average time/residue: 0.5831 time to fit residues: 67.4032 Evaluate side-chains 92 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 0.0270 chunk 258 optimal weight: 2.9990 overall best weight: 1.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 GLN A 521 ASN D 148 GLN D 256 ASN D 483 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.114089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.081316 restraints weight = 34733.334| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.03 r_work: 0.2902 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21815 Z= 0.144 Angle : 0.588 12.445 29695 Z= 0.294 Chirality : 0.045 0.259 3450 Planarity : 0.004 0.077 3729 Dihedral : 9.556 174.875 3969 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.58 % Favored : 94.19 % Rotamer: Outliers : 2.14 % Allowed : 20.84 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.40 (0.17), residues: 2600 helix: 1.57 (0.17), residues: 957 sheet: -0.94 (0.24), residues: 451 loop : -1.56 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 89 TYR 0.016 0.001 TYR D 476 PHE 0.015 0.001 PHE C 458 TRP 0.008 0.001 TRP C 792 HIS 0.005 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (21751) covalent geometry : angle 0.57933 / 0.29 (29515) SS BOND : bond 0.00162 / 0.11 ( 12) SS BOND : angle 0.82215 / 0.56 ( 24) hydrogen bonds : bond 0.04001 / 2.82 ( 838) hydrogen bonds : angle 5.14245 / 3.61 ( 2448) link_ALPHA1-4 : bond 0.01232 / 0.68 ( 5) link_ALPHA1-4 : angle 1.76254 / 0.94 ( 15) link_BETA1-4 : bond 0.00511 / 0.30 ( 17) link_BETA1-4 : angle 1.14197 / 0.82 ( 51) link_NAG-ASN : bond 0.00426 / 0.24 ( 30) link_NAG-ASN : angle 1.62597 / 1.05 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 102 time to evaluate : 0.908 Fit side-chains REVERT: B 89 ARG cc_start: 0.6637 (mmm160) cc_final: 0.6385 (mmm160) REVERT: B 358 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8289 (mtp) REVERT: B 390 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.7099 (p90) REVERT: B 720 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7655 (mpt) REVERT: C 101 HIS cc_start: 0.6914 (m90) cc_final: 0.6183 (t70) REVERT: C 240 MET cc_start: 0.8887 (mtp) cc_final: 0.8431 (ttm) REVERT: C 736 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8074 (mp) REVERT: D 371 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.7871 (tmm) outliers start: 48 outliers final: 16 residues processed: 139 average time/residue: 0.5194 time to fit residues: 84.4264 Evaluate side-chains 115 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 390 TYR Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain C residue 56 TRP Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 371 MET Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 716 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 181 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 256 optimal weight: 4.9990 chunk 244 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 182 optimal weight: 0.5980 chunk 144 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 94 optimal weight: 0.0030 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.115034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.082420 restraints weight = 34727.921| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.03 r_work: 0.2923 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21815 Z= 0.113 Angle : 0.542 11.487 29695 Z= 0.269 Chirality : 0.043 0.244 3450 Planarity : 0.004 0.077 3729 Dihedral : 8.501 172.475 3969 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.62 % Favored : 94.19 % Rotamer: Outliers : 2.32 % Allowed : 21.06 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2600 helix: 1.69 (0.17), residues: 969 sheet: -0.82 (0.24), residues: 446 loop : -1.55 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 318 TYR 0.015 0.001 TYR D 476 PHE 0.013 0.001 PHE C 458 TRP 0.010 0.001 TRP A 381 HIS 0.004 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (21751) covalent geometry : angle 0.53244 / 0.27 (29515) SS BOND : bond 0.00182 / 0.10 ( 12) SS BOND : angle 0.66370 / 0.46 ( 24) hydrogen bonds : bond 0.03475 / 2.43 ( 838) hydrogen bonds : angle 4.85461 / 3.40 ( 2448) link_ALPHA1-4 : bond 0.01047 / 0.59 ( 5) link_ALPHA1-4 : angle 1.71467 / 0.92 ( 15) link_BETA1-4 : bond 0.00458 / 0.28 ( 17) link_BETA1-4 : angle 1.23952 / 0.88 ( 51) link_NAG-ASN : bond 0.00247 / 0.17 ( 30) link_NAG-ASN : angle 1.52944 / 0.99 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 102 time to evaluate : 0.872 Fit side-chains REVERT: B 89 ARG cc_start: 0.6757 (mmm160) cc_final: 0.6410 (mmm160) REVERT: B 287 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7526 (mt0) REVERT: B 390 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.7078 (p90) REVERT: B 487 VAL cc_start: 0.8733 (t) cc_final: 0.8496 (m) REVERT: B 720 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7580 (mpt) REVERT: B 744 LYS cc_start: 0.7950 (mtmm) cc_final: 0.7703 (mtmt) REVERT: C 101 HIS cc_start: 0.6877 (m90) cc_final: 0.6136 (t70) REVERT: C 240 MET cc_start: 0.8892 (mtp) cc_final: 0.8470 (ttm) REVERT: C 246 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8546 (m) REVERT: C 736 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8093 (mp) outliers start: 52 outliers final: 17 residues processed: 147 average time/residue: 0.4986 time to fit residues: 85.5410 Evaluate side-chains 115 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 390 TYR Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain C residue 56 TRP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 660 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 11 optimal weight: 0.8980 chunk 195 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 67 optimal weight: 0.0770 chunk 140 optimal weight: 0.0020 chunk 135 optimal weight: 1.9990 chunk 125 optimal weight: 0.0060 chunk 206 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 ASN B 172 HIS D 395 GLN D 429 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.115907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.083569 restraints weight = 34610.842| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.02 r_work: 0.2947 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21815 Z= 0.099 Angle : 0.528 13.480 29695 Z= 0.260 Chirality : 0.043 0.245 3450 Planarity : 0.004 0.075 3729 Dihedral : 7.910 171.767 3969 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.54 % Favored : 94.27 % Rotamer: Outliers : 2.49 % Allowed : 21.15 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.11 (0.17), residues: 2600 helix: 1.85 (0.17), residues: 968 sheet: -0.75 (0.25), residues: 446 loop : -1.47 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 318 TYR 0.014 0.001 TYR D 476 PHE 0.012 0.001 PHE C 458 TRP 0.009 0.001 TRP A 381 HIS 0.004 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (21751) covalent geometry : angle 0.51908 / 0.26 (29515) SS BOND : bond 0.00166 / 0.10 ( 12) SS BOND : angle 0.64127 / 0.43 ( 24) hydrogen bonds : bond 0.03077 / 2.13 ( 838) hydrogen bonds : angle 4.67839 / 3.28 ( 2448) link_ALPHA1-4 : bond 0.00987 / 0.57 ( 5) link_ALPHA1-4 : angle 1.77041 / 0.95 ( 15) link_BETA1-4 : bond 0.00457 / 0.28 ( 17) link_BETA1-4 : angle 1.24448 / 0.91 ( 51) link_NAG-ASN : bond 0.00266 / 0.19 ( 30) link_NAG-ASN : angle 1.47074 / 0.96 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 107 time to evaluate : 0.853 Fit side-chains REVERT: B 191 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7070 (tp) REVERT: B 287 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7508 (mt0) REVERT: B 358 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8230 (mtp) REVERT: B 390 TYR cc_start: 0.7488 (OUTLIER) cc_final: 0.7074 (p90) REVERT: B 518 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8510 (mt-10) REVERT: C 101 HIS cc_start: 0.6836 (m90) cc_final: 0.6070 (t70) REVERT: C 240 MET cc_start: 0.8884 (mtp) cc_final: 0.8499 (ttm) REVERT: C 246 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8561 (m) REVERT: D 89 ARG cc_start: 0.7833 (ptm160) cc_final: 0.7351 (ttt90) REVERT: D 527 VAL cc_start: 0.8920 (OUTLIER) cc_final: 0.8670 (m) outliers start: 56 outliers final: 24 residues processed: 152 average time/residue: 0.5120 time to fit residues: 91.2642 Evaluate side-chains 126 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 390 TYR Chi-restraints excluded: chain C residue 56 TRP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 429 ASN Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 660 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 33 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 HIS D 429 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.111269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.078364 restraints weight = 34780.356| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.02 r_work: 0.2852 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 21815 Z= 0.234 Angle : 0.625 10.398 29695 Z= 0.310 Chirality : 0.047 0.256 3450 Planarity : 0.005 0.077 3729 Dihedral : 7.915 173.857 3969 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.85 % Favored : 93.96 % Rotamer: Outliers : 2.89 % Allowed : 20.84 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2600 helix: 1.69 (0.17), residues: 964 sheet: -0.94 (0.24), residues: 458 loop : -1.47 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 318 TYR 0.013 0.001 TYR C 692 PHE 0.019 0.002 PHE C 533 TRP 0.012 0.001 TRP B 375 HIS 0.006 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.23 (21751) covalent geometry : angle 0.61455 / 0.31 (29515) SS BOND : bond 0.00293 / 0.20 ( 12) SS BOND : angle 0.97911 / 0.66 ( 24) hydrogen bonds : bond 0.04158 / 2.90 ( 838) hydrogen bonds : angle 4.83832 / 3.39 ( 2448) link_ALPHA1-4 : bond 0.01075 / 0.60 ( 5) link_ALPHA1-4 : angle 1.81392 / 0.99 ( 15) link_BETA1-4 : bond 0.00447 / 0.24 ( 17) link_BETA1-4 : angle 1.42808 / 1.04 ( 51) link_NAG-ASN : bond 0.00320 / 0.21 ( 30) link_NAG-ASN : angle 1.77074 / 1.15 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 95 time to evaluate : 0.788 Fit side-chains REVERT: B 358 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8404 (mtp) REVERT: B 390 TYR cc_start: 0.7573 (OUTLIER) cc_final: 0.7122 (p90) REVERT: B 678 PHE cc_start: 0.6612 (OUTLIER) cc_final: 0.6400 (t80) REVERT: C 101 HIS cc_start: 0.6813 (m90) cc_final: 0.6093 (t70) REVERT: C 115 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8525 (mpt180) REVERT: C 240 MET cc_start: 0.8995 (mtp) cc_final: 0.8618 (ttm) REVERT: C 437 THR cc_start: 0.8509 (OUTLIER) cc_final: 0.8109 (p) REVERT: C 736 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8133 (mp) REVERT: D 61 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6613 (tm-30) outliers start: 65 outliers final: 36 residues processed: 148 average time/residue: 0.5079 time to fit residues: 87.9438 Evaluate side-chains 129 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 86 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 390 TYR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 678 PHE Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain C residue 56 TRP Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 747 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 54 optimal weight: 0.9990 chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 104 optimal weight: 0.0270 chunk 243 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 202 optimal weight: 0.0870 chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.114202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.081585 restraints weight = 34587.169| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.02 r_work: 0.2906 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21815 Z= 0.111 Angle : 0.537 10.150 29695 Z= 0.266 Chirality : 0.043 0.245 3450 Planarity : 0.004 0.076 3729 Dihedral : 7.655 173.216 3969 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.73 % Favored : 94.08 % Rotamer: Outliers : 2.00 % Allowed : 22.35 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.16 (0.17), residues: 2600 helix: 1.81 (0.17), residues: 966 sheet: -0.82 (0.24), residues: 451 loop : -1.47 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 488 TYR 0.014 0.001 TYR D 476 PHE 0.013 0.001 PHE C 458 TRP 0.010 0.001 TRP A 381 HIS 0.004 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (21751) covalent geometry : angle 0.52710 / 0.26 (29515) SS BOND : bond 0.00189 / 0.12 ( 12) SS BOND : angle 0.66443 / 0.46 ( 24) hydrogen bonds : bond 0.03225 / 2.23 ( 838) hydrogen bonds : angle 4.65296 / 3.26 ( 2448) link_ALPHA1-4 : bond 0.00960 / 0.55 ( 5) link_ALPHA1-4 : angle 1.79859 / 0.95 ( 15) link_BETA1-4 : bond 0.00428 / 0.26 ( 17) link_BETA1-4 : angle 1.28004 / 0.93 ( 51) link_NAG-ASN : bond 0.00257 / 0.18 ( 30) link_NAG-ASN : angle 1.52719 / 1.00 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 95 time to evaluate : 0.517 Fit side-chains REVERT: A 240 MET cc_start: 0.8216 (mmt) cc_final: 0.7984 (mmt) REVERT: A 786 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: B 203 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7688 (mt) REVERT: B 390 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.6888 (p90) REVERT: B 744 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7778 (mtmt) REVERT: C 101 HIS cc_start: 0.6881 (m90) cc_final: 0.6068 (t70) REVERT: C 115 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8541 (mpt180) REVERT: C 240 MET cc_start: 0.8912 (mtp) cc_final: 0.8546 (ttm) REVERT: C 246 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8585 (m) REVERT: C 437 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8016 (p) REVERT: C 736 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8071 (mp) outliers start: 45 outliers final: 24 residues processed: 135 average time/residue: 0.5326 time to fit residues: 83.2080 Evaluate side-chains 120 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 390 TYR Chi-restraints excluded: chain C residue 56 TRP Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 429 ASN Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 660 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 253 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 150 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 224 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.113748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.081072 restraints weight = 34544.039| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.01 r_work: 0.2900 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21815 Z= 0.123 Angle : 0.536 9.740 29695 Z= 0.266 Chirality : 0.044 0.249 3450 Planarity : 0.004 0.076 3729 Dihedral : 7.532 172.671 3969 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.81 % Favored : 94.00 % Rotamer: Outliers : 2.32 % Allowed : 22.13 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.13 (0.17), residues: 2600 helix: 1.84 (0.17), residues: 966 sheet: -0.82 (0.24), residues: 451 loop : -1.46 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 488 TYR 0.013 0.001 TYR D 476 PHE 0.014 0.001 PHE C 458 TRP 0.009 0.001 TRP A 381 HIS 0.004 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (21751) covalent geometry : angle 0.52606 / 0.26 (29515) SS BOND : bond 0.00199 / 0.14 ( 12) SS BOND : angle 0.69829 / 0.48 ( 24) hydrogen bonds : bond 0.03311 / 2.29 ( 838) hydrogen bonds : angle 4.62650 / 3.24 ( 2448) link_ALPHA1-4 : bond 0.00962 / 0.56 ( 5) link_ALPHA1-4 : angle 1.83974 / 0.97 ( 15) link_BETA1-4 : bond 0.00422 / 0.25 ( 17) link_BETA1-4 : angle 1.31014 / 0.95 ( 51) link_NAG-ASN : bond 0.00235 / 0.17 ( 30) link_NAG-ASN : angle 1.56969 / 1.03 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 96 time to evaluate : 0.821 Fit side-chains REVERT: A 674 ASN cc_start: 0.7800 (OUTLIER) cc_final: 0.7583 (t160) REVERT: B 65 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7811 (mp) REVERT: B 203 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7685 (mt) REVERT: B 390 TYR cc_start: 0.7438 (OUTLIER) cc_final: 0.6938 (p90) REVERT: B 744 LYS cc_start: 0.8042 (mtmm) cc_final: 0.7794 (mtmt) REVERT: C 101 HIS cc_start: 0.6957 (m90) cc_final: 0.6250 (t70) REVERT: C 118 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8364 (m) REVERT: C 240 MET cc_start: 0.8934 (mtp) cc_final: 0.8564 (ttm) REVERT: C 246 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8598 (m) REVERT: C 736 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8084 (mp) REVERT: D 89 ARG cc_start: 0.7596 (ptm160) cc_final: 0.7165 (ttt90) REVERT: D 120 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8497 (mm) REVERT: D 371 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7951 (tmm) outliers start: 52 outliers final: 26 residues processed: 140 average time/residue: 0.4912 time to fit residues: 80.7029 Evaluate side-chains 125 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 390 TYR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 56 TRP Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 371 MET Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 429 ASN Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 660 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 43 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 449 HIS C 273 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.113970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.081258 restraints weight = 34661.634| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.02 r_work: 0.2901 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21815 Z= 0.120 Angle : 0.539 11.580 29695 Z= 0.266 Chirality : 0.044 0.247 3450 Planarity : 0.004 0.076 3729 Dihedral : 7.429 172.502 3969 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.85 % Favored : 94.00 % Rotamer: Outliers : 2.32 % Allowed : 22.40 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.17), residues: 2600 helix: 1.84 (0.17), residues: 966 sheet: -0.79 (0.24), residues: 455 loop : -1.43 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 488 TYR 0.013 0.001 TYR D 476 PHE 0.013 0.001 PHE C 458 TRP 0.009 0.001 TRP A 381 HIS 0.004 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (21751) covalent geometry : angle 0.52862 / 0.26 (29515) SS BOND : bond 0.00218 / 0.14 ( 12) SS BOND : angle 0.71119 / 0.48 ( 24) hydrogen bonds : bond 0.03242 / 2.24 ( 838) hydrogen bonds : angle 4.60970 / 3.23 ( 2448) link_ALPHA1-4 : bond 0.00973 / 0.57 ( 5) link_ALPHA1-4 : angle 1.86041 / 0.98 ( 15) link_BETA1-4 : bond 0.00422 / 0.25 ( 17) link_BETA1-4 : angle 1.29247 / 0.94 ( 51) link_NAG-ASN : bond 0.00243 / 0.17 ( 30) link_NAG-ASN : angle 1.55576 / 1.02 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 96 time to evaluate : 0.831 Fit side-chains REVERT: A 674 ASN cc_start: 0.7799 (OUTLIER) cc_final: 0.7580 (t160) REVERT: A 786 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: B 65 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7877 (mp) REVERT: B 203 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7715 (mt) REVERT: B 390 TYR cc_start: 0.7424 (OUTLIER) cc_final: 0.6921 (p90) REVERT: B 518 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8505 (mt-10) REVERT: B 744 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7826 (mtmt) REVERT: C 36 ARG cc_start: 0.8539 (ttm-80) cc_final: 0.8232 (ttm110) REVERT: C 101 HIS cc_start: 0.6892 (m90) cc_final: 0.6191 (t70) REVERT: C 115 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8541 (mpt180) REVERT: C 118 VAL cc_start: 0.8596 (OUTLIER) cc_final: 0.8371 (m) REVERT: C 196 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8443 (mt0) REVERT: C 240 MET cc_start: 0.8927 (mtp) cc_final: 0.8555 (ttm) REVERT: C 246 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8573 (m) REVERT: C 437 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8049 (p) REVERT: C 736 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8092 (mp) REVERT: D 89 ARG cc_start: 0.7582 (ptm160) cc_final: 0.7142 (ttt90) REVERT: D 120 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8494 (mm) outliers start: 52 outliers final: 29 residues processed: 143 average time/residue: 0.5549 time to fit residues: 92.0796 Evaluate side-chains 131 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 90 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 390 TYR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain C residue 56 TRP Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 429 ASN Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 660 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 106 optimal weight: 10.0000 chunk 211 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 128 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 GLN C 146 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.111279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.078367 restraints weight = 34677.411| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.01 r_work: 0.2848 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21815 Z= 0.193 Angle : 0.604 9.921 29695 Z= 0.299 Chirality : 0.046 0.255 3450 Planarity : 0.004 0.076 3729 Dihedral : 7.490 173.312 3969 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.92 % Favored : 93.92 % Rotamer: Outliers : 2.23 % Allowed : 22.66 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.17), residues: 2600 helix: 1.74 (0.17), residues: 960 sheet: -0.99 (0.23), residues: 471 loop : -1.44 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 318 TYR 0.012 0.001 TYR C 410 PHE 0.018 0.002 PHE C 533 TRP 0.010 0.001 TRP B 375 HIS 0.004 0.001 HIS A 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.19 (21751) covalent geometry : angle 0.59246 / 0.30 (29515) SS BOND : bond 0.00256 / 0.19 ( 12) SS BOND : angle 0.94537 / 0.62 ( 24) hydrogen bonds : bond 0.03989 / 2.78 ( 838) hydrogen bonds : angle 4.77239 / 3.34 ( 2448) link_ALPHA1-4 : bond 0.01021 / 0.60 ( 5) link_ALPHA1-4 : angle 1.90899 / 1.00 ( 15) link_BETA1-4 : bond 0.00402 / 0.23 ( 17) link_BETA1-4 : angle 1.41393 / 1.03 ( 51) link_NAG-ASN : bond 0.00294 / 0.19 ( 30) link_NAG-ASN : angle 1.78140 / 1.16 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 91 time to evaluate : 0.839 Fit side-chains REVERT: A 209 MET cc_start: 0.7747 (mmm) cc_final: 0.7540 (mmt) REVERT: A 502 MET cc_start: 0.9160 (mmm) cc_final: 0.8723 (mmm) REVERT: A 674 ASN cc_start: 0.7759 (OUTLIER) cc_final: 0.7511 (t160) REVERT: B 65 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7938 (mp) REVERT: B 203 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7843 (mt) REVERT: B 390 TYR cc_start: 0.7523 (OUTLIER) cc_final: 0.7002 (p90) REVERT: B 744 LYS cc_start: 0.8209 (mtmm) cc_final: 0.7942 (mtmt) REVERT: C 36 ARG cc_start: 0.8576 (ttm-80) cc_final: 0.8247 (ttm110) REVERT: C 101 HIS cc_start: 0.6868 (m90) cc_final: 0.6090 (t70) REVERT: C 115 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8538 (mpt180) REVERT: C 240 MET cc_start: 0.8992 (mtp) cc_final: 0.8643 (ttm) REVERT: C 246 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8579 (m) REVERT: C 437 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8158 (p) REVERT: C 736 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8142 (mp) REVERT: D 61 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6516 (tm-30) REVERT: D 89 ARG cc_start: 0.7694 (ptm160) cc_final: 0.7256 (ttt90) REVERT: D 120 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8559 (mm) REVERT: D 371 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7974 (tmm) outliers start: 50 outliers final: 33 residues processed: 137 average time/residue: 0.5520 time to fit residues: 88.4717 Evaluate side-chains 132 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 88 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 390 TYR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain C residue 56 TRP Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 371 MET Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 429 ASN Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 660 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 118 optimal weight: 0.0370 chunk 236 optimal weight: 20.0000 chunk 137 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 224 optimal weight: 0.0000 chunk 246 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 243 optimal weight: 0.5980 chunk 175 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 overall best weight: 0.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 768 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.114372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.081802 restraints weight = 34634.176| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.02 r_work: 0.2908 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21815 Z= 0.103 Angle : 0.541 13.464 29695 Z= 0.267 Chirality : 0.043 0.239 3450 Planarity : 0.004 0.075 3729 Dihedral : 7.298 173.186 3969 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.62 % Favored : 94.23 % Rotamer: Outliers : 1.91 % Allowed : 23.11 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.17), residues: 2600 helix: 1.82 (0.17), residues: 966 sheet: -0.86 (0.24), residues: 472 loop : -1.45 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 488 TYR 0.013 0.001 TYR D 476 PHE 0.012 0.001 PHE C 458 TRP 0.011 0.001 TRP A 381 HIS 0.003 0.001 HIS D 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (21751) covalent geometry : angle 0.53205 / 0.26 (29515) SS BOND : bond 0.00180 / 0.12 ( 12) SS BOND : angle 0.66213 / 0.45 ( 24) hydrogen bonds : bond 0.03109 / 2.15 ( 838) hydrogen bonds : angle 4.60491 / 3.23 ( 2448) link_ALPHA1-4 : bond 0.01002 / 0.60 ( 5) link_ALPHA1-4 : angle 1.86148 / 0.96 ( 15) link_BETA1-4 : bond 0.00430 / 0.27 ( 17) link_BETA1-4 : angle 1.25386 / 0.91 ( 51) link_NAG-ASN : bond 0.00283 / 0.20 ( 30) link_NAG-ASN : angle 1.50276 / 0.98 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 96 time to evaluate : 0.882 Fit side-chains REVERT: A 209 MET cc_start: 0.7764 (mmm) cc_final: 0.7510 (mmt) REVERT: A 502 MET cc_start: 0.9173 (mmm) cc_final: 0.8729 (mmm) REVERT: A 786 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7595 (mp0) REVERT: B 390 TYR cc_start: 0.7403 (OUTLIER) cc_final: 0.6838 (p90) REVERT: B 744 LYS cc_start: 0.8223 (mtmm) cc_final: 0.7982 (mtmt) REVERT: C 36 ARG cc_start: 0.8533 (ttm-80) cc_final: 0.8224 (ttm110) REVERT: C 101 HIS cc_start: 0.6881 (m90) cc_final: 0.6097 (t70) REVERT: C 115 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8540 (mpt180) REVERT: C 240 MET cc_start: 0.8914 (mtp) cc_final: 0.8544 (ttm) REVERT: C 246 VAL cc_start: 0.8848 (OUTLIER) cc_final: 0.8577 (m) REVERT: C 437 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8129 (p) REVERT: C 736 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8074 (mp) REVERT: D 61 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7358 (tp30) REVERT: D 89 ARG cc_start: 0.7560 (ptm160) cc_final: 0.7130 (ttt90) REVERT: D 120 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8447 (mm) REVERT: D 527 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8767 (m) outliers start: 43 outliers final: 27 residues processed: 132 average time/residue: 0.5694 time to fit residues: 87.7633 Evaluate side-chains 126 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 390 TYR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 56 TRP Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 429 ASN Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 660 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 73 optimal weight: 3.9990 chunk 24 optimal weight: 0.1980 chunk 152 optimal weight: 0.9980 chunk 232 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 183 optimal weight: 0.6980 chunk 168 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.113315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.081024 restraints weight = 34657.237| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.97 r_work: 0.2898 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21815 Z= 0.117 Angle : 0.546 12.561 29695 Z= 0.267 Chirality : 0.043 0.245 3450 Planarity : 0.004 0.075 3729 Dihedral : 7.168 172.323 3969 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.85 % Favored : 94.00 % Rotamer: Outliers : 1.60 % Allowed : 23.37 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.11 (0.17), residues: 2600 helix: 1.84 (0.17), residues: 967 sheet: -0.87 (0.24), residues: 482 loop : -1.40 (0.18), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 318 TYR 0.013 0.001 TYR D 476 PHE 0.013 0.001 PHE C 458 TRP 0.009 0.001 TRP A 381 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (21751) covalent geometry : angle 0.53642 / 0.27 (29515) SS BOND : bond 0.00180 / 0.13 ( 12) SS BOND : angle 0.71496 / 0.47 ( 24) hydrogen bonds : bond 0.03228 / 2.23 ( 838) hydrogen bonds : angle 4.59469 / 3.22 ( 2448) link_ALPHA1-4 : bond 0.01088 / 0.66 ( 5) link_ALPHA1-4 : angle 1.85127 / 0.98 ( 15) link_BETA1-4 : bond 0.00414 / 0.25 ( 17) link_BETA1-4 : angle 1.28002 / 0.92 ( 51) link_NAG-ASN : bond 0.00232 / 0.16 ( 30) link_NAG-ASN : angle 1.53802 / 1.01 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4737.92 seconds wall clock time: 82 minutes 11.92 seconds (4931.92 seconds total)