Starting phenix.real_space_refine on Thu Feb 5 00:08:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ghr_40047/02_2026/8ghr_40047.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ghr_40047/02_2026/8ghr_40047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ghr_40047/02_2026/8ghr_40047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ghr_40047/02_2026/8ghr_40047.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ghr_40047/02_2026/8ghr_40047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ghr_40047/02_2026/8ghr_40047.map" } resolution = 3.2 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= 0.001 sd= 0.027 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 4 6.06 5 P 2 5.49 5 S 72 5.16 5 C 8870 2.51 5 N 2304 2.21 5 O 2610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13864 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5887 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 735, 5876 Classifications: {'peptide': 735} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 3, 'PTRANS': 51, 'TRANS': 680} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 86 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1, 'ARG:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 735, 5876 Classifications: {'peptide': 735} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 3, 'PTRANS': 51, 'TRANS': 680} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 86 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1, 'ARG:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 6040 Chain: "B" Number of atoms: 5887 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 735, 5876 Classifications: {'peptide': 735} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 3, 'PTRANS': 51, 'TRANS': 680} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 86 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1, 'ARG:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 735, 5876 Classifications: {'peptide': 735} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 3, 'PTRANS': 51, 'TRANS': 680} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 86 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1, 'ARG:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 6040 Chain: "C" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 932 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 932 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 54 Unusual residues: {' CA': 1, ' ZN': 2, 'AMP%rna3p': 1, 'NAG': 2} Classifications: {'RNA_mixed': 1, 'undetermined': 5} Modifications used: {'rna3p': 1} Link IDs: {None: 5} 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: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 54 Unusual residues: {' CA': 1, ' ZN': 2, 'AMP%rna3p': 1, 'NAG': 2} Classifications: {'RNA_mixed': 1, 'undetermined': 5} Modifications used: {'rna3p': 1} Link IDs: {None: 5} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ACYS A 626 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 626 " occ=0.50 residue: pdb=" N AASN A 700 " occ=0.75 ... (8 atoms not shown) pdb=" CB BASN A 700 " occ=0.25 residue: pdb=" N ACYS B 626 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 626 " occ=0.50 residue: pdb=" N AASN B 700 " occ=0.75 ... (8 atoms not shown) pdb=" CB BASN B 700 " occ=0.25 Time building chain proxies: 4.58, per 1000 atoms: 0.33 Number of scatterers: 13864 At special positions: 0 Unit cell: (120.61, 124.081, 105.859, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 2 19.99 S 72 16.00 P 2 15.00 O 2610 8.00 N 2304 7.00 C 8870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 241 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 868 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG ACYS A 626 " - pdb=" SG CYS A 726 " distance=2.03 Simple disulfide: pdb=" SG CYS A 628 " - pdb=" SG CYS A 711 " distance=2.03 Simple disulfide: pdb=" SG CYS A 726 " - pdb=" SG BCYS A 626 " distance=2.03 Simple disulfide: pdb=" SG CYS A 838 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 241 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 431 " - pdb=" SG CYS B 530 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 868 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG ACYS B 626 " - pdb=" SG CYS B 726 " distance=2.03 Simple disulfide: pdb=" SG CYS B 628 " - pdb=" SG CYS B 711 " distance=2.03 Simple disulfide: pdb=" SG CYS B 726 " - pdb=" SG BCYS B 626 " distance=2.03 Simple disulfide: pdb=" SG CYS B 838 " - pdb=" SG CYS B 848 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1304 " - " ASN A 285 " " NAG A1305 " - " ASN A 477 " " NAG B1304 " - " ASN B 285 " " NAG B1305 " - " ASN B 477 " " NAG E 1 " - " ASN A 341 " " NAG F 1 " - " ASN A 585 " " NAG G 1 " - " ASN B 341 " " NAG H 1 " - " ASN B 585 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 910.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" NE2 HIS A 380 " pdb="ZN ZN A1301 " - pdb=" NE2 HIS A 535 " pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A 424 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" NE2 HIS B 380 " pdb="ZN ZN B1301 " - pdb=" NE2 HIS B 535 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" NE2 HIS B 424 " 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 26 sheets defined 30.5% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 221 through 228 removed outlier: 4.036A pdb=" N LEU A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.690A pdb=" N ASN A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 263 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL A 264 " --> pdb=" O HIS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 292 through 301 removed outlier: 3.969A pdb=" N LYS A 295 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 296 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Proline residue: A 298 - end of helix Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.677A pdb=" N THR A 309 " --> pdb=" O PRO A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 332 removed outlier: 3.906A pdb=" N GLY A 331 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 358 Processing helix chain 'A' and resid 375 through 383 Processing helix chain 'A' and resid 386 through 410 removed outlier: 3.857A pdb=" N ILE A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 442 Processing helix chain 'A' and resid 470 through 478 removed outlier: 4.169A pdb=" N ILE A 474 " --> pdb=" O ASN A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 removed outlier: 4.104A pdb=" N GLN A 545 " --> pdb=" O SER A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 577 removed outlier: 3.681A pdb=" N LEU A 572 " --> pdb=" O GLU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 595 removed outlier: 3.838A pdb=" N LEU A 594 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 595 " --> pdb=" O ASN A 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 591 through 595' Processing helix chain 'A' and resid 637 through 642 Processing helix chain 'A' and resid 645 through 657 Processing helix chain 'A' and resid 721 through 724 Processing helix chain 'A' and resid 725 through 730 removed outlier: 3.896A pdb=" N TYR A 729 " --> pdb=" O LYS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 758 Processing helix chain 'A' and resid 768 through 789 removed outlier: 4.171A pdb=" N ILE A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU A 781 " --> pdb=" O HIS A 777 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG A 782 " --> pdb=" O ASP A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 816 removed outlier: 3.905A pdb=" N GLN A 815 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 848 removed outlier: 3.697A pdb=" N CYS A 848 " --> pdb=" O PRO A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 885 removed outlier: 4.473A pdb=" N TRP A 877 " --> pdb=" O HIS A 873 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL A 878 " --> pdb=" O ASP A 874 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU A 879 " --> pdb=" O SER A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 897 Processing helix chain 'A' and resid 907 through 916 Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 221 through 228 removed outlier: 4.037A pdb=" N LEU B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 232 through 241 Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.689A pdb=" N ASN B 259 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 263 " --> pdb=" O ASN B 259 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL B 264 " --> pdb=" O HIS B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 273 Processing helix chain 'B' and resid 292 through 301 removed outlier: 3.969A pdb=" N LYS B 295 " --> pdb=" O SER B 292 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B 296 " --> pdb=" O LYS B 293 " (cutoff:3.500A) Proline residue: B 298 - end of helix Processing helix chain 'B' and resid 305 through 313 removed outlier: 3.675A pdb=" N THR B 309 " --> pdb=" O PRO B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 332 removed outlier: 3.906A pdb=" N GLY B 331 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 375 through 383 Processing helix chain 'B' and resid 386 through 410 removed outlier: 3.857A pdb=" N ILE B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 442 Processing helix chain 'B' and resid 470 through 478 removed outlier: 4.170A pdb=" N ILE B 474 " --> pdb=" O ASN B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 545 removed outlier: 4.071A pdb=" N GLN B 545 " --> pdb=" O SER B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 577 removed outlier: 3.682A pdb=" N LEU B 572 " --> pdb=" O GLU B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 595 removed outlier: 3.843A pdb=" N LEU B 594 " --> pdb=" O LEU B 591 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 595 " --> pdb=" O ASN B 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 591 through 595' Processing helix chain 'B' and resid 637 through 642 Processing helix chain 'B' and resid 645 through 657 Processing helix chain 'B' and resid 721 through 724 Processing helix chain 'B' and resid 725 through 730 removed outlier: 3.897A pdb=" N TYR B 729 " --> pdb=" O LYS B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 758 Processing helix chain 'B' and resid 768 through 789 removed outlier: 4.171A pdb=" N ILE B 772 " --> pdb=" O SER B 768 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU B 781 " --> pdb=" O HIS B 777 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ARG B 782 " --> pdb=" O ASP B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 816 removed outlier: 3.908A pdb=" N GLN B 815 " --> pdb=" O GLU B 811 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B 816 " --> pdb=" O ASN B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 removed outlier: 3.694A pdb=" N CYS B 848 " --> pdb=" O PRO B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 885 removed outlier: 4.470A pdb=" N TRP B 877 " --> pdb=" O HIS B 873 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL B 878 " --> pdb=" O ASP B 874 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU B 879 " --> pdb=" O SER B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 897 Processing helix chain 'B' and resid 907 through 916 Processing helix chain 'C' and resid 63 through 66 Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.980A pdb=" N THR C 92 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 66 Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.980A pdb=" N THR D 92 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 243 through 244 removed outlier: 3.573A pdb=" N THR A 369 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 249 Processing sheet with id=AA3, first strand: chain 'A' and resid 279 through 281 Processing sheet with id=AA4, first strand: chain 'A' and resid 427 through 428 Processing sheet with id=AA5, first strand: chain 'A' and resid 447 through 450 removed outlier: 3.806A pdb=" N LEU A 457 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU A 510 " --> pdb=" O LEU A 457 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 663 through 664 Processing sheet with id=AA7, first strand: chain 'A' and resid 671 through 675 removed outlier: 6.552A pdb=" N MET A 680 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR A 693 " --> pdb=" O MET A 680 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLY A 682 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET A 689 " --> pdb=" O SER A 684 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 691 " --> pdb=" O PRO A 797 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA A 855 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 702 through 703 removed outlier: 4.589A pdb=" N SER A 702 " --> pdb=" O ASN A 746 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN A 746 " --> pdb=" O SER A 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 736 through 738 Processing sheet with id=AB1, first strand: chain 'A' and resid 818 through 820 Processing sheet with id=AB2, first strand: chain 'B' and resid 243 through 244 removed outlier: 3.572A pdb=" N THR B 369 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 248 through 249 Processing sheet with id=AB4, first strand: chain 'B' and resid 279 through 281 Processing sheet with id=AB5, first strand: chain 'B' and resid 427 through 428 Processing sheet with id=AB6, first strand: chain 'B' and resid 447 through 450 removed outlier: 3.808A pdb=" N LEU B 457 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU B 510 " --> pdb=" O LEU B 457 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 663 through 664 Processing sheet with id=AB8, first strand: chain 'B' and resid 671 through 675 removed outlier: 6.552A pdb=" N MET B 680 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR B 693 " --> pdb=" O MET B 680 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 682 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET B 689 " --> pdb=" O SER B 684 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 691 " --> pdb=" O PRO B 797 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA B 855 " --> pdb=" O ALA B 887 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 702 through 703 removed outlier: 4.589A pdb=" N SER B 702 " --> pdb=" O ASN B 746 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN B 746 " --> pdb=" O SER B 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 736 through 738 Processing sheet with id=AC2, first strand: chain 'B' and resid 818 through 820 Processing sheet with id=AC3, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AC4, first strand: chain 'C' and resid 11 through 12 removed outlier: 4.374A pdb=" N TYR C 34 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA C 50 " --> pdb=" O TRP C 37 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ARG C 39 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEU C 48 " --> pdb=" O ARG C 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.495A pdb=" N CYS C 97 " --> pdb=" O TRP C 114 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TRP C 114 " --> pdb=" O CYS C 97 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ARG C 99 " --> pdb=" O ASP C 112 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.373A pdb=" N TYR D 34 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ARG D 39 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LEU D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.493A pdb=" N CYS D 97 " --> pdb=" O TRP D 114 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRP D 114 " --> pdb=" O CYS D 97 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ARG D 99 " --> pdb=" O ASP D 112 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4407 1.34 - 1.46: 3509 1.46 - 1.58: 6242 1.58 - 1.70: 2 1.70 - 1.82: 102 Bond restraints: 14262 Sorted by residual: bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.84e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.80e+00 ... (remaining 14257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 19114 2.04 - 4.09: 286 4.09 - 6.13: 30 6.13 - 8.17: 4 8.17 - 10.22: 6 Bond angle restraints: 19440 Sorted by residual: angle pdb=" C SER A 709 " pdb=" N ASN A 710 " pdb=" CA ASN A 710 " ideal model delta sigma weight residual 121.54 127.51 -5.97 1.91e+00 2.74e-01 9.77e+00 angle pdb=" C SER B 709 " pdb=" N ASN B 710 " pdb=" CA ASN B 710 " ideal model delta sigma weight residual 121.54 127.47 -5.93 1.91e+00 2.74e-01 9.62e+00 angle pdb=" C PRO A 483 " pdb=" N ASN A 484 " pdb=" CA ASN A 484 " ideal model delta sigma weight residual 121.54 127.33 -5.79 1.91e+00 2.74e-01 9.19e+00 angle pdb=" C PRO B 483 " pdb=" N ASN B 484 " pdb=" CA ASN B 484 " ideal model delta sigma weight residual 121.54 127.31 -5.77 1.91e+00 2.74e-01 9.13e+00 angle pdb=" CA LEU A 359 " pdb=" CB LEU A 359 " pdb=" CG LEU A 359 " ideal model delta sigma weight residual 116.30 126.52 -10.22 3.50e+00 8.16e-02 8.52e+00 ... (remaining 19435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.47: 8132 24.47 - 48.94: 452 48.94 - 73.40: 32 73.40 - 97.87: 12 97.87 - 122.34: 2 Dihedral angle restraints: 8630 sinusoidal: 3590 harmonic: 5040 Sorted by residual: dihedral pdb=" CB CYS A 628 " pdb=" SG CYS A 628 " pdb=" SG CYS A 711 " pdb=" CB CYS A 711 " ideal model delta sinusoidal sigma weight residual -86.00 1.66 -87.66 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS B 628 " pdb=" SG CYS B 628 " pdb=" SG CYS B 711 " pdb=" CB CYS B 711 " ideal model delta sinusoidal sigma weight residual -86.00 1.64 -87.64 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS B 195 " pdb=" SG CYS B 195 " pdb=" SG CYS B 241 " pdb=" CB CYS B 241 " ideal model delta sinusoidal sigma weight residual -86.00 -162.28 76.28 1 1.00e+01 1.00e-02 7.32e+01 ... (remaining 8627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1685 0.049 - 0.098: 345 0.098 - 0.147: 82 0.147 - 0.196: 4 0.196 - 0.245: 2 Chirality restraints: 2118 Sorted by residual: chirality pdb=" C2' AMP A1303 " pdb=" C1' AMP A1303 " pdb=" C3' AMP A1303 " pdb=" O2' AMP A1303 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" C2' AMP B1303 " pdb=" C1' AMP B1303 " pdb=" C3' AMP B1303 " pdb=" O2' AMP B1303 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 585 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.97e-01 ... (remaining 2115 not shown) Planarity restraints: 2506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 721 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.06e+00 pdb=" N PRO B 722 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 722 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 722 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 721 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.04e+00 pdb=" N PRO A 722 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 722 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 722 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 257 " 0.015 2.00e-02 2.50e+03 1.34e-02 3.14e+00 pdb=" CG PHE B 257 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE B 257 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 257 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 257 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 257 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 257 " 0.001 2.00e-02 2.50e+03 ... (remaining 2503 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 73 2.52 - 3.11: 9535 3.11 - 3.71: 19723 3.71 - 4.30: 28318 4.30 - 4.90: 49299 Nonbonded interactions: 106948 Sorted by model distance: nonbonded pdb="ZN ZN B1301 " pdb=" O2P AMP B1303 " model vdw 1.923 2.230 nonbonded pdb="ZN ZN A1301 " pdb=" O2P AMP A1303 " model vdw 1.925 2.230 nonbonded pdb=" OD1 ASP A 218 " pdb="ZN ZN A1302 " model vdw 1.955 2.230 nonbonded pdb=" OD1 ASP B 218 " pdb="ZN ZN B1302 " model vdw 1.955 2.230 nonbonded pdb=" OD1 ASP A 376 " pdb="ZN ZN A1301 " model vdw 2.042 2.230 ... (remaining 106943 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 187 through 625 or resid 627 through 699 or resid 701 thro \ ugh 1306)) selection = (chain 'B' and (resid 187 through 625 or resid 627 through 699 or resid 701 thro \ ugh 1306)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.190 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 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 : 0.003 0.036 14300 Z= 0.132 Angle : 0.607 10.215 19516 Z= 0.294 Chirality : 0.043 0.245 2118 Planarity : 0.005 0.050 2498 Dihedral : 13.781 122.339 5350 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: -0.17 (0.20), residues: 1720 helix: 0.41 (0.28), residues: 350 sheet: 0.15 (0.26), residues: 362 loop : -0.33 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 814 TYR 0.017 0.001 TYR A 261 PHE 0.031 0.001 PHE B 257 TRP 0.010 0.001 TRP B 307 HIS 0.005 0.001 HIS B 272 Details of bonding type rmsd covalent geometry : bond 0.00283 (14262) covalent geometry : angle 0.60366 (19440) SS BOND : bond 0.00140 ( 20) SS BOND : angle 0.40940 ( 40) hydrogen bonds : bond 0.16660 ( 464) hydrogen bonds : angle 7.41930 ( 1242) metal coordination : bond 0.00433 ( 6) link_BETA1-4 : bond 0.00346 ( 4) link_BETA1-4 : angle 1.94532 ( 12) link_NAG-ASN : bond 0.00131 ( 8) link_NAG-ASN : angle 1.64486 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.429 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1087 time to fit residues: 30.6437 Evaluate side-chains 170 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.1980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 GLN A 815 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 GLN B 815 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.151827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.111933 restraints weight = 16877.782| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.52 r_work: 0.2843 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14300 Z= 0.193 Angle : 0.672 9.256 19516 Z= 0.332 Chirality : 0.046 0.211 2118 Planarity : 0.005 0.041 2498 Dihedral : 6.590 125.035 2160 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.67 % Allowed : 7.79 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: -0.30 (0.20), residues: 1720 helix: 0.57 (0.28), residues: 358 sheet: -0.22 (0.28), residues: 318 loop : -0.41 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 814 TYR 0.022 0.002 TYR A 261 PHE 0.042 0.002 PHE B 257 TRP 0.008 0.001 TRP B 307 HIS 0.010 0.002 HIS B 272 Details of bonding type rmsd covalent geometry : bond 0.00483 (14262) covalent geometry : angle 0.66767 (19440) SS BOND : bond 0.00269 ( 20) SS BOND : angle 1.02838 ( 40) hydrogen bonds : bond 0.05236 ( 464) hydrogen bonds : angle 5.82159 ( 1242) metal coordination : bond 0.01412 ( 6) link_BETA1-4 : bond 0.00186 ( 4) link_BETA1-4 : angle 1.64326 ( 12) link_NAG-ASN : bond 0.00142 ( 8) link_NAG-ASN : angle 1.86517 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 0.548 Fit side-chains REVERT: B 753 TYR cc_start: 0.8643 (t80) cc_final: 0.8025 (t80) outliers start: 10 outliers final: 10 residues processed: 168 average time/residue: 0.1169 time to fit residues: 28.5469 Evaluate side-chains 171 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 869 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 144 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 58 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.0370 chunk 113 optimal weight: 2.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.151668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.101122 restraints weight = 17081.950| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.45 r_work: 0.2800 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14300 Z= 0.131 Angle : 0.595 8.189 19516 Z= 0.292 Chirality : 0.044 0.191 2118 Planarity : 0.005 0.040 2498 Dihedral : 6.384 125.027 2160 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.87 % Allowed : 9.33 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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 (0.20), residues: 1720 helix: 0.78 (0.28), residues: 370 sheet: -0.04 (0.27), residues: 334 loop : -0.35 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 814 TYR 0.014 0.001 TYR A 261 PHE 0.030 0.002 PHE B 257 TRP 0.009 0.001 TRP B 307 HIS 0.008 0.001 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00320 (14262) covalent geometry : angle 0.59100 (19440) SS BOND : bond 0.00184 ( 20) SS BOND : angle 0.59562 ( 40) hydrogen bonds : bond 0.04135 ( 464) hydrogen bonds : angle 5.44908 ( 1242) metal coordination : bond 0.00863 ( 6) link_BETA1-4 : bond 0.00258 ( 4) link_BETA1-4 : angle 1.54777 ( 12) link_NAG-ASN : bond 0.00092 ( 8) link_NAG-ASN : angle 1.76817 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.519 Fit side-chains REVERT: A 753 TYR cc_start: 0.8604 (t80) cc_final: 0.8172 (t80) REVERT: B 753 TYR cc_start: 0.8570 (t80) cc_final: 0.8140 (t80) outliers start: 13 outliers final: 8 residues processed: 164 average time/residue: 0.1050 time to fit residues: 25.1260 Evaluate side-chains 165 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 157 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 798 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 106 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 chunk 156 optimal weight: 0.0980 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.151650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.100650 restraints weight = 16964.078| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.38 r_work: 0.2800 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14300 Z= 0.131 Angle : 0.592 9.284 19516 Z= 0.288 Chirality : 0.043 0.186 2118 Planarity : 0.005 0.039 2498 Dihedral : 6.341 125.928 2160 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.28 % Allowed : 9.87 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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 (0.20), residues: 1720 helix: 0.80 (0.28), residues: 372 sheet: -0.04 (0.27), residues: 334 loop : -0.35 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 814 TYR 0.013 0.001 TYR A 261 PHE 0.026 0.002 PHE B 257 TRP 0.009 0.001 TRP B 307 HIS 0.008 0.001 HIS B 272 Details of bonding type rmsd covalent geometry : bond 0.00323 (14262) covalent geometry : angle 0.58828 (19440) SS BOND : bond 0.00167 ( 20) SS BOND : angle 0.54354 ( 40) hydrogen bonds : bond 0.04007 ( 464) hydrogen bonds : angle 5.30260 ( 1242) metal coordination : bond 0.00829 ( 6) link_BETA1-4 : bond 0.00258 ( 4) link_BETA1-4 : angle 1.58477 ( 12) link_NAG-ASN : bond 0.00096 ( 8) link_NAG-ASN : angle 1.79398 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.527 Fit side-chains REVERT: A 753 TYR cc_start: 0.8649 (t80) cc_final: 0.8311 (t80) REVERT: B 753 TYR cc_start: 0.8620 (t80) cc_final: 0.8178 (t80) REVERT: C 92 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.8014 (t) REVERT: D 92 THR cc_start: 0.8223 (OUTLIER) cc_final: 0.8022 (t) outliers start: 19 outliers final: 13 residues processed: 173 average time/residue: 0.1104 time to fit residues: 28.0893 Evaluate side-chains 174 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 812 ASN Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 2 optimal weight: 0.5980 chunk 43 optimal weight: 20.0000 chunk 41 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN A 767 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.151157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.099327 restraints weight = 17056.359| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.29 r_work: 0.2825 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14300 Z= 0.130 Angle : 0.587 8.451 19516 Z= 0.286 Chirality : 0.043 0.182 2118 Planarity : 0.005 0.042 2498 Dihedral : 6.337 126.639 2160 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.07 % Allowed : 10.67 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: -0.04 (0.20), residues: 1720 helix: 1.00 (0.29), residues: 358 sheet: -0.21 (0.27), residues: 354 loop : -0.27 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 814 TYR 0.013 0.001 TYR A 337 PHE 0.023 0.002 PHE B 257 TRP 0.008 0.001 TRP B 307 HIS 0.008 0.001 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00319 (14262) covalent geometry : angle 0.58252 (19440) SS BOND : bond 0.00158 ( 20) SS BOND : angle 0.52453 ( 40) hydrogen bonds : bond 0.03913 ( 464) hydrogen bonds : angle 5.22449 ( 1242) metal coordination : bond 0.00826 ( 6) link_BETA1-4 : bond 0.00271 ( 4) link_BETA1-4 : angle 1.60620 ( 12) link_NAG-ASN : bond 0.00087 ( 8) link_NAG-ASN : angle 1.79909 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.551 Fit side-chains REVERT: A 753 TYR cc_start: 0.8584 (t80) cc_final: 0.8355 (t80) REVERT: B 753 TYR cc_start: 0.8581 (t80) cc_final: 0.8190 (t80) REVERT: C 61 TYR cc_start: 0.8805 (m-80) cc_final: 0.8455 (m-80) REVERT: D 61 TYR cc_start: 0.8817 (m-80) cc_final: 0.8467 (m-80) REVERT: D 92 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7982 (t) outliers start: 16 outliers final: 13 residues processed: 172 average time/residue: 0.1138 time to fit residues: 28.1234 Evaluate side-chains 174 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain D residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 142 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 143 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 815 GLN B 202 GLN B 815 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.152266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.100964 restraints weight = 16976.598| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.26 r_work: 0.2846 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14300 Z= 0.130 Angle : 0.589 9.968 19516 Z= 0.286 Chirality : 0.043 0.180 2118 Planarity : 0.005 0.039 2498 Dihedral : 6.336 127.036 2160 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.34 % Allowed : 11.21 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: -0.04 (0.20), residues: 1720 helix: 1.04 (0.29), residues: 358 sheet: -0.25 (0.26), residues: 354 loop : -0.26 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 814 TYR 0.013 0.001 TYR B 337 PHE 0.021 0.002 PHE B 257 TRP 0.008 0.001 TRP B 307 HIS 0.008 0.001 HIS B 272 Details of bonding type rmsd covalent geometry : bond 0.00319 (14262) covalent geometry : angle 0.58525 (19440) SS BOND : bond 0.00152 ( 20) SS BOND : angle 0.49581 ( 40) hydrogen bonds : bond 0.03889 ( 464) hydrogen bonds : angle 5.18955 ( 1242) metal coordination : bond 0.00790 ( 6) link_BETA1-4 : bond 0.00277 ( 4) link_BETA1-4 : angle 1.60831 ( 12) link_NAG-ASN : bond 0.00094 ( 8) link_NAG-ASN : angle 1.80629 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.414 Fit side-chains REVERT: C 61 TYR cc_start: 0.8797 (m-80) cc_final: 0.8432 (m-80) REVERT: D 61 TYR cc_start: 0.8806 (m-80) cc_final: 0.8444 (m-80) outliers start: 20 outliers final: 16 residues processed: 172 average time/residue: 0.1281 time to fit residues: 31.2251 Evaluate side-chains 173 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 834 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 117 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 815 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.149607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.100871 restraints weight = 17090.247| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.31 r_work: 0.2792 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14300 Z= 0.210 Angle : 0.666 10.357 19516 Z= 0.325 Chirality : 0.046 0.218 2118 Planarity : 0.005 0.039 2498 Dihedral : 6.655 130.438 2160 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.21 % Allowed : 11.48 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: -0.25 (0.20), residues: 1720 helix: 0.76 (0.28), residues: 358 sheet: -0.41 (0.27), residues: 334 loop : -0.35 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 814 TYR 0.017 0.002 TYR B 337 PHE 0.030 0.002 PHE B 257 TRP 0.009 0.001 TRP D 114 HIS 0.009 0.002 HIS B 272 Details of bonding type rmsd covalent geometry : bond 0.00529 (14262) covalent geometry : angle 0.66103 (19440) SS BOND : bond 0.00245 ( 20) SS BOND : angle 0.60774 ( 40) hydrogen bonds : bond 0.04924 ( 464) hydrogen bonds : angle 5.34428 ( 1242) metal coordination : bond 0.01403 ( 6) link_BETA1-4 : bond 0.00252 ( 4) link_BETA1-4 : angle 1.87929 ( 12) link_NAG-ASN : bond 0.00181 ( 8) link_NAG-ASN : angle 2.01885 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.520 Fit side-chains REVERT: A 815 GLN cc_start: 0.7536 (mm110) cc_final: 0.7240 (mm-40) REVERT: B 753 TYR cc_start: 0.8630 (t80) cc_final: 0.8219 (t80) REVERT: C 61 TYR cc_start: 0.8835 (m-80) cc_final: 0.8518 (m-80) REVERT: D 61 TYR cc_start: 0.8837 (m-80) cc_final: 0.8521 (m-80) outliers start: 18 outliers final: 17 residues processed: 173 average time/residue: 0.1218 time to fit residues: 29.7290 Evaluate side-chains 179 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 51 optimal weight: 4.9990 chunk 115 optimal weight: 30.0000 chunk 68 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 31 optimal weight: 0.0270 chunk 78 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.153056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.101982 restraints weight = 16875.417| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.28 r_work: 0.2836 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14300 Z= 0.115 Angle : 0.583 10.098 19516 Z= 0.284 Chirality : 0.042 0.172 2118 Planarity : 0.005 0.039 2498 Dihedral : 6.422 128.337 2160 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.21 % Allowed : 11.81 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: -0.06 (0.20), residues: 1720 helix: 1.03 (0.29), residues: 358 sheet: -0.27 (0.26), residues: 354 loop : -0.28 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 814 TYR 0.014 0.001 TYR B 337 PHE 0.018 0.001 PHE B 257 TRP 0.010 0.001 TRP B 307 HIS 0.007 0.001 HIS B 272 Details of bonding type rmsd covalent geometry : bond 0.00273 (14262) covalent geometry : angle 0.57857 (19440) SS BOND : bond 0.00129 ( 20) SS BOND : angle 0.46982 ( 40) hydrogen bonds : bond 0.03710 ( 464) hydrogen bonds : angle 5.13525 ( 1242) metal coordination : bond 0.00580 ( 6) link_BETA1-4 : bond 0.00283 ( 4) link_BETA1-4 : angle 1.59087 ( 12) link_NAG-ASN : bond 0.00101 ( 8) link_NAG-ASN : angle 1.78806 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.497 Fit side-chains REVERT: A 814 ARG cc_start: 0.8667 (tpp80) cc_final: 0.8301 (tpp80) REVERT: B 753 TYR cc_start: 0.8590 (t80) cc_final: 0.8298 (t80) outliers start: 18 outliers final: 17 residues processed: 171 average time/residue: 0.1199 time to fit residues: 29.2198 Evaluate side-chains 175 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 6 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 64 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 42 optimal weight: 30.0000 chunk 11 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.153245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.103073 restraints weight = 17029.247| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.35 r_work: 0.2824 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14300 Z= 0.113 Angle : 0.577 10.344 19516 Z= 0.282 Chirality : 0.042 0.161 2118 Planarity : 0.004 0.038 2498 Dihedral : 6.267 126.742 2160 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.14 % Allowed : 12.21 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.02 (0.20), residues: 1720 helix: 1.16 (0.29), residues: 358 sheet: -0.21 (0.26), residues: 354 loop : -0.26 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 814 TYR 0.013 0.001 TYR A 337 PHE 0.017 0.001 PHE B 257 TRP 0.011 0.001 TRP C 114 HIS 0.007 0.001 HIS B 272 Details of bonding type rmsd covalent geometry : bond 0.00275 (14262) covalent geometry : angle 0.57360 (19440) SS BOND : bond 0.00125 ( 20) SS BOND : angle 0.45233 ( 40) hydrogen bonds : bond 0.03534 ( 464) hydrogen bonds : angle 5.02370 ( 1242) metal coordination : bond 0.00608 ( 6) link_BETA1-4 : bond 0.00279 ( 4) link_BETA1-4 : angle 1.57128 ( 12) link_NAG-ASN : bond 0.00076 ( 8) link_NAG-ASN : angle 1.74711 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.381 Fit side-chains REVERT: A 814 ARG cc_start: 0.8678 (tpp80) cc_final: 0.8380 (tpp80) outliers start: 17 outliers final: 17 residues processed: 169 average time/residue: 0.1232 time to fit residues: 29.3865 Evaluate side-chains 173 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 6 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 7 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 129 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 90 optimal weight: 0.0770 chunk 161 optimal weight: 0.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 815 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.154372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.107664 restraints weight = 16830.802| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.36 r_work: 0.2830 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14300 Z= 0.118 Angle : 0.577 10.350 19516 Z= 0.281 Chirality : 0.042 0.164 2118 Planarity : 0.005 0.041 2498 Dihedral : 6.242 126.420 2160 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.14 % Allowed : 12.15 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.04 (0.20), residues: 1720 helix: 1.19 (0.29), residues: 358 sheet: -0.23 (0.26), residues: 354 loop : -0.24 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 814 TYR 0.013 0.001 TYR A 337 PHE 0.017 0.001 PHE A 257 TRP 0.009 0.001 TRP C 114 HIS 0.007 0.001 HIS B 272 Details of bonding type rmsd covalent geometry : bond 0.00287 (14262) covalent geometry : angle 0.57276 (19440) SS BOND : bond 0.00130 ( 20) SS BOND : angle 0.46046 ( 40) hydrogen bonds : bond 0.03626 ( 464) hydrogen bonds : angle 5.01846 ( 1242) metal coordination : bond 0.00657 ( 6) link_BETA1-4 : bond 0.00258 ( 4) link_BETA1-4 : angle 1.56946 ( 12) link_NAG-ASN : bond 0.00085 ( 8) link_NAG-ASN : angle 1.74921 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.542 Fit side-chains REVERT: A 814 ARG cc_start: 0.8693 (tpp80) cc_final: 0.8341 (tpp80) outliers start: 17 outliers final: 17 residues processed: 166 average time/residue: 0.1246 time to fit residues: 29.6770 Evaluate side-chains 169 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 6 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 52 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 159 optimal weight: 7.9990 chunk 156 optimal weight: 0.0670 chunk 135 optimal weight: 4.9990 chunk 90 optimal weight: 0.0970 chunk 51 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.153345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.112180 restraints weight = 16936.637| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.87 r_work: 0.2773 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14300 Z= 0.134 Angle : 0.597 11.240 19516 Z= 0.289 Chirality : 0.043 0.177 2118 Planarity : 0.005 0.040 2498 Dihedral : 6.327 127.390 2160 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.21 % Allowed : 12.08 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.20), residues: 1720 helix: 1.12 (0.29), residues: 358 sheet: -0.26 (0.27), residues: 354 loop : -0.28 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 814 TYR 0.015 0.001 TYR A 337 PHE 0.019 0.002 PHE A 257 TRP 0.010 0.001 TRP D 114 HIS 0.007 0.001 HIS B 272 Details of bonding type rmsd covalent geometry : bond 0.00331 (14262) covalent geometry : angle 0.59256 (19440) SS BOND : bond 0.00152 ( 20) SS BOND : angle 0.47914 ( 40) hydrogen bonds : bond 0.03889 ( 464) hydrogen bonds : angle 5.05668 ( 1242) metal coordination : bond 0.00815 ( 6) link_BETA1-4 : bond 0.00248 ( 4) link_BETA1-4 : angle 1.62976 ( 12) link_NAG-ASN : bond 0.00104 ( 8) link_NAG-ASN : angle 1.81317 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3870.40 seconds wall clock time: 66 minutes 40.01 seconds (4000.01 seconds total)