Starting phenix.real_space_refine on Fri Jul 3 12:05:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ghr_40047/07_2026/8ghr_40047.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ghr_40047/07_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_40047/07_2026/8ghr_40047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ghr_40047/07_2026/8ghr_40047.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ghr_40047/07_2026/8ghr_40047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ghr_40047/07_2026/8ghr_40047.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ghr_40047/07_2026/8ghr_40047.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ghr_40047/07_2026/8ghr_40047.cif" } 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-dev-6108/lib/python3.11/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 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 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 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 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, 'NAG': 2} Classifications: {'RNA': 1, 'undetermined': 5} Modifications used: {'rna3p': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 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, 'NAG': 2} Classifications: {'RNA': 1, 'undetermined': 5} Modifications used: {'rna3p': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 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: 5.17, per 1000 atoms: 0.37 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: 1.30 Conformation dependent library (CDL) restraints added in 862.2 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: 0.65 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: 2.62 Time building geometry restraints manager: 1.70 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: 19130 2.04 - 4.09: 280 4.09 - 6.13: 24 6.13 - 8.17: 2 8.17 - 10.22: 4 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: 7896 24.47 - 48.94: 440 48.94 - 73.40: 28 73.40 - 97.87: 12 97.87 - 122.34: 2 Dihedral angle restraints: 8378 sinusoidal: 3338 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 8375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1449 0.038 - 0.076: 485 0.076 - 0.114: 139 0.114 - 0.152: 41 0.152 - 0.189: 4 Chirality restraints: 2118 Sorted by residual: 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 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 585 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CA PHE A 257 " pdb=" N PHE A 257 " pdb=" C PHE A 257 " pdb=" CB PHE A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.36e-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: 3.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.390 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 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= 0.130 Angle : 0.587 10.215 19516 Z= 0.290 Chirality : 0.043 0.189 2118 Planarity : 0.005 0.050 2498 Dihedral : 13.895 122.339 5098 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/Z covalent geometry : bond 0.00279 / 0.13 (14262) covalent geometry : angle 0.58301 / 0.29 (19440) SS BOND : bond 0.00140 / 0.10 ( 20) SS BOND : angle 0.40940 / 0.28 ( 40) hydrogen bonds : bond 0.16660 / 9.99 ( 464) hydrogen bonds : angle 7.41930 / 5.37 ( 1242) metal coordination : bond 0.00433 / 0.24 ( 6) link_BETA1-4 : bond 0.00346 / 0.18 ( 4) link_BETA1-4 : angle 1.94532 / 1.12 ( 12) link_NAG-ASN : bond 0.00131 / 0.08 ( 8) link_NAG-ASN : angle 1.64486 / 1.14 ( 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 : 0.540 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1210 time to fit residues: 34.0986 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... ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 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 = 0.3708 r_free = 0.3708 target = 0.151538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.100500 restraints weight = 16887.668| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.26 r_work: 0.2825 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.0886 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= 0.191 Angle : 0.660 9.157 19516 Z= 0.328 Chirality : 0.046 0.209 2118 Planarity : 0.005 0.041 2498 Dihedral : 6.285 126.034 1908 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.67 % Allowed : 7.72 % Favored : 91.61 % 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: 0.58 (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 0.021 0.002 TYR A 261 PHE 0.043 0.002 PHE B 257 TRP 0.008 0.001 TRP B 307 HIS 0.010 0.002 HIS B 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.19 (14262) covalent geometry : angle 0.65624 / 0.33 (19440) SS BOND : bond 0.00353 / 0.21 ( 20) SS BOND : angle 0.92110 / 0.60 ( 40) hydrogen bonds : bond 0.05234 / 3.33 ( 464) hydrogen bonds : angle 5.81696 / 4.16 ( 1242) metal coordination : bond 0.01411 / 0.81 ( 6) link_BETA1-4 : bond 0.00172 / 0.09 ( 4) link_BETA1-4 : angle 1.46214 / 0.86 ( 12) link_NAG-ASN : bond 0.00140 / 0.09 ( 8) link_NAG-ASN : angle 1.73470 / 1.19 ( 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 175 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 0.508 Fit side-chains REVERT: B 753 TYR cc_start: 0.8679 (t80) cc_final: 0.8056 (t80) outliers start: 10 outliers final: 10 residues processed: 169 average time/residue: 0.1245 time to fit residues: 30.4904 Evaluate side-chains 173 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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: 1.9990 chunk 163 optimal weight: 1.9990 chunk 95 optimal weight: 0.0570 chunk 133 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.151805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.110350 restraints weight = 17073.291| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.76 r_work: 0.2775 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.0991 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= 0.130 Angle : 0.585 8.155 19516 Z= 0.289 Chirality : 0.043 0.189 2118 Planarity : 0.005 0.040 2498 Dihedral : 6.179 125.011 1908 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.94 % Allowed : 9.26 % 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: -0.11 (0.27), residues: 338 loop : -0.32 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 814 TYR 0.013 0.001 TYR A 261 PHE 0.027 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/Z covalent geometry : bond 0.00318 / 0.13 (14262) covalent geometry : angle 0.58148 / 0.29 (19440) SS BOND : bond 0.00187 / 0.12 ( 20) SS BOND : angle 0.61523 / 0.42 ( 40) hydrogen bonds : bond 0.04155 / 2.66 ( 464) hydrogen bonds : angle 5.45934 / 3.90 ( 1242) metal coordination : bond 0.00829 / 0.49 ( 6) link_BETA1-4 : bond 0.00282 / 0.14 ( 4) link_BETA1-4 : angle 1.30765 / 0.78 ( 12) link_NAG-ASN : bond 0.00090 / 0.06 ( 8) link_NAG-ASN : angle 1.62366 / 1.11 ( 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 177 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.534 Fit side-chains REVERT: A 753 TYR cc_start: 0.8628 (t80) cc_final: 0.8203 (t80) REVERT: B 753 TYR cc_start: 0.8603 (t80) cc_final: 0.8172 (t80) outliers start: 14 outliers final: 9 residues processed: 165 average time/residue: 0.1211 time to fit residues: 28.9553 Evaluate side-chains 172 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 820 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 106 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 167 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 118 optimal weight: 10.0000 chunk 156 optimal weight: 0.0470 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: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3701 r_free = 0.3701 target = 0.151159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.109345 restraints weight = 16970.019| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.82 r_work: 0.2767 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14300 Z= 0.149 Angle : 0.595 9.425 19516 Z= 0.294 Chirality : 0.043 0.196 2118 Planarity : 0.005 0.040 2498 Dihedral : 6.218 125.737 1908 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.34 % Allowed : 9.80 % 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: -0.14 (0.20), residues: 1720 helix: 0.76 (0.28), residues: 370 sheet: -0.05 (0.27), residues: 334 loop : -0.38 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 814 TYR 0.014 0.001 TYR A 261 PHE 0.027 0.002 PHE A 257 TRP 0.009 0.001 TRP A 190 HIS 0.008 0.001 HIS B 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (14262) covalent geometry : angle 0.59158 / 0.29 (19440) SS BOND : bond 0.00186 / 0.13 ( 20) SS BOND : angle 0.57307 / 0.40 ( 40) hydrogen bonds : bond 0.04268 / 2.74 ( 464) hydrogen bonds : angle 5.35912 / 3.82 ( 1242) metal coordination : bond 0.00979 / 0.58 ( 6) link_BETA1-4 : bond 0.00366 / 0.19 ( 4) link_BETA1-4 : angle 1.43343 / 0.86 ( 12) link_NAG-ASN : bond 0.00109 / 0.07 ( 8) link_NAG-ASN : angle 1.69634 / 1.16 ( 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 179 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.532 Fit side-chains REVERT: A 753 TYR cc_start: 0.8609 (t80) cc_final: 0.8281 (t80) REVERT: B 753 TYR cc_start: 0.8571 (t80) cc_final: 0.8185 (t80) REVERT: D 92 THR cc_start: 0.8239 (OUTLIER) cc_final: 0.8038 (t) outliers start: 20 outliers final: 15 residues processed: 169 average time/residue: 0.1162 time to fit residues: 28.7811 Evaluate side-chains 175 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 75 ILE Chi-restraints excluded: chain D residue 75 ILE 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: 0.7980 chunk 43 optimal weight: 20.0000 chunk 41 optimal weight: 0.2980 chunk 87 optimal weight: 0.0030 chunk 76 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 143 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.153622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.113940 restraints weight = 16974.795| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.30 r_work: 0.2871 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14300 Z= 0.105 Angle : 0.554 9.243 19516 Z= 0.272 Chirality : 0.042 0.167 2118 Planarity : 0.004 0.039 2498 Dihedral : 6.066 123.854 1908 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.67 % Allowed : 10.74 % Favored : 88.59 % 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: 0.05 (0.20), residues: 1720 helix: 1.09 (0.29), residues: 360 sheet: -0.17 (0.27), residues: 354 loop : -0.21 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 814 TYR 0.012 0.001 TYR A 337 PHE 0.018 0.001 PHE B 257 TRP 0.010 0.001 TRP B 307 HIS 0.008 0.001 HIS B 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (14262) covalent geometry : angle 0.55092 / 0.27 (19440) SS BOND : bond 0.00125 / 0.09 ( 20) SS BOND : angle 0.46862 / 0.33 ( 40) hydrogen bonds : bond 0.03462 / 2.24 ( 464) hydrogen bonds : angle 5.14555 / 3.67 ( 1242) metal coordination : bond 0.00533 / 0.32 ( 6) link_BETA1-4 : bond 0.00314 / 0.16 ( 4) link_BETA1-4 : angle 1.25746 / 0.75 ( 12) link_NAG-ASN : bond 0.00080 / 0.05 ( 8) link_NAG-ASN : angle 1.53871 / 1.05 ( 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 179 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 169 time to evaluate : 0.594 Fit side-chains REVERT: A 753 TYR cc_start: 0.8546 (t80) cc_final: 0.8327 (t80) REVERT: C 61 TYR cc_start: 0.8743 (m-80) cc_final: 0.8491 (m-80) REVERT: D 61 TYR cc_start: 0.8754 (m-80) cc_final: 0.8503 (m-80) outliers start: 10 outliers final: 8 residues processed: 176 average time/residue: 0.1188 time to fit residues: 29.8437 Evaluate side-chains 172 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 834 VAL 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 834 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 142 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 104 optimal weight: 0.0000 chunk 122 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 GLN A 815 GLN B 202 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 = 0.3732 r_free = 0.3732 target = 0.153845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.112918 restraints weight = 16928.584| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.82 r_work: 0.2813 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14300 Z= 0.108 Angle : 0.553 9.733 19516 Z= 0.272 Chirality : 0.042 0.162 2118 Planarity : 0.004 0.039 2498 Dihedral : 6.033 123.516 1908 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.94 % Allowed : 10.81 % 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: 0.08 (0.20), residues: 1720 helix: 1.16 (0.29), residues: 358 sheet: -0.19 (0.26), residues: 354 loop : -0.19 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 814 TYR 0.012 0.001 TYR D 96 PHE 0.018 0.001 PHE B 257 TRP 0.009 0.001 TRP B 307 HIS 0.007 0.001 HIS B 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (14262) covalent geometry : angle 0.55053 / 0.27 (19440) SS BOND : bond 0.00124 / 0.09 ( 20) SS BOND : angle 0.45523 / 0.32 ( 40) hydrogen bonds : bond 0.03490 / 2.25 ( 464) hydrogen bonds : angle 5.09669 / 3.63 ( 1242) metal coordination : bond 0.00556 / 0.33 ( 6) link_BETA1-4 : bond 0.00335 / 0.17 ( 4) link_BETA1-4 : angle 1.29451 / 0.78 ( 12) link_NAG-ASN : bond 0.00065 / 0.04 ( 8) link_NAG-ASN : angle 1.54171 / 1.05 ( 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 176 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.451 Fit side-chains REVERT: A 758 LEU cc_start: 0.8916 (mt) cc_final: 0.8673 (mt) REVERT: C 61 TYR cc_start: 0.8728 (m-80) cc_final: 0.8390 (m-80) REVERT: D 61 TYR cc_start: 0.8735 (m-80) cc_final: 0.8397 (m-80) outliers start: 14 outliers final: 10 residues processed: 172 average time/residue: 0.1245 time to fit residues: 30.7002 Evaluate side-chains 170 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 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 834 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 117 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 51 optimal weight: 0.0970 chunk 14 optimal weight: 0.0040 chunk 127 optimal weight: 3.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.152481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.101178 restraints weight = 17017.723| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.28 r_work: 0.2832 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- 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 = 0.22 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 = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1273 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= 0.139 Angle : 0.588 10.167 19516 Z= 0.288 Chirality : 0.043 0.182 2118 Planarity : 0.005 0.038 2498 Dihedral : 6.135 125.031 1908 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.07 % Allowed : 11.41 % Favored : 87.52 % 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: -0.01 (0.20), residues: 1720 helix: 1.09 (0.29), residues: 358 sheet: -0.23 (0.26), residues: 354 loop : -0.25 (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 A 337 PHE 0.021 0.002 PHE A 257 TRP 0.008 0.001 TRP A 190 HIS 0.008 0.001 HIS B 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (14262) covalent geometry : angle 0.58460 / 0.29 (19440) SS BOND : bond 0.00158 / 0.11 ( 20) SS BOND : angle 0.49543 / 0.34 ( 40) hydrogen bonds : bond 0.03994 / 2.57 ( 464) hydrogen bonds : angle 5.13770 / 3.64 ( 1242) metal coordination : bond 0.00889 / 0.53 ( 6) link_BETA1-4 : bond 0.00313 / 0.16 ( 4) link_BETA1-4 : angle 1.42318 / 0.85 ( 12) link_NAG-ASN : bond 0.00109 / 0.07 ( 8) link_NAG-ASN : angle 1.67615 / 1.15 ( 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 175 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.494 Fit side-chains REVERT: C 61 TYR cc_start: 0.8757 (m-80) cc_final: 0.8435 (m-80) REVERT: D 61 TYR cc_start: 0.8763 (m-80) cc_final: 0.8440 (m-80) outliers start: 16 outliers final: 16 residues processed: 167 average time/residue: 0.1196 time to fit residues: 28.8027 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 : 0.530 ------------------------------------------------------------------------------- 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 820 ILE Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 854 LEU 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 B residue 854 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 51 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 31 optimal weight: 0.0070 chunk 78 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 145 optimal weight: 0.4980 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.154454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.108309 restraints weight = 16803.675| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.23 r_work: 0.2844 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1304 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= 0.120 Angle : 0.564 10.372 19516 Z= 0.277 Chirality : 0.042 0.169 2118 Planarity : 0.004 0.038 2498 Dihedral : 6.073 124.370 1908 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.07 % Allowed : 11.48 % 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: 0.07 (0.20), residues: 1720 helix: 1.19 (0.29), residues: 358 sheet: -0.21 (0.26), residues: 354 loop : -0.21 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 814 TYR 0.027 0.001 TYR A 753 PHE 0.018 0.001 PHE A 257 TRP 0.009 0.001 TRP A 307 HIS 0.007 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (14262) covalent geometry : angle 0.56081 / 0.28 (19440) SS BOND : bond 0.00131 / 0.09 ( 20) SS BOND : angle 0.47016 / 0.33 ( 40) hydrogen bonds : bond 0.03616 / 2.33 ( 464) hydrogen bonds : angle 5.03400 / 3.57 ( 1242) metal coordination : bond 0.00678 / 0.41 ( 6) link_BETA1-4 : bond 0.00304 / 0.16 ( 4) link_BETA1-4 : angle 1.33186 / 0.79 ( 12) link_NAG-ASN : bond 0.00076 / 0.05 ( 8) link_NAG-ASN : angle 1.59033 / 1.09 ( 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 179 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.482 Fit side-chains REVERT: A 427 GLU cc_start: 0.8579 (tp30) cc_final: 0.8335 (tp30) REVERT: B 427 GLU cc_start: 0.8571 (tp30) cc_final: 0.8328 (tp30) outliers start: 16 outliers final: 16 residues processed: 173 average time/residue: 0.1276 time to fit residues: 31.8456 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 : 0.335 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 40 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 chunk 11 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 815 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.153393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.104976 restraints weight = 17029.939| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.36 r_work: 0.2836 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 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 = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1321 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= 0.117 Angle : 0.564 10.371 19516 Z= 0.277 Chirality : 0.042 0.166 2118 Planarity : 0.004 0.038 2498 Dihedral : 6.054 123.983 1908 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.14 % Allowed : 11.68 % Favored : 87.18 % 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: 0.08 (0.20), residues: 1720 helix: 1.22 (0.29), residues: 358 sheet: -0.19 (0.26), residues: 354 loop : -0.21 (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 A 337 PHE 0.017 0.001 PHE B 257 TRP 0.008 0.001 TRP B 307 HIS 0.007 0.001 HIS B 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (14262) covalent geometry : angle 0.56130 / 0.28 (19440) SS BOND : bond 0.00131 / 0.09 ( 20) SS BOND : angle 0.45401 / 0.32 ( 40) hydrogen bonds : bond 0.03580 / 2.31 ( 464) hydrogen bonds : angle 4.98927 / 3.53 ( 1242) metal coordination : bond 0.00636 / 0.38 ( 6) link_BETA1-4 : bond 0.00329 / 0.17 ( 4) link_BETA1-4 : angle 1.34769 / 0.81 ( 12) link_NAG-ASN : bond 0.00078 / 0.05 ( 8) link_NAG-ASN : angle 1.57760 / 1.08 ( 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 174 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.431 Fit side-chains REVERT: A 427 GLU cc_start: 0.8572 (tp30) cc_final: 0.8341 (tp30) REVERT: B 427 GLU cc_start: 0.8553 (tp30) cc_final: 0.8322 (tp30) outliers start: 17 outliers final: 16 residues processed: 167 average time/residue: 0.1186 time to fit residues: 28.3268 Evaluate side-chains 174 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 131 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 77 optimal weight: 0.0570 chunk 167 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 161 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 815 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.155309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.109007 restraints weight = 16809.968| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.29 r_work: 0.2861 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1354 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= 0.106 Angle : 0.553 11.149 19516 Z= 0.270 Chirality : 0.041 0.164 2118 Planarity : 0.004 0.038 2498 Dihedral : 5.991 123.100 1908 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.14 % Allowed : 11.61 % Favored : 87.25 % 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: 0.14 (0.20), residues: 1720 helix: 1.30 (0.29), residues: 358 sheet: -0.18 (0.26), residues: 354 loop : -0.18 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 814 TYR 0.012 0.001 TYR B 337 PHE 0.016 0.001 PHE B 257 TRP 0.011 0.001 TRP D 114 HIS 0.007 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (14262) covalent geometry : angle 0.54987 / 0.27 (19440) SS BOND : bond 0.00115 / 0.08 ( 20) SS BOND : angle 0.43251 / 0.30 ( 40) hydrogen bonds : bond 0.03334 / 2.16 ( 464) hydrogen bonds : angle 4.91497 / 3.48 ( 1242) metal coordination : bond 0.00527 / 0.32 ( 6) link_BETA1-4 : bond 0.00312 / 0.16 ( 4) link_BETA1-4 : angle 1.28473 / 0.76 ( 12) link_NAG-ASN : bond 0.00075 / 0.05 ( 8) link_NAG-ASN : angle 1.50102 / 1.02 ( 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 179 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.428 Fit side-chains REVERT: A 427 GLU cc_start: 0.8569 (tp30) cc_final: 0.8341 (tp30) REVERT: B 427 GLU cc_start: 0.8560 (tp30) cc_final: 0.8332 (tp30) REVERT: C 61 TYR cc_start: 0.8772 (m-80) cc_final: 0.8549 (m-80) REVERT: D 61 TYR cc_start: 0.8779 (m-80) cc_final: 0.8554 (m-80) outliers start: 17 outliers final: 17 residues processed: 171 average time/residue: 0.1293 time to fit residues: 31.4493 Evaluate side-chains 178 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 559 ILE 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 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: 10.0000 chunk 49 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 159 optimal weight: 8.9990 chunk 156 optimal weight: 0.0770 chunk 135 optimal weight: 0.0030 chunk 90 optimal weight: 0.3980 chunk 51 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 overall best weight: 0.6350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.155266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.109221 restraints weight = 16826.767| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.27 r_work: 0.2863 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1363 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= 0.108 Angle : 0.556 10.932 19516 Z= 0.272 Chirality : 0.041 0.161 2118 Planarity : 0.004 0.038 2498 Dihedral : 5.983 122.906 1908 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.21 % Allowed : 11.74 % Favored : 87.05 % 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: 0.15 (0.20), residues: 1720 helix: 1.31 (0.29), residues: 358 sheet: -0.15 (0.26), residues: 354 loop : -0.18 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 814 TYR 0.012 0.001 TYR A 337 PHE 0.016 0.001 PHE A 257 TRP 0.008 0.001 TRP B 307 HIS 0.007 0.001 HIS B 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (14262) covalent geometry : angle 0.55347 / 0.27 (19440) SS BOND : bond 0.00119 / 0.08 ( 20) SS BOND : angle 0.42794 / 0.30 ( 40) hydrogen bonds : bond 0.03376 / 2.18 ( 464) hydrogen bonds : angle 4.90075 / 3.47 ( 1242) metal coordination : bond 0.00563 / 0.34 ( 6) link_BETA1-4 : bond 0.00306 / 0.16 ( 4) link_BETA1-4 : angle 1.30614 / 0.78 ( 12) link_NAG-ASN : bond 0.00072 / 0.05 ( 8) link_NAG-ASN : angle 1.51817 / 1.04 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3867.80 seconds wall clock time: 66 minutes 43.92 seconds (4003.92 seconds total)