Starting phenix.real_space_refine on Sat Sep 12 05:42:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ghr_40047/09_2026/8ghr_40047.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ghr_40047/09_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_40047/09_2026/8ghr_40047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ghr_40047/09_2026/8ghr_40047.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ghr_40047/09_2026/8ghr_40047.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ghr_40047/09_2026/8ghr_40047.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ghr_40047/09_2026/8ghr_40047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ghr_40047/09_2026/8ghr_40047.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 4 6.06 5 P 2 5.49 5 S 72 5.16 5 C 8870 2.51 5 N 2304 2.21 5 O 2610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: {'RNAv2': 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: {'RNAv2': 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: 4.64, per 1000 atoms: 0.33 Number of scatterers: 13864 At special positions: 0 Unit cell: (120.61, 124.081, 105.859, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 2 19.99 S 72 16.00 P 2 15.00 O 2610 8.00 N 2304 7.00 C 8870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 241 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 868 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG ACYS A 626 " - pdb=" SG CYS A 726 " distance=2.03 Simple disulfide: pdb=" SG CYS A 628 " - pdb=" SG CYS A 711 " distance=2.03 Simple disulfide: pdb=" SG CYS A 726 " - pdb=" SG BCYS A 626 " distance=2.03 Simple disulfide: pdb=" SG CYS A 838 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 241 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 431 " - pdb=" SG CYS B 530 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 868 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG ACYS B 626 " - pdb=" SG CYS B 726 " distance=2.03 Simple disulfide: pdb=" SG CYS B 628 " - pdb=" SG CYS B 711 " distance=2.03 Simple disulfide: pdb=" SG CYS B 726 " - pdb=" SG BCYS B 626 " distance=2.03 Simple disulfide: pdb=" SG CYS B 838 " - pdb=" SG CYS B 848 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1304 " - " ASN A 285 " " NAG A1305 " - " ASN A 477 " " NAG B1304 " - " ASN B 285 " " NAG B1305 " - " ASN B 477 " " NAG E 1 " - " ASN A 341 " " NAG F 1 " - " ASN A 585 " " NAG G 1 " - " ASN B 341 " " NAG H 1 " - " ASN B 585 " Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 893.1 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: 0.49 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: 2.30 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4407 1.34 - 1.46: 3509 1.46 - 1.58: 6242 1.58 - 1.70: 2 1.70 - 1.82: 102 Bond restraints: 14262 Sorted by residual: bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.84e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.80e+00 ... (remaining 14257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 19114 2.04 - 4.09: 286 4.09 - 6.13: 30 6.13 - 8.17: 4 8.17 - 10.22: 6 Bond angle restraints: 19440 Sorted by residual: angle pdb=" C SER A 709 " pdb=" N ASN A 710 " pdb=" CA ASN A 710 " ideal model delta sigma weight residual 121.54 127.51 -5.97 1.91e+00 2.74e-01 9.77e+00 angle pdb=" C SER B 709 " pdb=" N ASN B 710 " pdb=" CA ASN B 710 " ideal model delta sigma weight residual 121.54 127.47 -5.93 1.91e+00 2.74e-01 9.62e+00 angle pdb=" C PRO A 483 " pdb=" N ASN A 484 " pdb=" CA ASN A 484 " ideal model delta sigma weight residual 121.54 127.33 -5.79 1.91e+00 2.74e-01 9.19e+00 angle pdb=" C PRO B 483 " pdb=" N ASN B 484 " pdb=" CA ASN B 484 " ideal model delta sigma weight residual 121.54 127.31 -5.77 1.91e+00 2.74e-01 9.13e+00 angle pdb=" CA LEU A 359 " pdb=" CB LEU A 359 " pdb=" CG LEU A 359 " ideal model delta sigma weight residual 116.30 126.52 -10.22 3.50e+00 8.16e-02 8.52e+00 ... (remaining 19435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.47: 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 - 0.049: 1685 0.049 - 0.098: 345 0.098 - 0.147: 82 0.147 - 0.196: 4 0.196 - 0.245: 2 Chirality restraints: 2118 Sorted by residual: chirality pdb=" C2' AMP A1303 " pdb=" C1' AMP A1303 " pdb=" C3' AMP A1303 " pdb=" O2' AMP A1303 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" C2' AMP B1303 " pdb=" C1' AMP B1303 " pdb=" C3' AMP B1303 " pdb=" O2' AMP B1303 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 585 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.97e-01 ... (remaining 2115 not shown) Planarity restraints: 2506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 721 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.06e+00 pdb=" N PRO B 722 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 722 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 722 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 721 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.04e+00 pdb=" N PRO A 722 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 722 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 722 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 257 " 0.015 2.00e-02 2.50e+03 1.34e-02 3.14e+00 pdb=" CG PHE B 257 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE B 257 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 257 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 257 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 257 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 257 " 0.001 2.00e-02 2.50e+03 ... (remaining 2503 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 73 2.52 - 3.11: 9535 3.11 - 3.71: 19723 3.71 - 4.30: 28318 4.30 - 4.90: 49299 Nonbonded interactions: 106948 Sorted by model distance: nonbonded pdb="ZN ZN B1301 " pdb=" O2P AMP B1303 " model vdw 1.923 2.230 nonbonded pdb="ZN ZN A1301 " pdb=" O2P AMP A1303 " model vdw 1.925 2.230 nonbonded pdb=" OD1 ASP A 218 " pdb="ZN ZN A1302 " model vdw 1.955 2.230 nonbonded pdb=" OD1 ASP B 218 " pdb="ZN ZN B1302 " model vdw 1.955 2.230 nonbonded pdb=" OD1 ASP A 376 " pdb="ZN ZN A1301 " model vdw 2.042 2.230 ... (remaining 106943 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 187 through 625 or resid 627 through 699 or resid 701 thro \ ugh 1306)) selection = (chain 'B' and (resid 187 through 625 or resid 627 through 699 or resid 701 thro \ ugh 1306)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.580 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.140 ------------------------------------------------------------------------------- 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= 0.132 Angle : 0.607 10.215 19516 Z= 0.294 Chirality : 0.043 0.245 2118 Planarity : 0.005 0.050 2498 Dihedral : 13.892 122.339 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 0.00283 / 0.13 (14262) covalent geometry : angle 0.60366 / 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 : 0.542 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1123 time to fit residues: 32.0727 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 : 0.364 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.151335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.111720 restraints weight = 16894.717| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.41 r_work: 0.2827 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.0927 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= 0.195 Angle : 0.677 9.545 19516 Z= 0.334 Chirality : 0.046 0.220 2118 Planarity : 0.005 0.041 2498 Dihedral : 6.177 125.040 1908 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.67 % Allowed : 7.85 % Favored : 91.48 % 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: -0.31 (0.20), residues: 1720 helix: 0.59 (0.28), residues: 358 sheet: -0.23 (0.28), residues: 318 loop : -0.42 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 814 TYR 0.022 0.002 TYR B 261 PHE 0.045 0.002 PHE B 257 TRP 0.008 0.001 TRP A 190 HIS 0.010 0.002 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.19 (14262) covalent geometry : angle 0.67404 / 0.33 (19440) SS BOND : bond 0.00473 / 0.28 ( 20) SS BOND : angle 0.76456 / 0.51 ( 40) hydrogen bonds : bond 0.05058 / 3.24 ( 464) hydrogen bonds : angle 5.75367 / 4.11 ( 1242) metal coordination : bond 0.01497 / 0.86 ( 6) link_BETA1-4 : bond 0.00149 / 0.08 ( 4) link_BETA1-4 : angle 1.47337 / 0.88 ( 12) link_NAG-ASN : bond 0.00159 / 0.10 ( 8) link_NAG-ASN : angle 1.75740 / 1.21 ( 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 : 0.512 Fit side-chains REVERT: B 753 TYR cc_start: 0.8648 (t80) cc_final: 0.8136 (t80) outliers start: 10 outliers final: 10 residues processed: 169 average time/residue: 0.1182 time to fit residues: 29.2885 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 : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 869 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 144 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 163 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 113 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** B 815 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.152470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.111235 restraints weight = 17063.955| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.78 r_work: 0.2790 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.0987 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= 0.114 Angle : 0.578 8.154 19516 Z= 0.283 Chirality : 0.043 0.177 2118 Planarity : 0.004 0.040 2498 Dihedral : 5.976 124.078 1908 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.87 % Allowed : 9.06 % Favored : 90.07 % 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: 0.81 (0.28), residues: 372 sheet: -0.09 (0.27), residues: 338 loop : -0.30 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 814 TYR 0.014 0.001 TYR B 775 PHE 0.025 0.001 PHE B 257 TRP 0.009 0.001 TRP B 307 HIS 0.008 0.001 HIS B 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.11 (14262) covalent geometry : angle 0.57542 / 0.28 (19440) SS BOND : bond 0.00171 / 0.11 ( 20) SS BOND : angle 0.57859 / 0.40 ( 40) hydrogen bonds : bond 0.03877 / 2.49 ( 464) hydrogen bonds : angle 5.40851 / 3.86 ( 1242) metal coordination : bond 0.00667 / 0.39 ( 6) link_BETA1-4 : bond 0.00261 / 0.13 ( 4) link_BETA1-4 : angle 1.23334 / 0.73 ( 12) link_NAG-ASN : bond 0.00094 / 0.06 ( 8) link_NAG-ASN : angle 1.56324 / 1.06 ( 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 180 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.526 Fit side-chains REVERT: A 753 TYR cc_start: 0.8595 (t80) cc_final: 0.8160 (t80) REVERT: B 753 TYR cc_start: 0.8581 (t80) cc_final: 0.8135 (t80) outliers start: 13 outliers final: 4 residues processed: 169 average time/residue: 0.1195 time to fit residues: 29.3291 Evaluate side-chains 170 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 166 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 798 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 106 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 167 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 118 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.151782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.100076 restraints weight = 16960.611| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.29 r_work: 0.2824 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- 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 = 0.24 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 = 0.24 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: 0.8944 moved from start: 0.1108 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= 0.140 Angle : 0.593 9.340 19516 Z= 0.290 Chirality : 0.043 0.189 2118 Planarity : 0.005 0.039 2498 Dihedral : 6.055 125.974 1908 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.21 % Allowed : 9.93 % 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: -0.11 (0.20), residues: 1720 helix: 0.80 (0.28), residues: 372 sheet: -0.05 (0.27), residues: 334 loop : -0.36 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 814 TYR 0.014 0.001 TYR A 261 PHE 0.026 0.002 PHE B 257 TRP 0.008 0.001 TRP B 190 HIS 0.008 0.001 HIS B 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 (14262) covalent geometry : angle 0.58955 / 0.29 (19440) SS BOND : bond 0.00179 / 0.12 ( 20) SS BOND : angle 0.56486 / 0.39 ( 40) hydrogen bonds : bond 0.04133 / 2.65 ( 464) hydrogen bonds : angle 5.31197 / 3.79 ( 1242) metal coordination : bond 0.00876 / 0.52 ( 6) link_BETA1-4 : bond 0.00262 / 0.13 ( 4) link_BETA1-4 : angle 1.38753 / 0.82 ( 12) link_NAG-ASN : bond 0.00098 / 0.06 ( 8) link_NAG-ASN : angle 1.66495 / 1.14 ( 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 176 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.538 Fit side-chains REVERT: A 753 TYR cc_start: 0.8638 (t80) cc_final: 0.8311 (t80) REVERT: B 753 TYR cc_start: 0.8609 (t80) cc_final: 0.8166 (t80) outliers start: 18 outliers final: 14 residues processed: 168 average time/residue: 0.1182 time to fit residues: 29.0403 Evaluate side-chains 170 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 812 ASN 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 812 ASN Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 834 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 2 optimal weight: 0.0980 chunk 43 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 chunk 87 optimal weight: 0.0060 chunk 76 optimal weight: 0.4980 chunk 153 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 167 optimal weight: 7.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 GLN A 815 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 815 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.154471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.114153 restraints weight = 16971.094| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 3.65 r_work: 0.2876 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14300 Z= 0.096 Angle : 0.548 8.017 19516 Z= 0.267 Chirality : 0.042 0.165 2118 Planarity : 0.004 0.039 2498 Dihedral : 5.839 123.969 1908 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.94 % Allowed : 10.60 % Favored : 88.46 % 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: 1.18 (0.29), residues: 358 sheet: -0.16 (0.27), residues: 354 loop : -0.18 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 814 TYR 0.016 0.001 TYR A 775 PHE 0.016 0.001 PHE B 257 TRP 0.010 0.001 TRP A 307 HIS 0.007 0.001 HIS B 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (14262) covalent geometry : angle 0.54573 / 0.27 (19440) SS BOND : bond 0.00108 / 0.08 ( 20) SS BOND : angle 0.44737 / 0.31 ( 40) hydrogen bonds : bond 0.03220 / 2.08 ( 464) hydrogen bonds : angle 5.08962 / 3.63 ( 1242) metal coordination : bond 0.00427 / 0.25 ( 6) link_BETA1-4 : bond 0.00335 / 0.17 ( 4) link_BETA1-4 : angle 1.19789 / 0.72 ( 12) link_NAG-ASN : bond 0.00077 / 0.05 ( 8) link_NAG-ASN : angle 1.46627 / 0.99 ( 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 182 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.347 Fit side-chains REVERT: C 61 TYR cc_start: 0.8725 (m-80) cc_final: 0.8491 (m-80) REVERT: D 61 TYR cc_start: 0.8730 (m-80) cc_final: 0.8494 (m-80) outliers start: 14 outliers final: 11 residues processed: 175 average time/residue: 0.1217 time to fit residues: 30.8914 Evaluate side-chains 177 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 834 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 142 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 143 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 815 GLN B 202 GLN B 815 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.152482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.105323 restraints weight = 16992.623| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.24 r_work: 0.2904 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1250 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= 0.145 Angle : 0.596 9.986 19516 Z= 0.291 Chirality : 0.044 0.183 2118 Planarity : 0.005 0.039 2498 Dihedral : 6.019 126.266 1908 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.28 % Allowed : 10.81 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.20), residues: 1720 helix: 1.04 (0.29), residues: 358 sheet: -0.19 (0.27), residues: 354 loop : -0.27 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 814 TYR 0.013 0.001 TYR A 337 PHE 0.024 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 0.00362 / 0.15 (14262) covalent geometry : angle 0.59235 / 0.29 (19440) SS BOND : bond 0.00170 / 0.12 ( 20) SS BOND : angle 0.53442 / 0.37 ( 40) hydrogen bonds : bond 0.04080 / 2.62 ( 464) hydrogen bonds : angle 5.18880 / 3.69 ( 1242) metal coordination : bond 0.00951 / 0.57 ( 6) link_BETA1-4 : bond 0.00277 / 0.14 ( 4) link_BETA1-4 : angle 1.42795 / 0.84 ( 12) link_NAG-ASN : bond 0.00110 / 0.07 ( 8) link_NAG-ASN : angle 1.67672 / 1.15 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.501 Fit side-chains REVERT: C 61 TYR cc_start: 0.8798 (m-80) cc_final: 0.8502 (m-80) REVERT: D 61 TYR cc_start: 0.8798 (m-80) cc_final: 0.8501 (m-80) outliers start: 19 outliers final: 16 residues processed: 172 average time/residue: 0.1252 time to fit residues: 30.9666 Evaluate side-chains 176 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 844 THR 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 810 LEU 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 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: 1.9990 chunk 84 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.151622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.100230 restraints weight = 17053.119| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.51 r_work: 0.2793 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 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 : 0.004 0.042 14300 Z= 0.163 Angle : 0.620 10.189 19516 Z= 0.302 Chirality : 0.044 0.198 2118 Planarity : 0.005 0.039 2498 Dihedral : 6.223 128.883 1908 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.34 % Allowed : 11.34 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.20), residues: 1720 helix: 0.96 (0.29), residues: 358 sheet: -0.36 (0.27), residues: 334 loop : -0.29 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 814 TYR 0.026 0.001 TYR A 753 PHE 0.025 0.002 PHE A 257 TRP 0.008 0.001 TRP A 190 HIS 0.008 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.16 (14262) covalent geometry : angle 0.61666 / 0.30 (19440) SS BOND : bond 0.00189 / 0.13 ( 20) SS BOND : angle 0.52824 / 0.37 ( 40) hydrogen bonds : bond 0.04363 / 2.80 ( 464) hydrogen bonds : angle 5.22343 / 3.70 ( 1242) metal coordination : bond 0.01112 / 0.66 ( 6) link_BETA1-4 : bond 0.00266 / 0.14 ( 4) link_BETA1-4 : angle 1.49666 / 0.88 ( 12) link_NAG-ASN : bond 0.00130 / 0.08 ( 8) link_NAG-ASN : angle 1.76879 / 1.22 ( 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 182 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.385 Fit side-chains REVERT: B 753 TYR cc_start: 0.8624 (t80) cc_final: 0.8335 (t80) outliers start: 20 outliers final: 20 residues processed: 173 average time/residue: 0.1178 time to fit residues: 29.2355 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 : 0.955 ------------------------------------------------------------------------------- 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 A residue 844 THR 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 810 LEU Chi-restraints excluded: chain B residue 815 GLN Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 51 optimal weight: 0.0570 chunk 115 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.152292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.104875 restraints weight = 16906.862| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.27 r_work: 0.2808 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 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 = 0.2693 r_free = 0.2693 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: 0.2693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14300 Z= 0.179 Angle : 0.628 10.387 19516 Z= 0.308 Chirality : 0.045 0.204 2118 Planarity : 0.005 0.039 2498 Dihedral : 6.296 129.538 1908 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.41 % Allowed : 11.21 % Favored : 87.38 % 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: 0.90 (0.29), residues: 358 sheet: -0.37 (0.27), residues: 334 loop : -0.33 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 814 TYR 0.017 0.002 TYR A 775 PHE 0.026 0.002 PHE B 257 TRP 0.008 0.001 TRP B 190 HIS 0.008 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.18 (14262) covalent geometry : angle 0.62447 / 0.31 (19440) SS BOND : bond 0.00209 / 0.15 ( 20) SS BOND : angle 0.56490 / 0.39 ( 40) hydrogen bonds : bond 0.04508 / 2.89 ( 464) hydrogen bonds : angle 5.24165 / 3.71 ( 1242) metal coordination : bond 0.01202 / 0.72 ( 6) link_BETA1-4 : bond 0.00269 / 0.14 ( 4) link_BETA1-4 : angle 1.56204 / 0.92 ( 12) link_NAG-ASN : bond 0.00138 / 0.09 ( 8) link_NAG-ASN : angle 1.79805 / 1.24 ( 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: 21 poor density : 158 time to evaluate : 0.519 Fit side-chains REVERT: B 753 TYR cc_start: 0.8594 (t80) cc_final: 0.8312 (t80) outliers start: 21 outliers final: 20 residues processed: 170 average time/residue: 0.1294 time to fit residues: 31.5540 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 : 0.531 ------------------------------------------------------------------------------- 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 A residue 844 THR 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 810 LEU Chi-restraints excluded: chain B residue 815 GLN Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 64 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 40 optimal weight: 0.0980 chunk 123 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.153300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.104343 restraints weight = 17020.235| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.53 r_work: 0.2794 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1367 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= 0.114 Angle : 0.584 10.261 19516 Z= 0.285 Chirality : 0.042 0.170 2118 Planarity : 0.005 0.050 2498 Dihedral : 6.127 127.972 1908 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.07 % Allowed : 12.08 % Favored : 86.85 % 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: -0.19 (0.27), residues: 354 loop : -0.27 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 814 TYR 0.014 0.001 TYR A 337 PHE 0.017 0.001 PHE B 257 TRP 0.010 0.001 TRP B 307 HIS 0.007 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.11 (14262) covalent geometry : angle 0.58050 / 0.28 (19440) SS BOND : bond 0.00131 / 0.09 ( 20) SS BOND : angle 0.46136 / 0.32 ( 40) hydrogen bonds : bond 0.03696 / 2.39 ( 464) hydrogen bonds : angle 5.10078 / 3.62 ( 1242) metal coordination : bond 0.00606 / 0.36 ( 6) link_BETA1-4 : bond 0.00316 / 0.16 ( 4) link_BETA1-4 : angle 1.33404 / 0.79 ( 12) link_NAG-ASN : bond 0.00085 / 0.05 ( 8) link_NAG-ASN : angle 1.65207 / 1.13 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.525 Fit side-chains outliers start: 16 outliers final: 16 residues processed: 171 average time/residue: 0.1183 time to fit residues: 29.1975 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 : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 844 THR 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 815 GLN Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain D residue 2 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 7 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 129 optimal weight: 0.0980 chunk 139 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 167 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 90 optimal weight: 0.0030 chunk 161 optimal weight: 0.7980 overall best weight: 0.4590 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.153803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.103018 restraints weight = 16886.329| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.38 r_work: 0.2806 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 14300 Z= 0.117 Angle : 0.789 59.199 19516 Z= 0.429 Chirality : 0.042 0.170 2118 Planarity : 0.005 0.047 2498 Dihedral : 6.123 127.903 1908 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.28 % Allowed : 11.81 % Favored : 86.91 % 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: 1.14 (0.29), residues: 358 sheet: -0.20 (0.26), residues: 354 loop : -0.27 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 814 TYR 0.014 0.001 TYR A 337 PHE 0.019 0.001 PHE B 257 TRP 0.010 0.001 TRP B 307 HIS 0.007 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (14262) covalent geometry : angle 0.78700 / 0.43 (19440) SS BOND : bond 0.00118 / 0.08 ( 20) SS BOND : angle 0.45539 / 0.32 ( 40) hydrogen bonds : bond 0.03659 / 2.37 ( 464) hydrogen bonds : angle 5.09722 / 3.62 ( 1242) metal coordination : bond 0.00478 / 0.28 ( 6) link_BETA1-4 : bond 0.00566 / 0.28 ( 4) link_BETA1-4 : angle 1.36091 / 0.81 ( 12) link_NAG-ASN : bond 0.00091 / 0.06 ( 8) link_NAG-ASN : angle 1.65801 / 1.13 ( 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 178 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.541 Fit side-chains outliers start: 19 outliers final: 18 residues processed: 170 average time/residue: 0.1257 time to fit residues: 30.7969 Evaluate side-chains 177 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 GLU 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 A residue 844 THR Chi-restraints excluded: chain B residue 427 GLU 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 846 LEU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain D residue 2 VAL 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: 3.9990 chunk 82 optimal weight: 0.4980 chunk 159 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.153085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.112097 restraints weight = 16942.969| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.83 r_work: 0.2791 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 14300 Z= 0.117 Angle : 0.789 59.199 19516 Z= 0.429 Chirality : 0.042 0.170 2118 Planarity : 0.005 0.047 2498 Dihedral : 6.123 127.903 1908 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.28 % Allowed : 11.81 % Favored : 86.91 % 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: 1.14 (0.29), residues: 358 sheet: -0.20 (0.26), residues: 354 loop : -0.27 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 814 TYR 0.014 0.001 TYR A 337 PHE 0.019 0.001 PHE B 257 TRP 0.010 0.001 TRP B 307 HIS 0.007 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (14262) covalent geometry : angle 0.78701 / 0.43 (19440) SS BOND : bond 0.00118 / 0.08 ( 20) SS BOND : angle 0.45539 / 0.32 ( 40) hydrogen bonds : bond 0.03659 / 2.37 ( 464) hydrogen bonds : angle 5.09722 / 3.62 ( 1242) metal coordination : bond 0.00478 / 0.28 ( 6) link_BETA1-4 : bond 0.00566 / 0.28 ( 4) link_BETA1-4 : angle 1.36091 / 0.81 ( 12) link_NAG-ASN : bond 0.00091 / 0.06 ( 8) link_NAG-ASN : angle 1.65801 / 1.13 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3883.20 seconds wall clock time: 67 minutes 2.73 seconds (4022.73 seconds total)