Starting phenix.real_space_refine on Sat Jul 4 06:49:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yvk_39605/07_2026/8yvk_39605.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yvk_39605/07_2026/8yvk_39605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yvk_39605/07_2026/8yvk_39605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yvk_39605/07_2026/8yvk_39605.map" model { file = "/net/cci-nas-00/data/ceres_data/8yvk_39605/07_2026/8yvk_39605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yvk_39605/07_2026/8yvk_39605.cif" } resolution = 3.09 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= 0.075 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 120 5.16 5 C 12024 2.51 5 N 3296 2.21 5 O 3720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19164 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3003 Classifications: {'peptide': 389} Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 369} Chain: "B" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3003 Classifications: {'peptide': 389} Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 369} Chain: "C" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3003 Classifications: {'peptide': 389} Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 369} Chain: "D" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3003 Classifications: {'peptide': 389} Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 369} Chain: "E" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "F" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "G" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "H" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "I" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "J" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "K" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.77, per 1000 atoms: 0.20 Number of scatterers: 19164 At special positions: 0 Unit cell: (136.3, 136.3, 96.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 120 16.00 O 3720 8.00 N 3296 7.00 C 12024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 91 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 123 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 232 " distance=2.53 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.02 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 334 " distance=2.04 Simple disulfide: pdb=" SG CYS A 422 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 418 " distance=2.04 Simple disulfide: pdb=" SG CYS B 123 " - pdb=" SG CYS B 128 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 232 " distance=2.53 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.02 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 317 " - pdb=" SG CYS B 334 " distance=2.04 Simple disulfide: pdb=" SG CYS B 422 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 418 " distance=2.04 Simple disulfide: pdb=" SG CYS C 123 " - pdb=" SG CYS C 128 " distance=2.03 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 232 " distance=2.53 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 317 " - pdb=" SG CYS C 334 " distance=2.04 Simple disulfide: pdb=" SG CYS C 422 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS D 91 " - pdb=" SG CYS D 418 " distance=2.04 Simple disulfide: pdb=" SG CYS D 123 " - pdb=" SG CYS D 128 " distance=2.03 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.02 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 232 " distance=2.53 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.03 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 317 " - pdb=" SG CYS D 334 " distance=2.04 Simple disulfide: pdb=" SG CYS D 422 " - pdb=" SG CYS D 447 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 89 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 145 " " NAG B 501 " - " ASN B 145 " " NAG C 501 " - " ASN C 145 " " NAG D 501 " - " ASN D 145 " Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 746.5 milliseconds 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4400 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 52 sheets defined 4.2% alpha, 44.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.644A pdb=" N ILE A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 removed outlier: 3.567A pdb=" N SER A 144 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN A 145 " --> pdb=" O LYS A 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 141 through 145' Processing helix chain 'A' and resid 410 through 415 Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.644A pdb=" N ILE B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 removed outlier: 3.604A pdb=" N SER B 144 " --> pdb=" O ASP B 141 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN B 145 " --> pdb=" O LYS B 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 141 through 145' Processing helix chain 'B' and resid 410 through 415 Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.644A pdb=" N ILE C 107 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 145 removed outlier: 3.604A pdb=" N SER C 144 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN C 145 " --> pdb=" O LYS C 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 141 through 145' Processing helix chain 'C' and resid 410 through 415 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.645A pdb=" N ILE D 107 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 145 removed outlier: 3.568A pdb=" N SER D 144 " --> pdb=" O ASP D 141 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN D 145 " --> pdb=" O LYS D 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 141 through 145' Processing helix chain 'D' and resid 410 through 415 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.592A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.784A pdb=" N THR E 91 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.865A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.784A pdb=" N THR G 91 " --> pdb=" O VAL G 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.783A pdb=" N THR I 91 " --> pdb=" O VAL I 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.784A pdb=" N THR K 91 " --> pdb=" O VAL K 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 101 removed outlier: 6.446A pdb=" N ALA A 445 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS A 101 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N SER A 443 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 123 removed outlier: 4.921A pdb=" N PHE A 114 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ALA A 137 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ILE A 116 " --> pdb=" O GLN A 135 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLN A 135 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU A 118 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU A 133 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU A 157 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 3.672A pdb=" N SER A 179 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TYR A 207 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.637A pdb=" N VAL A 231 " --> pdb=" O TYR A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 224 removed outlier: 4.536A pdb=" N TYR A 252 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ILE A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.562A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 350 through 354 removed outlier: 4.602A pdb=" N PHE A 350 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER A 370 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP A 396 " --> pdb=" O SER A 370 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE A 372 " --> pdb=" O ILE A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 95 through 101 removed outlier: 6.446A pdb=" N ALA B 445 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS B 101 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N SER B 443 " --> pdb=" O LYS B 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 123 removed outlier: 4.922A pdb=" N PHE B 114 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ALA B 137 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ILE B 116 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN B 135 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLU B 118 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU B 133 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU B 157 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 179 through 184 removed outlier: 3.673A pdb=" N SER B 179 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TYR B 207 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 223 through 224 removed outlier: 3.639A pdb=" N VAL B 231 " --> pdb=" O TYR B 238 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 223 through 224 removed outlier: 4.535A pdb=" N TYR B 252 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 276 through 283 removed outlier: 5.562A pdb=" N GLU B 277 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ARG B 292 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 350 through 354 removed outlier: 4.601A pdb=" N PHE B 350 " --> pdb=" O GLY B 361 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER B 370 " --> pdb=" O ASP B 396 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP B 396 " --> pdb=" O SER B 370 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE B 372 " --> pdb=" O ILE B 394 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 95 through 101 removed outlier: 6.446A pdb=" N ALA C 445 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS C 101 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N SER C 443 " --> pdb=" O LYS C 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 114 through 123 removed outlier: 4.922A pdb=" N PHE C 114 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ALA C 137 " --> pdb=" O PHE C 114 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ILE C 116 " --> pdb=" O GLN C 135 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN C 135 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLU C 118 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU C 133 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU C 157 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 179 through 184 removed outlier: 3.671A pdb=" N SER C 179 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TYR C 207 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE C 211 " --> pdb=" O TYR C 207 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 223 through 224 removed outlier: 3.639A pdb=" N VAL C 231 " --> pdb=" O TYR C 238 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 223 through 224 removed outlier: 4.536A pdb=" N TYR C 252 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG C 258 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 276 through 283 removed outlier: 5.562A pdb=" N GLU C 277 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG C 292 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 350 through 354 removed outlier: 4.602A pdb=" N PHE C 350 " --> pdb=" O GLY C 361 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER C 370 " --> pdb=" O ASP C 396 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP C 396 " --> pdb=" O SER C 370 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE C 372 " --> pdb=" O ILE C 394 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 95 through 101 removed outlier: 6.447A pdb=" N ALA D 445 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS D 101 " --> pdb=" O SER D 443 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N SER D 443 " --> pdb=" O LYS D 101 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 114 through 123 removed outlier: 4.922A pdb=" N PHE D 114 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ALA D 137 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N ILE D 116 " --> pdb=" O GLN D 135 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLN D 135 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU D 118 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU D 133 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU D 157 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 179 through 184 removed outlier: 3.672A pdb=" N SER D 179 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TYR D 207 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE D 211 " --> pdb=" O TYR D 207 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 223 through 224 removed outlier: 3.639A pdb=" N VAL D 231 " --> pdb=" O TYR D 238 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 223 through 224 removed outlier: 4.537A pdb=" N TYR D 252 " --> pdb=" O VAL D 268 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG D 258 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 276 through 283 removed outlier: 5.593A pdb=" N GLU D 277 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ARG D 292 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 350 through 354 removed outlier: 4.601A pdb=" N PHE D 350 " --> pdb=" O GLY D 361 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER D 370 " --> pdb=" O ASP D 396 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASP D 396 " --> pdb=" O SER D 370 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N PHE D 372 " --> pdb=" O ILE D 394 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.135A pdb=" N GLY E 10 " --> pdb=" O THR E 120 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N MET E 34 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N HIS E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR E 59 " --> pdb=" O HIS E 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.135A pdb=" N GLY E 10 " --> pdb=" O THR E 120 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU E 112 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AD6, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.682A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.682A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.136A pdb=" N GLY G 10 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR G 59 " --> pdb=" O HIS G 50 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.136A pdb=" N GLY G 10 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU G 112 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.683A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU H 34 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASP H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.683A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.135A pdb=" N GLY I 10 " --> pdb=" O THR I 120 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N MET I 34 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N HIS I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR I 59 " --> pdb=" O HIS I 50 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.135A pdb=" N GLY I 10 " --> pdb=" O THR I 120 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU I 112 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.495A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU J 34 " --> pdb=" O ASP J 50 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASP J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.495A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.135A pdb=" N GLY K 10 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR K 59 " --> pdb=" O HIS K 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.135A pdb=" N GLY K 10 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU K 112 " --> pdb=" O ARG K 98 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.495A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU L 34 " --> pdb=" O ASP L 50 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASP L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.495A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) 694 hydrogen bonds defined for protein. 1767 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: 2.93 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3234 1.32 - 1.45: 6119 1.45 - 1.59: 10135 1.59 - 1.72: 0 1.72 - 1.85: 156 Bond restraints: 19644 Sorted by residual: bond pdb=" CA SER I 53 " pdb=" CB SER I 53 " ideal model delta sigma weight residual 1.528 1.456 0.073 1.56e-02 4.11e+03 2.19e+01 bond pdb=" CA SER E 53 " pdb=" CB SER E 53 " ideal model delta sigma weight residual 1.529 1.453 0.076 1.64e-02 3.72e+03 2.14e+01 bond pdb=" N ARG D 292 " pdb=" CA ARG D 292 " ideal model delta sigma weight residual 1.455 1.512 -0.057 1.25e-02 6.40e+03 2.09e+01 bond pdb=" N ILE G 51 " pdb=" CA ILE G 51 " ideal model delta sigma weight residual 1.456 1.504 -0.049 1.15e-02 7.56e+03 1.79e+01 bond pdb=" CA SER G 53 " pdb=" CB SER G 53 " ideal model delta sigma weight residual 1.529 1.455 0.075 1.78e-02 3.16e+03 1.76e+01 ... (remaining 19639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 25590 2.44 - 4.89: 984 4.89 - 7.33: 58 7.33 - 9.77: 13 9.77 - 12.21: 3 Bond angle restraints: 26648 Sorted by residual: angle pdb=" N ARG I 54 " pdb=" CA ARG I 54 " pdb=" C ARG I 54 " ideal model delta sigma weight residual 110.55 99.39 11.16 1.35e+00 5.49e-01 6.83e+01 angle pdb=" C ASN A 324 " pdb=" CA ASN A 324 " pdb=" CB ASN A 324 " ideal model delta sigma weight residual 110.62 98.41 12.21 1.57e+00 4.06e-01 6.05e+01 angle pdb=" N ARG B 88 " pdb=" CA ARG B 88 " pdb=" C ARG B 88 " ideal model delta sigma weight residual 111.36 117.98 -6.62 1.09e+00 8.42e-01 3.68e+01 angle pdb=" CA ARG B 88 " pdb=" C ARG B 88 " pdb=" O ARG B 88 " ideal model delta sigma weight residual 120.42 114.33 6.09 1.06e+00 8.90e-01 3.30e+01 angle pdb=" C ARG E 54 " pdb=" CA ARG E 54 " pdb=" CB ARG E 54 " ideal model delta sigma weight residual 110.01 119.54 -9.53 1.80e+00 3.09e-01 2.80e+01 ... (remaining 26643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.49: 10339 15.49 - 30.97: 1014 30.97 - 46.46: 189 46.46 - 61.94: 39 61.94 - 77.43: 11 Dihedral angle restraints: 11592 sinusoidal: 4632 harmonic: 6960 Sorted by residual: dihedral pdb=" C ASN A 324 " pdb=" N ASN A 324 " pdb=" CA ASN A 324 " pdb=" CB ASN A 324 " ideal model delta harmonic sigma weight residual -122.60 -106.89 -15.71 0 2.50e+00 1.60e-01 3.95e+01 dihedral pdb=" C TYR A 345 " pdb=" N TYR A 345 " pdb=" CA TYR A 345 " pdb=" CB TYR A 345 " ideal model delta harmonic sigma weight residual -122.60 -136.97 14.37 0 2.50e+00 1.60e-01 3.30e+01 dihedral pdb=" CB CYS D 317 " pdb=" SG CYS D 317 " pdb=" SG CYS D 334 " pdb=" CB CYS D 334 " ideal model delta sinusoidal sigma weight residual -86.00 -39.09 -46.91 1 1.00e+01 1.00e-02 3.04e+01 ... (remaining 11589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2571 0.100 - 0.199: 225 0.199 - 0.299: 26 0.299 - 0.398: 3 0.398 - 0.498: 3 Chirality restraints: 2828 Sorted by residual: chirality pdb=" CA ARG B 88 " pdb=" N ARG B 88 " pdb=" C ARG B 88 " pdb=" CB ARG B 88 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.20e+00 chirality pdb=" CA TYR A 345 " pdb=" N TYR A 345 " pdb=" C TYR A 345 " pdb=" CB TYR A 345 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" CA ASN A 324 " pdb=" N ASN A 324 " pdb=" C ASN A 324 " pdb=" CB ASN A 324 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 4.97e+00 ... (remaining 2825 not shown) Planarity restraints: 3452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 501 " -0.100 2.00e-02 2.50e+03 8.27e-02 8.56e+01 pdb=" C7 NAG B 501 " 0.029 2.00e-02 2.50e+03 pdb=" C8 NAG B 501 " -0.076 2.00e-02 2.50e+03 pdb=" N2 NAG B 501 " 0.132 2.00e-02 2.50e+03 pdb=" O7 NAG B 501 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 501 " -0.088 2.00e-02 2.50e+03 7.26e-02 6.58e+01 pdb=" C7 NAG C 501 " 0.026 2.00e-02 2.50e+03 pdb=" C8 NAG C 501 " -0.067 2.00e-02 2.50e+03 pdb=" N2 NAG C 501 " 0.115 2.00e-02 2.50e+03 pdb=" O7 NAG C 501 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 501 " -0.077 2.00e-02 2.50e+03 6.56e-02 5.39e+01 pdb=" C7 NAG D 501 " 0.019 2.00e-02 2.50e+03 pdb=" C8 NAG D 501 " 0.019 2.00e-02 2.50e+03 pdb=" N2 NAG D 501 " 0.104 2.00e-02 2.50e+03 pdb=" O7 NAG D 501 " -0.064 2.00e-02 2.50e+03 ... (remaining 3449 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 128 2.60 - 3.18: 14824 3.18 - 3.75: 26008 3.75 - 4.33: 40112 4.33 - 4.90: 71879 Nonbonded interactions: 152951 Sorted by model distance: nonbonded pdb=" O GLY C 297 " pdb="CA CA C 502 " model vdw 2.027 3.250 nonbonded pdb=" OG1 THR B 214 " pdb=" OG SER C 451 " model vdw 2.143 3.040 nonbonded pdb=" OG1 THR C 214 " pdb=" OG SER D 451 " model vdw 2.155 3.040 nonbonded pdb=" OG SER A 451 " pdb=" OG1 THR D 214 " model vdw 2.173 3.040 nonbonded pdb=" O GLY D 297 " pdb="CA CA D 502 " model vdw 2.175 3.250 ... (remaining 152946 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 15.190 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 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 : 0.010 0.503 19692 Z= 0.538 Angle : 1.066 21.776 26748 Z= 0.660 Chirality : 0.063 0.498 2828 Planarity : 0.007 0.083 3448 Dihedral : 12.479 77.426 7060 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.12 % Favored : 93.80 % Rotamer: Outliers : 0.38 % Allowed : 1.25 % Favored : 98.37 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 17.86 % 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: -1.67 (0.15), residues: 2452 helix: -4.79 (0.22), residues: 24 sheet: 0.10 (0.16), residues: 948 loop : -1.97 (0.14), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 88 TYR 0.027 0.002 TYR I 59 PHE 0.019 0.002 PHE D 120 TRP 0.027 0.002 TRP D 456 HIS 0.009 0.002 HIS K 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00721 / 0.40 (19644) covalent geometry : angle 0.99824 / 0.64 (26648) SS BOND : bond 0.15168 / 9.84 ( 44) SS BOND : angle 5.79664 / 3.93 ( 88) hydrogen bonds : bond 0.11848 / 7.79 ( 662) hydrogen bonds : angle 7.84958 / 5.64 ( 1767) link_NAG-ASN : bond 0.01058 / 0.51 ( 4) link_NAG-ASN : angle 8.45705 / 4.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 246 time to evaluate : 0.498 Fit side-chains REVERT: A 398 ASP cc_start: 0.8326 (m-30) cc_final: 0.8008 (m-30) REVERT: C 102 ASP cc_start: 0.7652 (m-30) cc_final: 0.7328 (m-30) REVERT: D 102 ASP cc_start: 0.7649 (m-30) cc_final: 0.7329 (m-30) REVERT: D 398 ASP cc_start: 0.8422 (m-30) cc_final: 0.8135 (m-30) REVERT: E 43 LYS cc_start: 0.7564 (mtpt) cc_final: 0.7358 (tttt) REVERT: G 4 LEU cc_start: 0.8754 (mt) cc_final: 0.8471 (mt) REVERT: G 46 GLU cc_start: 0.7948 (tt0) cc_final: 0.7518 (tt0) REVERT: G 76 LYS cc_start: 0.7392 (mppt) cc_final: 0.7135 (mptt) REVERT: H 14 SER cc_start: 0.8396 (m) cc_final: 0.8010 (p) REVERT: H 83 ASP cc_start: 0.6924 (m-30) cc_final: 0.6555 (m-30) REVERT: J 83 ASP cc_start: 0.6987 (m-30) cc_final: 0.6496 (m-30) outliers start: 8 outliers final: 1 residues processed: 253 average time/residue: 0.1404 time to fit residues: 52.0407 Evaluate side-chains 212 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 106 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.088015 restraints weight = 25506.837| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.63 r_work: 0.2814 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 19692 Z= 0.181 Angle : 0.682 10.241 26748 Z= 0.365 Chirality : 0.048 0.181 2828 Planarity : 0.005 0.055 3448 Dihedral : 5.372 21.056 2786 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.29 % Allowed : 7.44 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -1.55 (0.15), residues: 2452 helix: -4.67 (0.23), residues: 24 sheet: 0.34 (0.17), residues: 900 loop : -1.96 (0.13), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 155 TYR 0.015 0.001 TYR I 60 PHE 0.018 0.002 PHE C 120 TRP 0.024 0.002 TRP B 178 HIS 0.007 0.001 HIS K 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (19644) covalent geometry : angle 0.65964 / 0.36 (26648) SS BOND : bond 0.01183 / 0.77 ( 44) SS BOND : angle 2.81514 / 1.91 ( 88) hydrogen bonds : bond 0.04373 / 3.05 ( 662) hydrogen bonds : angle 6.31422 / 4.50 ( 1767) link_NAG-ASN : bond 0.00159 / 0.08 ( 4) link_NAG-ASN : angle 3.39493 / 2.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 215 time to evaluate : 0.656 Fit side-chains REVERT: A 247 ASP cc_start: 0.8370 (p0) cc_final: 0.8130 (p0) REVERT: A 398 ASP cc_start: 0.8621 (m-30) cc_final: 0.8364 (m-30) REVERT: B 247 ASP cc_start: 0.8364 (p0) cc_final: 0.8116 (p0) REVERT: E 46 GLU cc_start: 0.8155 (tt0) cc_final: 0.7800 (tt0) REVERT: F 6 GLN cc_start: 0.8235 (tt0) cc_final: 0.8024 (tt0) REVERT: F 83 ASP cc_start: 0.7338 (m-30) cc_final: 0.7093 (m-30) REVERT: G 76 LYS cc_start: 0.7374 (mppt) cc_final: 0.7093 (mptt) REVERT: H 18 ARG cc_start: 0.7900 (ttp80) cc_final: 0.7693 (ttp80) REVERT: H 83 ASP cc_start: 0.7348 (m-30) cc_final: 0.6964 (m-30) REVERT: I 76 LYS cc_start: 0.7577 (mptt) cc_final: 0.7363 (mptt) REVERT: L 83 ASP cc_start: 0.7270 (m-30) cc_final: 0.7025 (m-30) outliers start: 6 outliers final: 2 residues processed: 220 average time/residue: 0.1255 time to fit residues: 42.2306 Evaluate side-chains 198 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain G residue 51 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 51 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 162 optimal weight: 0.3980 chunk 95 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 35 ASN E 39 GLN G 35 ASN H 32 ASN I 35 ASN J 32 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.088027 restraints weight = 25778.700| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.64 r_work: 0.2813 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19692 Z= 0.177 Angle : 0.634 7.009 26748 Z= 0.341 Chirality : 0.047 0.173 2828 Planarity : 0.005 0.056 3448 Dihedral : 5.251 28.827 2784 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.15 % Allowed : 10.03 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -1.38 (0.15), residues: 2452 helix: -4.59 (0.24), residues: 24 sheet: 0.45 (0.16), residues: 928 loop : -1.87 (0.14), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 19 TYR 0.012 0.001 TYR K 60 PHE 0.018 0.002 PHE B 120 TRP 0.021 0.001 TRP B 178 HIS 0.007 0.001 HIS I 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (19644) covalent geometry : angle 0.62617 / 0.34 (26648) SS BOND : bond 0.00961 / 0.65 ( 44) SS BOND : angle 1.54248 / 1.04 ( 88) hydrogen bonds : bond 0.04227 / 2.97 ( 662) hydrogen bonds : angle 6.03709 / 4.30 ( 1767) link_NAG-ASN : bond 0.00102 / 0.05 ( 4) link_NAG-ASN : angle 2.86570 / 1.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 0.621 Fit side-chains REVERT: A 398 ASP cc_start: 0.8569 (m-30) cc_final: 0.8314 (m-30) REVERT: D 398 ASP cc_start: 0.8624 (m-30) cc_final: 0.8377 (m-30) REVERT: E 46 GLU cc_start: 0.8089 (tt0) cc_final: 0.7734 (tt0) REVERT: F 83 ASP cc_start: 0.7336 (m-30) cc_final: 0.7106 (m-30) REVERT: G 46 GLU cc_start: 0.8294 (tt0) cc_final: 0.7950 (tt0) REVERT: H 83 ASP cc_start: 0.7327 (m-30) cc_final: 0.7033 (m-30) REVERT: K 46 GLU cc_start: 0.8296 (tt0) cc_final: 0.7945 (tt0) REVERT: L 83 ASP cc_start: 0.7354 (m-30) cc_final: 0.7130 (m-30) outliers start: 24 outliers final: 11 residues processed: 230 average time/residue: 0.1360 time to fit residues: 47.2981 Evaluate side-chains 203 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 192 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain L residue 18 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 234 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 30 optimal weight: 0.0370 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 35 ASN F 32 ASN F 39 HIS G 35 ASN H 32 ASN I 35 ASN J 32 ASN K 35 ASN L 32 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.115358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.089533 restraints weight = 25716.316| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.66 r_work: 0.2832 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19692 Z= 0.128 Angle : 0.597 11.327 26748 Z= 0.321 Chirality : 0.046 0.173 2828 Planarity : 0.005 0.055 3448 Dihedral : 5.030 32.514 2784 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.49 % Allowed : 12.19 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.22 (0.16), residues: 2452 helix: -4.50 (0.24), residues: 24 sheet: 0.51 (0.16), residues: 964 loop : -1.78 (0.14), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 344 TYR 0.010 0.001 TYR E 60 PHE 0.015 0.001 PHE B 120 TRP 0.019 0.001 TRP B 178 HIS 0.006 0.001 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (19644) covalent geometry : angle 0.58502 / 0.32 (26648) SS BOND : bond 0.00935 / 0.61 ( 44) SS BOND : angle 1.93139 / 1.32 ( 88) hydrogen bonds : bond 0.03740 / 2.64 ( 662) hydrogen bonds : angle 5.81370 / 4.13 ( 1767) link_NAG-ASN : bond 0.00074 / 0.04 ( 4) link_NAG-ASN : angle 2.55821 / 1.51 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 0.684 Fit side-chains REVERT: A 398 ASP cc_start: 0.8595 (m-30) cc_final: 0.8339 (m-30) REVERT: B 398 ASP cc_start: 0.8590 (m-30) cc_final: 0.8347 (m-30) REVERT: B 435 LYS cc_start: 0.9255 (mmtp) cc_final: 0.9047 (mttp) REVERT: C 398 ASP cc_start: 0.8577 (m-30) cc_final: 0.8337 (m-30) REVERT: D 398 ASP cc_start: 0.8596 (m-30) cc_final: 0.8345 (m-30) REVERT: F 83 ASP cc_start: 0.7351 (m-30) cc_final: 0.7143 (m-30) REVERT: F 100 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8408 (pm20) REVERT: G 46 GLU cc_start: 0.8307 (tt0) cc_final: 0.7985 (tt0) REVERT: G 83 MET cc_start: 0.8353 (mtm) cc_final: 0.8141 (mtm) REVERT: H 83 ASP cc_start: 0.7291 (m-30) cc_final: 0.7054 (m-30) REVERT: K 46 GLU cc_start: 0.8346 (tt0) cc_final: 0.8028 (tt0) REVERT: K 83 MET cc_start: 0.8464 (mtm) cc_final: 0.8261 (mtm) outliers start: 31 outliers final: 16 residues processed: 222 average time/residue: 0.1347 time to fit residues: 45.7350 Evaluate side-chains 220 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 18 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 1 optimal weight: 0.7980 chunk 187 optimal weight: 0.0770 chunk 169 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 199 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 35 ASN F 32 ASN G 35 ASN H 32 ASN I 35 ASN J 32 ASN K 35 ASN L 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.115728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.089831 restraints weight = 25601.584| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.66 r_work: 0.2837 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19692 Z= 0.127 Angle : 0.577 7.408 26748 Z= 0.309 Chirality : 0.045 0.200 2828 Planarity : 0.005 0.054 3448 Dihedral : 4.904 29.627 2784 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.44 % Allowed : 12.81 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -1.10 (0.16), residues: 2452 helix: -4.35 (0.25), residues: 24 sheet: 0.62 (0.16), residues: 956 loop : -1.70 (0.14), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 344 TYR 0.009 0.001 TYR K 60 PHE 0.015 0.001 PHE B 120 TRP 0.017 0.001 TRP B 178 HIS 0.007 0.001 HIS K 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (19644) covalent geometry : angle 0.56833 / 0.31 (26648) SS BOND : bond 0.00944 / 0.60 ( 44) SS BOND : angle 1.60393 / 1.17 ( 88) hydrogen bonds : bond 0.03598 / 2.54 ( 662) hydrogen bonds : angle 5.68552 / 4.03 ( 1767) link_NAG-ASN : bond 0.00055 / 0.03 ( 4) link_NAG-ASN : angle 2.46398 / 1.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.761 Fit side-chains REVERT: A 398 ASP cc_start: 0.8573 (m-30) cc_final: 0.8343 (m-30) REVERT: B 398 ASP cc_start: 0.8622 (m-30) cc_final: 0.8391 (m-30) REVERT: C 398 ASP cc_start: 0.8593 (m-30) cc_final: 0.8362 (m-30) REVERT: D 398 ASP cc_start: 0.8603 (m-30) cc_final: 0.8373 (m-30) REVERT: F 100 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8387 (pm20) REVERT: G 46 GLU cc_start: 0.8323 (tt0) cc_final: 0.7984 (tt0) REVERT: H 83 ASP cc_start: 0.7285 (m-30) cc_final: 0.7084 (m-30) REVERT: K 46 GLU cc_start: 0.8344 (tt0) cc_final: 0.8018 (tt0) outliers start: 30 outliers final: 17 residues processed: 217 average time/residue: 0.1418 time to fit residues: 47.2641 Evaluate side-chains 220 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 18 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 120 optimal weight: 7.9990 chunk 84 optimal weight: 0.0670 chunk 164 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 189 optimal weight: 8.9990 overall best weight: 1.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 35 ASN F 32 ASN G 35 ASN H 32 ASN I 35 ASN J 32 ASN K 35 ASN L 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.116316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.091961 restraints weight = 25570.077| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.61 r_work: 0.2852 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19692 Z= 0.123 Angle : 0.608 16.187 26748 Z= 0.322 Chirality : 0.045 0.162 2828 Planarity : 0.005 0.055 3448 Dihedral : 4.961 36.108 2784 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.49 % Allowed : 13.20 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.07 (0.16), residues: 2452 helix: -4.19 (0.27), residues: 24 sheet: 0.60 (0.17), residues: 940 loop : -1.63 (0.14), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 19 TYR 0.010 0.001 TYR I 95 PHE 0.014 0.001 PHE D 120 TRP 0.017 0.001 TRP A 178 HIS 0.006 0.001 HIS G 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (19644) covalent geometry : angle 0.59033 / 0.32 (26648) SS BOND : bond 0.00876 / 0.57 ( 44) SS BOND : angle 2.43837 / 1.65 ( 88) hydrogen bonds : bond 0.03541 / 2.51 ( 662) hydrogen bonds : angle 5.62527 / 3.99 ( 1767) link_NAG-ASN : bond 0.00048 / 0.02 ( 4) link_NAG-ASN : angle 2.38823 / 1.41 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 210 time to evaluate : 0.798 Fit side-chains REVERT: A 398 ASP cc_start: 0.8550 (m-30) cc_final: 0.8325 (m-30) REVERT: B 398 ASP cc_start: 0.8598 (m-30) cc_final: 0.8368 (m-30) REVERT: C 398 ASP cc_start: 0.8570 (m-30) cc_final: 0.8341 (m-30) REVERT: D 398 ASP cc_start: 0.8575 (m-30) cc_final: 0.8329 (m-30) REVERT: F 100 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8361 (pm20) REVERT: G 46 GLU cc_start: 0.8286 (tt0) cc_final: 0.7952 (tt0) REVERT: H 83 ASP cc_start: 0.7294 (m-30) cc_final: 0.7045 (m-30) outliers start: 31 outliers final: 19 residues processed: 220 average time/residue: 0.1315 time to fit residues: 44.6157 Evaluate side-chains 227 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 18 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 177 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 chunk 201 optimal weight: 5.9990 chunk 62 optimal weight: 0.0370 chunk 70 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 172 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 229 optimal weight: 0.7980 chunk 161 optimal weight: 6.9990 overall best weight: 2.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 35 ASN F 32 ASN G 35 ASN H 32 ASN I 35 ASN J 32 ASN K 35 ASN L 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.113697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.088161 restraints weight = 25773.790| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.61 r_work: 0.2809 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19692 Z= 0.198 Angle : 0.665 14.930 26748 Z= 0.352 Chirality : 0.047 0.188 2828 Planarity : 0.005 0.055 3448 Dihedral : 5.204 34.562 2784 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.92 % Allowed : 13.24 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.07 (0.16), residues: 2452 helix: -4.26 (0.28), residues: 24 sheet: 0.59 (0.16), residues: 980 loop : -1.69 (0.14), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 344 TYR 0.010 0.001 TYR I 95 PHE 0.018 0.002 PHE A 120 TRP 0.019 0.001 TRP D 178 HIS 0.009 0.001 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 (19644) covalent geometry : angle 0.65152 / 0.35 (26648) SS BOND : bond 0.01129 / 0.73 ( 44) SS BOND : angle 2.20450 / 1.50 ( 88) hydrogen bonds : bond 0.04184 / 2.96 ( 662) hydrogen bonds : angle 5.79954 / 4.12 ( 1767) link_NAG-ASN : bond 0.00090 / 0.05 ( 4) link_NAG-ASN : angle 2.64997 / 1.57 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 0.678 Fit side-chains REVERT: D 398 ASP cc_start: 0.8623 (m-30) cc_final: 0.8409 (m-30) REVERT: F 100 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8387 (pm20) outliers start: 40 outliers final: 16 residues processed: 226 average time/residue: 0.1331 time to fit residues: 45.7201 Evaluate side-chains 216 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 18 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 116 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 214 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 35 ASN F 32 ASN G 35 ASN H 32 ASN I 35 ASN J 32 ASN K 35 ASN L 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.115839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.091375 restraints weight = 25549.852| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.61 r_work: 0.2839 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19692 Z= 0.126 Angle : 0.590 11.681 26748 Z= 0.314 Chirality : 0.045 0.200 2828 Planarity : 0.005 0.053 3448 Dihedral : 4.942 34.154 2784 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.34 % Allowed : 14.40 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.03 (0.16), residues: 2452 helix: -4.00 (0.33), residues: 24 sheet: 0.61 (0.17), residues: 940 loop : -1.59 (0.14), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 344 TYR 0.009 0.001 TYR K 60 PHE 0.014 0.001 PHE D 120 TRP 0.018 0.001 TRP D 178 HIS 0.006 0.001 HIS I 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 (19644) covalent geometry : angle 0.57613 / 0.31 (26648) SS BOND : bond 0.00778 / 0.51 ( 44) SS BOND : angle 2.16067 / 1.45 ( 88) hydrogen bonds : bond 0.03527 / 2.50 ( 662) hydrogen bonds : angle 5.62337 / 3.99 ( 1767) link_NAG-ASN : bond 0.00057 / 0.03 ( 4) link_NAG-ASN : angle 2.39139 / 1.41 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 0.485 Fit side-chains REVERT: A 398 ASP cc_start: 0.8584 (m-30) cc_final: 0.8360 (m-30) REVERT: B 398 ASP cc_start: 0.8608 (m-30) cc_final: 0.8392 (m-30) REVERT: C 398 ASP cc_start: 0.8586 (m-30) cc_final: 0.8366 (m-30) REVERT: D 398 ASP cc_start: 0.8614 (m-30) cc_final: 0.8382 (m-30) REVERT: F 100 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8370 (pm20) REVERT: K 46 GLU cc_start: 0.8382 (tt0) cc_final: 0.8092 (tt0) REVERT: L 100 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8225 (pm20) outliers start: 28 outliers final: 17 residues processed: 217 average time/residue: 0.1268 time to fit residues: 42.1838 Evaluate side-chains 226 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 207 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 100 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 113 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 225 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 216 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 35 ASN F 32 ASN G 35 ASN H 32 ASN I 35 ASN J 32 ASN K 35 ASN L 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.089955 restraints weight = 25507.787| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.61 r_work: 0.2818 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19692 Z= 0.170 Angle : 0.624 11.489 26748 Z= 0.331 Chirality : 0.047 0.203 2828 Planarity : 0.005 0.055 3448 Dihedral : 5.057 32.908 2784 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.68 % Allowed : 14.16 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.01 (0.16), residues: 2452 helix: -3.79 (0.44), residues: 24 sheet: 0.63 (0.16), residues: 980 loop : -1.64 (0.14), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 344 TYR 0.010 0.001 TYR I 95 PHE 0.017 0.002 PHE D 120 TRP 0.019 0.001 TRP D 178 HIS 0.009 0.001 HIS I 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (19644) covalent geometry : angle 0.61120 / 0.33 (26648) SS BOND : bond 0.00900 / 0.58 ( 44) SS BOND : angle 2.05644 / 1.39 ( 88) hydrogen bonds : bond 0.03913 / 2.77 ( 662) hydrogen bonds : angle 5.71106 / 4.06 ( 1767) link_NAG-ASN : bond 0.00078 / 0.04 ( 4) link_NAG-ASN : angle 2.49962 / 1.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 0.672 Fit side-chains REVERT: A 398 ASP cc_start: 0.8616 (m-30) cc_final: 0.8392 (m-30) REVERT: B 252 TYR cc_start: 0.9144 (OUTLIER) cc_final: 0.8915 (m-80) REVERT: C 398 ASP cc_start: 0.8610 (m-30) cc_final: 0.8393 (m-30) REVERT: D 252 TYR cc_start: 0.9144 (OUTLIER) cc_final: 0.8918 (m-80) REVERT: D 398 ASP cc_start: 0.8621 (m-30) cc_final: 0.8409 (m-30) REVERT: F 100 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8364 (pm20) REVERT: K 46 GLU cc_start: 0.8387 (tt0) cc_final: 0.8096 (tt0) REVERT: L 100 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8226 (pm20) outliers start: 35 outliers final: 19 residues processed: 222 average time/residue: 0.1321 time to fit residues: 44.8983 Evaluate side-chains 226 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 252 TYR Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 100 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 224 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 216 optimal weight: 8.9990 chunk 149 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 35 ASN F 32 ASN G 35 ASN H 32 ASN I 35 ASN J 32 ASN K 35 ASN L 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.093147 restraints weight = 25647.398| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.60 r_work: 0.2868 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19692 Z= 0.102 Angle : 0.550 9.822 26748 Z= 0.293 Chirality : 0.044 0.198 2828 Planarity : 0.004 0.052 3448 Dihedral : 4.688 32.307 2784 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.39 % Allowed : 14.59 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.91 (0.16), residues: 2452 helix: -3.12 (0.64), residues: 24 sheet: 0.69 (0.17), residues: 940 loop : -1.52 (0.14), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 344 TYR 0.010 0.001 TYR K 60 PHE 0.013 0.001 PHE A 120 TRP 0.015 0.001 TRP C 178 HIS 0.005 0.001 HIS G 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (19644) covalent geometry : angle 0.53791 / 0.29 (26648) SS BOND : bond 0.00671 / 0.44 ( 44) SS BOND : angle 1.89162 / 1.28 ( 88) hydrogen bonds : bond 0.03164 / 2.24 ( 662) hydrogen bonds : angle 5.45121 / 3.86 ( 1767) link_NAG-ASN : bond 0.00026 / 0.01 ( 4) link_NAG-ASN : angle 2.10096 / 1.23 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 0.694 Fit side-chains REVERT: A 398 ASP cc_start: 0.8547 (m-30) cc_final: 0.8319 (m-30) REVERT: B 398 ASP cc_start: 0.8563 (m-30) cc_final: 0.8336 (m-30) REVERT: C 398 ASP cc_start: 0.8552 (m-30) cc_final: 0.8324 (m-30) REVERT: D 398 ASP cc_start: 0.8572 (m-30) cc_final: 0.8347 (m-30) REVERT: F 100 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8330 (pm20) REVERT: G 46 GLU cc_start: 0.8280 (tt0) cc_final: 0.7978 (tt0) REVERT: H 83 ASP cc_start: 0.7451 (m-30) cc_final: 0.7173 (m-30) REVERT: K 46 GLU cc_start: 0.8309 (tt0) cc_final: 0.8042 (tt0) outliers start: 29 outliers final: 22 residues processed: 239 average time/residue: 0.1222 time to fit residues: 45.2174 Evaluate side-chains 231 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 18 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 66 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 237 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 216 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 189 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 35 ASN F 32 ASN G 35 ASN H 32 ASN I 35 ASN J 32 ASN K 35 ASN L 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.117029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.092660 restraints weight = 25596.623| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.61 r_work: 0.2865 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 19692 Z= 0.172 Angle : 0.716 37.974 26748 Z= 0.413 Chirality : 0.045 0.197 2828 Planarity : 0.006 0.123 3448 Dihedral : 4.695 32.458 2784 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.34 % Allowed : 14.68 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.87 (0.16), residues: 2452 helix: -2.81 (0.74), residues: 24 sheet: 0.72 (0.17), residues: 940 loop : -1.50 (0.14), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 344 TYR 0.009 0.001 TYR K 60 PHE 0.014 0.001 PHE A 120 TRP 0.019 0.001 TRP E 36 HIS 0.015 0.002 HIS K 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (19644) covalent geometry : angle 0.70832 / 0.41 (26648) SS BOND : bond 0.00740 / 0.48 ( 44) SS BOND : angle 1.86041 / 1.25 ( 88) hydrogen bonds : bond 0.03454 / 2.43 ( 662) hydrogen bonds : angle 5.51244 / 3.91 ( 1767) link_NAG-ASN : bond 0.00045 / 0.02 ( 4) link_NAG-ASN : angle 2.13585 / 1.26 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4120.41 seconds wall clock time: 71 minutes 15.98 seconds (4275.98 seconds total)