Starting phenix.real_space_refine on Thu Sep 18 18:24:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yvk_39605/09_2025/8yvk_39605.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yvk_39605/09_2025/8yvk_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_39605/09_2025/8yvk_39605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yvk_39605/09_2025/8yvk_39605.map" model { file = "/net/cci-nas-00/data/ceres_data/8yvk_39605/09_2025/8yvk_39605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yvk_39605/09_2025/8yvk_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-2.0-5805/lib/python3.9/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, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 4.57, per 1000 atoms: 0.24 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: 1.69 Conformation dependent library (CDL) restraints added in 887.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.02 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: 4.23 Time building geometry restraints manager: 2.27 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 2.510 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 2.510 ... (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: 0.04 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.680 Find NCS groups from input model: 0.420 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 aren 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 covalent geometry : bond 0.00721 (19644) covalent geometry : angle 0.99824 (26648) SS BOND : bond 0.15168 ( 44) SS BOND : angle 5.79664 ( 88) hydrogen bonds : bond 0.11848 ( 662) hydrogen bonds : angle 7.84958 ( 1767) link_NAG-ASN : bond 0.01058 ( 4) link_NAG-ASN : angle 8.45705 ( 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 : 0.738 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: 0.8397 (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: 0.6497 (m-30) outliers start: 8 outliers final: 1 residues processed: 253 average time/residue: 0.1747 time to fit residues: 64.1883 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 : 0.762 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: K 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.113132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.087864 restraints weight = 25531.412| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.61 r_work: 0.2828 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 19692 Z= 0.180 Angle : 0.680 10.087 26748 Z= 0.365 Chirality : 0.048 0.181 2828 Planarity : 0.005 0.055 3448 Dihedral : 5.382 21.105 2786 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.81 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 aren not related in a simple way. whole: -1.56 (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 K 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 covalent geometry : bond 0.00436 (19644) covalent geometry : angle 0.65897 (26648) SS BOND : bond 0.01044 ( 44) SS BOND : angle 2.76797 ( 88) hydrogen bonds : bond 0.04342 ( 662) hydrogen bonds : angle 6.32404 ( 1767) link_NAG-ASN : bond 0.00132 ( 4) link_NAG-ASN : angle 3.41524 ( 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 223 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 217 time to evaluate : 0.902 Fit side-chains REVERT: A 247 ASP cc_start: 0.8340 (p0) cc_final: 0.8096 (p0) REVERT: A 398 ASP cc_start: 0.8595 (m-30) cc_final: 0.8336 (m-30) REVERT: B 247 ASP cc_start: 0.8336 (p0) cc_final: 0.8087 (p0) REVERT: D 398 ASP cc_start: 0.8676 (m-30) cc_final: 0.8425 (m-30) REVERT: E 46 GLU cc_start: 0.8128 (tt0) cc_final: 0.7769 (tt0) REVERT: F 6 GLN cc_start: 0.8231 (tt0) cc_final: 0.8019 (tt0) REVERT: F 83 ASP cc_start: 0.7315 (m-30) cc_final: 0.7071 (m-30) REVERT: G 76 LYS cc_start: 0.7372 (mppt) cc_final: 0.7088 (mptt) REVERT: H 18 ARG cc_start: 0.7897 (ttp80) cc_final: 0.7695 (ttp80) REVERT: H 83 ASP cc_start: 0.7345 (m-30) cc_final: 0.6960 (m-30) REVERT: L 83 ASP cc_start: 0.7304 (m-30) cc_final: 0.7061 (m-30) outliers start: 6 outliers final: 2 residues processed: 222 average time/residue: 0.1547 time to fit residues: 52.2493 Evaluate side-chains 197 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 195 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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: 6.9990 chunk 207 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 162 optimal weight: 0.0770 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: 10.0000 chunk 15 optimal weight: 3.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B 226 GLN C 226 GLN D 226 GLN E 35 ASN E 39 GLN G 35 ASN H 32 ASN I 35 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.088408 restraints weight = 25824.581| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.57 r_work: 0.2799 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19692 Z= 0.190 Angle : 0.652 7.301 26748 Z= 0.350 Chirality : 0.048 0.179 2828 Planarity : 0.005 0.056 3448 Dihedral : 5.314 28.032 2784 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.15 % Allowed : 10.84 % Favored : 88.00 % 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 aren not related in a simple way. whole: -1.44 (0.15), residues: 2452 helix: -4.60 (0.24), residues: 24 sheet: 0.41 (0.16), residues: 908 loop : -1.89 (0.14), residues: 1520 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 0.022 0.002 TRP B 178 HIS 0.008 0.001 HIS I 99 Details of bonding type rmsd covalent geometry : bond 0.00461 (19644) covalent geometry : angle 0.64283 (26648) SS BOND : bond 0.00902 ( 44) SS BOND : angle 1.67580 ( 88) hydrogen bonds : bond 0.04355 ( 662) hydrogen bonds : angle 6.08546 ( 1767) link_NAG-ASN : bond 0.00098 ( 4) link_NAG-ASN : angle 2.93199 ( 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 233 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 0.761 Fit side-chains REVERT: D 398 ASP cc_start: 0.8634 (m-30) cc_final: 0.8394 (m-30) REVERT: D 435 LYS cc_start: 0.9191 (mmtp) cc_final: 0.8984 (mttp) REVERT: E 46 GLU cc_start: 0.8141 (tt0) cc_final: 0.7811 (tt0) REVERT: F 83 ASP cc_start: 0.7457 (m-30) cc_final: 0.7233 (m-30) REVERT: H 83 ASP cc_start: 0.7429 (m-30) cc_final: 0.7120 (m-30) REVERT: K 46 GLU cc_start: 0.8327 (tt0) cc_final: 0.8006 (tt0) REVERT: L 83 ASP cc_start: 0.7484 (m-30) cc_final: 0.7276 (m-30) outliers start: 24 outliers final: 11 residues processed: 221 average time/residue: 0.1510 time to fit residues: 50.2295 Evaluate side-chains 206 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 195 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER 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: 2.9990 chunk 134 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 chunk 59 optimal weight: 0.5980 chunk 141 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 35 ASN F 32 ASN G 35 ASN H 32 ASN I 35 ASN J 32 ASN L 32 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.115294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.090295 restraints weight = 25728.547| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.56 r_work: 0.2845 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19692 Z= 0.119 Angle : 0.585 11.183 26748 Z= 0.315 Chirality : 0.045 0.165 2828 Planarity : 0.005 0.054 3448 Dihedral : 4.985 32.963 2784 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.49 % Allowed : 12.38 % Favored : 86.13 % 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 aren not related in a simple way. whole: -1.21 (0.16), residues: 2452 helix: -4.47 (0.24), residues: 24 sheet: 0.55 (0.16), residues: 956 loop : -1.78 (0.14), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 344 TYR 0.011 0.001 TYR E 60 PHE 0.014 0.001 PHE A 120 TRP 0.018 0.001 TRP C 178 HIS 0.006 0.001 HIS I 99 Details of bonding type rmsd covalent geometry : bond 0.00271 (19644) covalent geometry : angle 0.57392 (26648) SS BOND : bond 0.00845 ( 44) SS BOND : angle 1.84454 ( 88) hydrogen bonds : bond 0.03643 ( 662) hydrogen bonds : angle 5.80421 ( 1767) link_NAG-ASN : bond 0.00071 ( 4) link_NAG-ASN : angle 2.50465 ( 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 254 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 0.777 Fit side-chains REVERT: A 398 ASP cc_start: 0.8543 (m-30) cc_final: 0.8297 (m-30) REVERT: B 398 ASP cc_start: 0.8558 (m-30) cc_final: 0.8328 (m-30) REVERT: B 435 LYS cc_start: 0.9219 (mmtp) cc_final: 0.9009 (mttp) REVERT: C 398 ASP cc_start: 0.8544 (m-30) cc_final: 0.8317 (m-30) REVERT: D 398 ASP cc_start: 0.8558 (m-30) cc_final: 0.8335 (m-30) REVERT: D 435 LYS cc_start: 0.9223 (mmtp) cc_final: 0.9008 (mttp) REVERT: F 83 ASP cc_start: 0.7434 (m-30) cc_final: 0.7230 (m-30) REVERT: F 100 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8386 (pm20) REVERT: G 46 GLU cc_start: 0.8300 (tt0) cc_final: 0.7986 (tt0) REVERT: H 83 ASP cc_start: 0.7324 (m-30) cc_final: 0.7093 (m-30) REVERT: K 46 GLU cc_start: 0.8322 (tt0) cc_final: 0.8013 (tt0) outliers start: 31 outliers final: 14 residues processed: 234 average time/residue: 0.1509 time to fit residues: 53.3068 Evaluate side-chains 223 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 208 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 56 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 1 optimal weight: 0.7980 chunk 187 optimal weight: 0.3980 chunk 169 optimal weight: 0.9990 chunk 46 optimal weight: 0.0670 chunk 199 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3353 r_free = 0.3353 target = 0.117579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.091971 restraints weight = 25600.429| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.67 r_work: 0.2864 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19692 Z= 0.095 Angle : 0.534 6.951 26748 Z= 0.287 Chirality : 0.044 0.190 2828 Planarity : 0.004 0.053 3448 Dihedral : 4.642 26.192 2784 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.39 % Allowed : 12.57 % Favored : 86.04 % 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 aren not related in a simple way. whole: -1.05 (0.16), residues: 2452 helix: -4.23 (0.25), residues: 24 sheet: 0.59 (0.17), residues: 944 loop : -1.60 (0.14), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 344 TYR 0.010 0.001 TYR E 60 PHE 0.012 0.001 PHE C 120 TRP 0.015 0.001 TRP C 178 HIS 0.005 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00203 (19644) covalent geometry : angle 0.52552 (26648) SS BOND : bond 0.00746 ( 44) SS BOND : angle 1.48920 ( 88) hydrogen bonds : bond 0.03186 ( 662) hydrogen bonds : angle 5.56268 ( 1767) link_NAG-ASN : bond 0.00025 ( 4) link_NAG-ASN : angle 2.28250 ( 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 251 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 222 time to evaluate : 0.544 Fit side-chains REVERT: A 398 ASP cc_start: 0.8546 (m-30) cc_final: 0.8301 (m-30) REVERT: B 398 ASP cc_start: 0.8565 (m-30) cc_final: 0.8338 (m-30) REVERT: B 435 LYS cc_start: 0.9241 (mmtp) cc_final: 0.9033 (mttp) REVERT: C 398 ASP cc_start: 0.8529 (m-30) cc_final: 0.8316 (m-30) REVERT: D 398 ASP cc_start: 0.8559 (m-30) cc_final: 0.8335 (m-30) REVERT: D 435 LYS cc_start: 0.9251 (mmtp) cc_final: 0.9038 (mttp) REVERT: F 100 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8381 (pm20) outliers start: 29 outliers final: 22 residues processed: 231 average time/residue: 0.1489 time to fit residues: 52.1190 Evaluate side-chains 237 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 427 MET 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 35 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 120 optimal weight: 0.7980 chunk 84 optimal weight: 0.0000 chunk 164 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 218 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 189 optimal weight: 7.9990 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.114529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.089195 restraints weight = 25614.927| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.61 r_work: 0.2834 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19692 Z= 0.148 Angle : 0.622 15.718 26748 Z= 0.329 Chirality : 0.045 0.162 2828 Planarity : 0.005 0.055 3448 Dihedral : 4.913 35.659 2784 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.68 % Allowed : 12.38 % Favored : 85.94 % 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 aren not related in a simple way. whole: -1.01 (0.16), residues: 2452 helix: -4.16 (0.28), residues: 24 sheet: 0.67 (0.17), residues: 956 loop : -1.63 (0.14), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 344 TYR 0.009 0.001 TYR K 95 PHE 0.016 0.002 PHE C 120 TRP 0.016 0.001 TRP A 178 HIS 0.007 0.001 HIS I 99 Details of bonding type rmsd covalent geometry : bond 0.00355 (19644) covalent geometry : angle 0.60442 (26648) SS BOND : bond 0.00933 ( 44) SS BOND : angle 2.48302 ( 88) hydrogen bonds : bond 0.03684 ( 662) hydrogen bonds : angle 5.63361 ( 1767) link_NAG-ASN : bond 0.00055 ( 4) link_NAG-ASN : angle 2.40274 ( 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 252 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 0.765 Fit side-chains REVERT: A 398 ASP cc_start: 0.8562 (m-30) cc_final: 0.8339 (m-30) REVERT: B 398 ASP cc_start: 0.8597 (m-30) cc_final: 0.8371 (m-30) REVERT: C 398 ASP cc_start: 0.8561 (m-30) cc_final: 0.8341 (m-30) REVERT: D 398 ASP cc_start: 0.8567 (m-30) cc_final: 0.8342 (m-30) REVERT: D 435 LYS cc_start: 0.9276 (mmtp) cc_final: 0.9076 (mttp) REVERT: F 100 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8367 (pm20) REVERT: J 83 ASP cc_start: 0.7655 (m-30) cc_final: 0.7234 (m-30) outliers start: 35 outliers final: 18 residues processed: 230 average time/residue: 0.1364 time to fit residues: 48.5387 Evaluate side-chains 228 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 209 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 226 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 172 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 229 optimal weight: 7.9990 chunk 161 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3254 r_free = 0.3254 target = 0.110297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.084597 restraints weight = 25969.972| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.62 r_work: 0.2765 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.052 19692 Z= 0.346 Angle : 0.816 16.030 26748 Z= 0.427 Chirality : 0.053 0.191 2828 Planarity : 0.007 0.056 3448 Dihedral : 5.739 34.857 2784 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.63 % Allowed : 14.01 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 aren not related in a simple way. whole: -1.34 (0.15), residues: 2452 helix: -4.49 (0.25), residues: 24 sheet: 0.50 (0.16), residues: 904 loop : -1.83 (0.14), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 344 TYR 0.012 0.002 TYR K 95 PHE 0.023 0.003 PHE A 120 TRP 0.025 0.002 TRP A 178 HIS 0.012 0.002 HIS K 99 Details of bonding type rmsd covalent geometry : bond 0.00863 (19644) covalent geometry : angle 0.80232 (26648) SS BOND : bond 0.01513 ( 44) SS BOND : angle 2.43860 ( 88) hydrogen bonds : bond 0.05305 ( 662) hydrogen bonds : angle 6.16528 ( 1767) link_NAG-ASN : bond 0.00199 ( 4) link_NAG-ASN : angle 3.19450 ( 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 239 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 0.731 Fit side-chains REVERT: F 83 ASP cc_start: 0.7655 (m-30) cc_final: 0.7414 (m-30) REVERT: F 100 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8374 (pm20) REVERT: L 83 ASP cc_start: 0.7642 (m-30) cc_final: 0.7380 (m-30) outliers start: 34 outliers final: 12 residues processed: 218 average time/residue: 0.1612 time to fit residues: 51.5807 Evaluate side-chains 213 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 69 THR 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 116 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3332 r_free = 0.3332 target = 0.116086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.091668 restraints weight = 25489.415| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.58 r_work: 0.2856 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19692 Z= 0.104 Angle : 0.564 10.208 26748 Z= 0.303 Chirality : 0.045 0.204 2828 Planarity : 0.005 0.052 3448 Dihedral : 4.907 32.519 2784 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.73 % Allowed : 14.01 % 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 aren not related in a simple way. whole: -1.09 (0.16), residues: 2452 helix: -4.11 (0.30), residues: 24 sheet: 0.60 (0.17), residues: 964 loop : -1.69 (0.14), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 19 TYR 0.010 0.001 TYR K 60 PHE 0.012 0.001 PHE A 120 TRP 0.018 0.001 TRP C 178 HIS 0.005 0.001 HIS K 99 Details of bonding type rmsd covalent geometry : bond 0.00233 (19644) covalent geometry : angle 0.55423 (26648) SS BOND : bond 0.00710 ( 44) SS BOND : angle 1.76057 ( 88) hydrogen bonds : bond 0.03272 ( 662) hydrogen bonds : angle 5.59652 ( 1767) link_NAG-ASN : bond 0.00053 ( 4) link_NAG-ASN : angle 2.23250 ( 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 255 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 219 time to evaluate : 0.825 Fit side-chains REVERT: A 398 ASP cc_start: 0.8573 (m-30) cc_final: 0.8348 (m-30) REVERT: B 398 ASP cc_start: 0.8584 (m-30) cc_final: 0.8342 (m-30) REVERT: C 398 ASP cc_start: 0.8572 (m-30) cc_final: 0.8330 (m-30) REVERT: D 398 ASP cc_start: 0.8584 (m-30) cc_final: 0.8345 (m-30) REVERT: F 100 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8363 (pm20) REVERT: G 46 GLU cc_start: 0.8290 (tt0) cc_final: 0.7998 (tt0) REVERT: L 100 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8217 (pm20) outliers start: 36 outliers final: 18 residues processed: 238 average time/residue: 0.1596 time to fit residues: 57.5943 Evaluate side-chains 234 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain D residue 317 CYS 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 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 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 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: 3.9990 chunk 103 optimal weight: 3.9990 chunk 225 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 chunk 216 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3266 r_free = 0.3266 target = 0.111348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.085935 restraints weight = 25659.103| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.58 r_work: 0.2788 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 19692 Z= 0.250 Angle : 0.706 12.015 26748 Z= 0.372 Chirality : 0.049 0.215 2828 Planarity : 0.006 0.056 3448 Dihedral : 5.349 32.946 2784 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.49 % Allowed : 14.54 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 aren not related in a simple way. whole: -1.23 (0.16), residues: 2452 helix: -4.13 (0.35), residues: 24 sheet: 0.48 (0.16), residues: 944 loop : -1.75 (0.14), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 344 TYR 0.011 0.002 TYR A 252 PHE 0.021 0.002 PHE C 120 TRP 0.021 0.002 TRP C 178 HIS 0.010 0.002 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00625 (19644) covalent geometry : angle 0.69171 (26648) SS BOND : bond 0.01017 ( 44) SS BOND : angle 2.38709 ( 88) hydrogen bonds : bond 0.04525 ( 662) hydrogen bonds : angle 5.87916 ( 1767) link_NAG-ASN : bond 0.00093 ( 4) link_NAG-ASN : angle 2.69255 ( 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 234 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 0.760 Fit side-chains REVERT: B 252 TYR cc_start: 0.9142 (OUTLIER) cc_final: 0.8898 (m-80) REVERT: C 252 TYR cc_start: 0.9139 (OUTLIER) cc_final: 0.8895 (m-80) REVERT: D 252 TYR cc_start: 0.9140 (OUTLIER) cc_final: 0.8883 (m-80) REVERT: F 100 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8374 (pm20) REVERT: J 100 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8212 (pm20) REVERT: K 46 GLU cc_start: 0.8355 (tt0) cc_final: 0.8079 (tt0) REVERT: L 100 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8264 (pm20) outliers start: 31 outliers final: 15 residues processed: 216 average time/residue: 0.1688 time to fit residues: 54.2571 Evaluate side-chains 224 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 CYS 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 C residue 252 TYR Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 252 TYR 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 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 100 GLN 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: 1.9990 chunk 61 optimal weight: 5.9990 chunk 216 optimal weight: 6.9990 chunk 149 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 196 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3340 r_free = 0.3340 target = 0.116708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.091014 restraints weight = 25715.766| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.69 r_work: 0.2859 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19692 Z= 0.103 Angle : 0.561 9.634 26748 Z= 0.299 Chirality : 0.045 0.201 2828 Planarity : 0.004 0.051 3448 Dihedral : 4.782 32.575 2784 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.10 % Allowed : 14.78 % Favored : 84.12 % 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 aren not related in a simple way. whole: -0.97 (0.16), residues: 2452 helix: -3.29 (0.61), residues: 24 sheet: 0.66 (0.17), residues: 964 loop : -1.61 (0.14), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 19 TYR 0.010 0.001 TYR K 60 PHE 0.013 0.001 PHE C 120 TRP 0.017 0.001 TRP C 178 HIS 0.005 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00233 (19644) covalent geometry : angle 0.54737 (26648) SS BOND : bond 0.00668 ( 44) SS BOND : angle 2.07600 ( 88) hydrogen bonds : bond 0.03141 ( 662) hydrogen bonds : angle 5.48868 ( 1767) link_NAG-ASN : bond 0.00034 ( 4) link_NAG-ASN : angle 2.10511 ( 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 249 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.765 Fit side-chains REVERT: A 398 ASP cc_start: 0.8558 (m-30) cc_final: 0.8344 (m-30) REVERT: B 398 ASP cc_start: 0.8581 (m-30) cc_final: 0.8343 (m-30) REVERT: C 398 ASP cc_start: 0.8553 (m-30) cc_final: 0.8318 (m-30) REVERT: D 398 ASP cc_start: 0.8556 (m-30) cc_final: 0.8324 (m-30) REVERT: F 100 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8358 (pm20) REVERT: G 46 GLU cc_start: 0.8328 (tt0) cc_final: 0.8035 (tt0) REVERT: H 83 ASP cc_start: 0.7578 (m-30) cc_final: 0.7273 (m-30) REVERT: J 83 ASP cc_start: 0.7547 (m-30) cc_final: 0.7184 (m-30) REVERT: K 46 GLU cc_start: 0.8319 (tt0) cc_final: 0.8063 (tt0) REVERT: L 100 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8238 (pm20) outliers start: 23 outliers final: 19 residues processed: 236 average time/residue: 0.1589 time to fit residues: 56.5374 Evaluate side-chains 242 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 221 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 317 CYS 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 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 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 35 ASN 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 66 optimal weight: 8.9990 chunk 24 optimal weight: 0.4980 chunk 124 optimal weight: 3.9990 chunk 237 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 189 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3329 r_free = 0.3329 target = 0.115971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.090497 restraints weight = 25742.403| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.61 r_work: 0.2840 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19692 Z= 0.144 Angle : 0.595 10.460 26748 Z= 0.316 Chirality : 0.046 0.203 2828 Planarity : 0.005 0.054 3448 Dihedral : 4.889 32.578 2784 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.34 % Allowed : 14.64 % 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 aren not related in a simple way. whole: -0.96 (0.16), residues: 2452 helix: -2.66 (0.87), residues: 24 sheet: 0.65 (0.17), residues: 964 loop : -1.60 (0.14), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 344 TYR 0.010 0.001 TYR A 252 PHE 0.016 0.002 PHE C 120 TRP 0.018 0.001 TRP C 178 HIS 0.008 0.001 HIS I 99 Details of bonding type rmsd covalent geometry : bond 0.00346 (19644) covalent geometry : angle 0.58272 (26648) SS BOND : bond 0.00807 ( 44) SS BOND : angle 2.05452 ( 88) hydrogen bonds : bond 0.03572 ( 662) hydrogen bonds : angle 5.54921 ( 1767) link_NAG-ASN : bond 0.00042 ( 4) link_NAG-ASN : angle 2.26187 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4715.76 seconds wall clock time: 81 minutes 24.55 seconds (4884.55 seconds total)