Starting phenix.real_space_refine on Sat Jul 4 10:45:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o4q_70111/07_2026/9o4q_70111.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o4q_70111/07_2026/9o4q_70111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o4q_70111/07_2026/9o4q_70111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o4q_70111/07_2026/9o4q_70111.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o4q_70111/07_2026/9o4q_70111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o4q_70111/07_2026/9o4q_70111.map" } resolution = 2.76 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= 0.000 sd= 0.007 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 9 9.91 5 S 128 5.16 5 C 12264 2.51 5 N 3312 2.21 5 O 3852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19565 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2980 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 364} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2980 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 364} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2980 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 364} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2980 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 364} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "F" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "G" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "H" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "I" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "J" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "K" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "L" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "M" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.93, per 1000 atoms: 0.20 Number of scatterers: 19565 At special positions: 0 Unit cell: (144.275, 144.275, 83.375, 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 9 19.99 S 128 16.00 O 3852 8.00 N 3312 7.00 C 12264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.04 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 318 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.04 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 318 " - pdb=" SG CYS B 336 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.04 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 318 " - pdb=" SG CYS C 336 " distance=2.03 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.03 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.04 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 318 " - pdb=" SG CYS D 336 " distance=2.03 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " BETA1-6 " NAG M 1 " - " FUC M 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG N 1 " - " FUC N 3 " " NAG O 1 " - " FUC O 3 " " NAG P 1 " - " FUC P 3 " NAG-ASN " NAG A 501 " - " ASN A 88 " " NAG A 502 " - " ASN A 234 " " NAG B 501 " - " ASN B 88 " " NAG B 502 " - " ASN B 234 " " NAG C 501 " - " ASN C 88 " " NAG C 502 " - " ASN C 234 " " NAG D 501 " - " ASN D 88 " " NAG D 502 " - " ASN D 234 " " NAG M 1 " - " ASN A 146 " " NAG N 1 " - " ASN B 146 " " NAG O 1 " - " ASN C 146 " " NAG P 1 " - " ASN D 146 " Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 968.9 milliseconds 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4496 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 56 sheets defined 3.2% alpha, 43.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 104 through 112 removed outlier: 4.517A pdb=" N LYS A 111 " --> pdb=" O ARG A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 412A through 414 Processing helix chain 'B' and resid 104 through 112 removed outlier: 4.517A pdb=" N LYS B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 412A through 414 Processing helix chain 'C' and resid 104 through 112 removed outlier: 4.517A pdb=" N LYS C 111 " --> pdb=" O ARG C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'C' and resid 412A through 414 Processing helix chain 'D' and resid 104 through 112 removed outlier: 4.517A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 412A through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.349A pdb=" N SER A 445 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LYS A 102 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N SER A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.813A pdb=" N PHE A 115 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ALA A 138 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLN A 136 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 158 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 6.389A pdb=" N TYR A 207 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 5.531A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.925A pdb=" N TYR A 252 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU A 267 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 254 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER A 265 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG A 256 " --> pdb=" O VAL A 263 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.539A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.713A pdb=" N PHE A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 363 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASN A 372 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY A 399 " --> pdb=" O ASN A 372 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 392 " --> pdb=" O TRP A 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.349A pdb=" N SER B 445 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LYS B 102 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N SER B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.813A pdb=" N PHE B 115 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ALA B 138 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLN B 136 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU B 158 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.389A pdb=" N TYR B 207 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 5.531A 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 Processing sheet with id=AB3, first strand: chain 'B' and resid 223 through 224 removed outlier: 6.925A pdb=" N TYR B 252 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU B 267 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE B 254 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER B 265 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG B 256 " --> pdb=" O VAL B 263 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 276 through 283 removed outlier: 5.539A pdb=" N GLU B 277 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ARG B 292 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 352 through 356 removed outlier: 4.713A pdb=" N PHE B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY B 363 " --> pdb=" O PHE B 352 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASN B 372 " --> pdb=" O GLY B 399 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY B 399 " --> pdb=" O ASN B 372 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE B 374 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 392 " --> pdb=" O TRP B 378 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.349A pdb=" N SER C 445 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LYS C 102 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N SER C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.813A pdb=" N PHE C 115 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ALA C 138 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLN C 136 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU C 158 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 179 through 184 removed outlier: 6.389A pdb=" N TYR C 207 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 5.531A 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 Processing sheet with id=AC1, first strand: chain 'C' and resid 223 through 224 removed outlier: 6.925A pdb=" N TYR C 252 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU C 267 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE C 254 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER C 265 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG C 256 " --> pdb=" O VAL C 263 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 276 through 283 removed outlier: 5.539A pdb=" N GLU C 277 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ARG C 292 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 352 through 356 removed outlier: 4.713A pdb=" N PHE C 352 " --> pdb=" O GLY C 363 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY C 363 " --> pdb=" O PHE C 352 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASN C 372 " --> pdb=" O GLY C 399 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY C 399 " --> pdb=" O ASN C 372 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE C 374 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 392 " --> pdb=" O TRP C 378 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 96 through 102 removed outlier: 6.349A pdb=" N SER D 445 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LYS D 102 " --> pdb=" O SER D 443 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N SER D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.813A pdb=" N PHE D 115 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ALA D 138 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLN D 136 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU D 158 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 179 through 184 removed outlier: 6.389A pdb=" N TYR D 207 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 5.531A 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 Processing sheet with id=AC8, first strand: chain 'D' and resid 223 through 224 removed outlier: 6.925A pdb=" N TYR D 252 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU D 267 " --> pdb=" O TYR D 252 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE D 254 " --> pdb=" O SER D 265 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER D 265 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG D 256 " --> pdb=" O VAL D 263 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 276 through 283 removed outlier: 5.539A pdb=" N GLU D 277 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ARG D 292 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 352 through 356 removed outlier: 4.713A pdb=" N PHE D 352 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY D 363 " --> pdb=" O PHE D 352 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASN D 372 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY D 399 " --> pdb=" O ASN D 372 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE D 374 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE D 392 " --> pdb=" O TRP D 378 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.721A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.583A pdb=" N MET E 34 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.441A pdb=" N VAL E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 97 through 98 Processing sheet with id=AD6, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.721A pdb=" N GLN F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER F 25 " --> pdb=" O GLN F 3 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.583A pdb=" N MET F 34 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.441A pdb=" N VAL F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 97 through 98 Processing sheet with id=AE1, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.721A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.583A pdb=" N MET G 34 " --> pdb=" O ILE G 50 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 10 through 12 removed outlier: 4.441A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 97 through 98 Processing sheet with id=AE5, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.721A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.583A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.441A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 97 through 98 Processing sheet with id=AE9, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.845A pdb=" N ASP I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.676A pdb=" N GLU I 105 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL I 85 " --> pdb=" O GLN I 38 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AF4, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.845A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.676A pdb=" N GLU J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL J 85 " --> pdb=" O GLN J 38 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.845A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.676A pdb=" N GLU K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.845A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.676A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 740 hydrogen bonds defined for protein. 1872 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: 3.99 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6300 1.34 - 1.47: 5284 1.47 - 1.59: 8296 1.59 - 1.71: 0 1.71 - 1.84: 176 Bond restraints: 20056 Sorted by residual: bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C1 NAG C 502 " pdb=" O5 NAG C 502 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.76e+00 ... (remaining 20051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 25064 1.42 - 2.84: 1784 2.84 - 4.26: 276 4.26 - 5.68: 116 5.68 - 7.10: 28 Bond angle restraints: 27268 Sorted by residual: angle pdb=" CA ARG E 71 " pdb=" CB ARG E 71 " pdb=" CG ARG E 71 " ideal model delta sigma weight residual 114.10 121.20 -7.10 2.00e+00 2.50e-01 1.26e+01 angle pdb=" CA ARG F 71 " pdb=" CB ARG F 71 " pdb=" CG ARG F 71 " ideal model delta sigma weight residual 114.10 121.20 -7.10 2.00e+00 2.50e-01 1.26e+01 angle pdb=" CA ARG H 71 " pdb=" CB ARG H 71 " pdb=" CG ARG H 71 " ideal model delta sigma weight residual 114.10 121.20 -7.10 2.00e+00 2.50e-01 1.26e+01 angle pdb=" CA ARG G 71 " pdb=" CB ARG G 71 " pdb=" CG ARG G 71 " ideal model delta sigma weight residual 114.10 121.20 -7.10 2.00e+00 2.50e-01 1.26e+01 angle pdb=" N ARG A 428 " pdb=" CA ARG A 428 " pdb=" C ARG A 428 " ideal model delta sigma weight residual 107.69 101.05 6.64 2.01e+00 2.48e-01 1.09e+01 ... (remaining 27263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 11088 16.60 - 33.20: 796 33.20 - 49.79: 164 49.79 - 66.39: 48 66.39 - 82.99: 16 Dihedral angle restraints: 12112 sinusoidal: 5012 harmonic: 7100 Sorted by residual: dihedral pdb=" CD ARG G 83 " pdb=" NE ARG G 83 " pdb=" CZ ARG G 83 " pdb=" NH1 ARG G 83 " ideal model delta sinusoidal sigma weight residual 0.00 82.99 -82.99 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CD ARG H 83 " pdb=" NE ARG H 83 " pdb=" CZ ARG H 83 " pdb=" NH1 ARG H 83 " ideal model delta sinusoidal sigma weight residual 0.00 82.99 -82.99 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CD ARG E 83 " pdb=" NE ARG E 83 " pdb=" CZ ARG E 83 " pdb=" NH1 ARG E 83 " ideal model delta sinusoidal sigma weight residual 0.00 82.99 -82.99 1 1.00e+01 1.00e-02 8.43e+01 ... (remaining 12109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1788 0.041 - 0.081: 788 0.081 - 0.122: 252 0.122 - 0.162: 124 0.162 - 0.203: 8 Chirality restraints: 2960 Sorted by residual: chirality pdb=" CA ILE A 215 " pdb=" N ILE A 215 " pdb=" C ILE A 215 " pdb=" CB ILE A 215 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ILE D 215 " pdb=" N ILE D 215 " pdb=" C ILE D 215 " pdb=" CB ILE D 215 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ILE B 215 " pdb=" N ILE B 215 " pdb=" C ILE B 215 " pdb=" CB ILE B 215 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2957 not shown) Planarity restraints: 3524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 83 " -0.978 9.50e-02 1.11e+02 4.39e-01 1.22e+02 pdb=" NE ARG E 83 " 0.074 2.00e-02 2.50e+03 pdb=" CZ ARG E 83 " -0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG E 83 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 83 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 83 " -0.978 9.50e-02 1.11e+02 4.39e-01 1.22e+02 pdb=" NE ARG F 83 " 0.074 2.00e-02 2.50e+03 pdb=" CZ ARG F 83 " -0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG F 83 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 83 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 83 " -0.978 9.50e-02 1.11e+02 4.39e-01 1.22e+02 pdb=" NE ARG H 83 " 0.074 2.00e-02 2.50e+03 pdb=" CZ ARG H 83 " -0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG H 83 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG H 83 " -0.005 2.00e-02 2.50e+03 ... (remaining 3521 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1060 2.72 - 3.27: 19388 3.27 - 3.81: 33468 3.81 - 4.36: 44024 4.36 - 4.90: 75716 Nonbonded interactions: 173656 Sorted by model distance: nonbonded pdb=" O GLY B 345 " pdb="CA CA B 503 " model vdw 2.181 3.250 nonbonded pdb=" O GLY C 345 " pdb="CA CA C 503 " model vdw 2.181 3.250 nonbonded pdb=" O GLY A 345 " pdb="CA CA A 503 " model vdw 2.181 3.250 nonbonded pdb=" O GLY D 345 " pdb="CA CA D 503 " model vdw 2.181 3.250 nonbonded pdb=" OD2 ASP C 324 " pdb="CA CA C 503 " model vdw 2.188 3.250 ... (remaining 173651 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 83 through 504) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 11.990 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: 0.070 Set scattering table: 0.050 Process input model: 18.220 Find NCS groups from input model: 0.450 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: 0.010 Load rotamer database and sin/cos tables:8.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 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 : 0.005 0.064 20116 Z= 0.228 Angle : 0.863 7.101 27408 Z= 0.451 Chirality : 0.054 0.203 2960 Planarity : 0.020 0.439 3512 Dihedral : 12.498 82.990 7496 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.93 % Allowed : 1.31 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.16), residues: 2476 helix: -1.76 (0.62), residues: 24 sheet: 0.14 (0.16), residues: 972 loop : -0.58 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.050 0.003 ARG H 71 TYR 0.055 0.003 TYR C 252 PHE 0.024 0.003 PHE D 255 TRP 0.017 0.002 TRP A 178 HIS 0.008 0.002 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.23 (20056) covalent geometry : angle 0.85462 / 0.45 (27268) SS BOND : bond 0.00298 / 0.19 ( 40) SS BOND : angle 1.72102 / 1.11 ( 80) hydrogen bonds : bond 0.13008 / 9.25 ( 664) hydrogen bonds : angle 8.86519 / 6.23 ( 1872) link_BETA1-4 : bond 0.00596 / 0.28 ( 4) link_BETA1-4 : angle 0.90577 / 0.53 ( 12) link_BETA1-6 : bond 0.00350 / 0.17 ( 4) link_BETA1-6 : angle 1.14530 / 0.61 ( 12) link_NAG-ASN : bond 0.00280 / 0.19 ( 12) link_NAG-ASN : angle 2.55058 / 1.52 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 368 time to evaluate : 0.714 Fit side-chains REVERT: A 269 ASN cc_start: 0.9008 (t0) cc_final: 0.8590 (t0) REVERT: B 269 ASN cc_start: 0.9008 (t0) cc_final: 0.8590 (t0) REVERT: C 269 ASN cc_start: 0.9009 (t0) cc_final: 0.8590 (t0) REVERT: D 269 ASN cc_start: 0.9008 (t0) cc_final: 0.8590 (t0) REVERT: E 71 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8450 (tmm160) REVERT: E 72 ASP cc_start: 0.8507 (t0) cc_final: 0.8291 (t0) REVERT: E 83 ARG cc_start: 0.8390 (ptp90) cc_final: 0.7936 (ptp90) REVERT: F 71 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8448 (tmm160) REVERT: F 72 ASP cc_start: 0.8507 (t0) cc_final: 0.8290 (t0) REVERT: F 83 ARG cc_start: 0.8390 (ptp90) cc_final: 0.7936 (ptp90) REVERT: G 71 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8448 (tmm160) REVERT: G 72 ASP cc_start: 0.8505 (t0) cc_final: 0.8287 (t0) REVERT: G 83 ARG cc_start: 0.8391 (ptp90) cc_final: 0.7937 (ptp90) REVERT: H 71 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8447 (tmm160) REVERT: H 72 ASP cc_start: 0.8506 (t0) cc_final: 0.8289 (t0) REVERT: H 83 ARG cc_start: 0.8390 (ptp90) cc_final: 0.7937 (ptp90) REVERT: I 3 VAL cc_start: 0.9425 (t) cc_final: 0.9162 (m) REVERT: J 3 VAL cc_start: 0.9426 (t) cc_final: 0.9163 (m) REVERT: K 3 VAL cc_start: 0.9427 (t) cc_final: 0.9163 (m) REVERT: L 3 VAL cc_start: 0.9427 (t) cc_final: 0.9164 (m) outliers start: 20 outliers final: 4 residues processed: 380 average time/residue: 0.6130 time to fit residues: 259.6324 Evaluate side-chains 288 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 280 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain B residue 430 ARG Chi-restraints excluded: chain C residue 430 ARG Chi-restraints excluded: chain D residue 430 ARG Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 71 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN B 136 GLN C 136 GLN D 136 GLN E 3 GLN E 6 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN F 6 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN G 6 GLN ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 6 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 GLN J 45 GLN K 45 GLN L 45 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.089949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.070217 restraints weight = 35840.332| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.49 r_work: 0.2780 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.068 20116 Z= 0.367 Angle : 0.745 12.835 27408 Z= 0.388 Chirality : 0.053 0.173 2960 Planarity : 0.006 0.048 3512 Dihedral : 6.991 55.605 3160 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.54 % Allowed : 9.70 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2476 helix: -1.07 (0.57), residues: 24 sheet: 0.29 (0.17), residues: 980 loop : -0.46 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 61 TYR 0.031 0.002 TYR A 252 PHE 0.021 0.003 PHE C 410 TRP 0.023 0.003 TRP D 178 HIS 0.008 0.002 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00871 / 0.37 (20056) covalent geometry : angle 0.73958 / 0.39 (27268) SS BOND : bond 0.00366 / 0.23 ( 40) SS BOND : angle 0.90185 / 0.58 ( 80) hydrogen bonds : bond 0.04847 / 3.32 ( 664) hydrogen bonds : angle 6.92437 / 4.89 ( 1872) link_BETA1-4 : bond 0.00225 / 0.10 ( 4) link_BETA1-4 : angle 1.45198 / 0.80 ( 12) link_BETA1-6 : bond 0.00029 / 0.01 ( 4) link_BETA1-6 : angle 1.51965 / 0.82 ( 12) link_NAG-ASN : bond 0.00503 / 0.35 ( 12) link_NAG-ASN : angle 2.19475 / 1.34 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 244 time to evaluate : 0.552 Fit side-chains REVERT: A 402 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8453 (mm-30) REVERT: B 402 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8451 (mm-30) REVERT: C 402 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8447 (mm-30) REVERT: D 402 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8459 (mm-30) REVERT: E 71 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8543 (ptm-80) REVERT: E 72 ASP cc_start: 0.8469 (t0) cc_final: 0.8077 (OUTLIER) REVERT: F 71 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8535 (ptm-80) REVERT: F 72 ASP cc_start: 0.8464 (t0) cc_final: 0.8073 (OUTLIER) REVERT: G 71 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8544 (ptm-80) REVERT: G 72 ASP cc_start: 0.8471 (t0) cc_final: 0.8081 (OUTLIER) REVERT: H 71 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8550 (ptm-80) REVERT: H 72 ASP cc_start: 0.8472 (t0) cc_final: 0.8083 (OUTLIER) REVERT: I 100 GLN cc_start: 0.8949 (pt0) cc_final: 0.8407 (pm20) REVERT: J 100 GLN cc_start: 0.8951 (pt0) cc_final: 0.8409 (pm20) REVERT: K 100 GLN cc_start: 0.8951 (pt0) cc_final: 0.8411 (pm20) REVERT: L 100 GLN cc_start: 0.8956 (pt0) cc_final: 0.8417 (pm20) outliers start: 76 outliers final: 28 residues processed: 280 average time/residue: 0.6644 time to fit residues: 205.9253 Evaluate side-chains 260 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 232 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 53 optimal weight: 0.9990 chunk 118 optimal weight: 0.0980 chunk 223 optimal weight: 7.9990 chunk 200 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 137 optimal weight: 0.0070 chunk 208 optimal weight: 8.9990 chunk 110 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412AHIS B 412AHIS C 412AHIS ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412AHIS E 3 GLN E 105 GLN F 3 GLN F 105 GLN G 3 GLN G 105 GLN H 3 GLN H 105 GLN J 100 GLN K 100 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.094637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.074827 restraints weight = 35351.155| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.55 r_work: 0.2866 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20116 Z= 0.129 Angle : 0.598 8.612 27408 Z= 0.312 Chirality : 0.046 0.141 2960 Planarity : 0.004 0.037 3512 Dihedral : 5.935 53.789 3144 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.89 % Allowed : 10.73 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.17), residues: 2476 helix: -1.38 (0.56), residues: 24 sheet: 0.26 (0.17), residues: 1000 loop : -0.24 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 96 TYR 0.018 0.001 TYR A 252 PHE 0.014 0.002 PHE D 410 TRP 0.018 0.001 TRP C 178 HIS 0.005 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (20056) covalent geometry : angle 0.59465 / 0.31 (27268) SS BOND : bond 0.00152 / 0.09 ( 40) SS BOND : angle 0.51290 / 0.34 ( 80) hydrogen bonds : bond 0.03675 / 2.50 ( 664) hydrogen bonds : angle 6.42800 / 4.53 ( 1872) link_BETA1-4 : bond 0.00398 / 0.20 ( 4) link_BETA1-4 : angle 1.28726 / 0.69 ( 12) link_BETA1-6 : bond 0.00231 / 0.11 ( 4) link_BETA1-6 : angle 1.27457 / 0.70 ( 12) link_NAG-ASN : bond 0.00266 / 0.18 ( 12) link_NAG-ASN : angle 1.77203 / 1.08 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 280 time to evaluate : 0.764 Fit side-chains REVERT: A 269 ASN cc_start: 0.9115 (t0) cc_final: 0.8709 (t0) REVERT: B 269 ASN cc_start: 0.9112 (t0) cc_final: 0.8705 (t0) REVERT: C 269 ASN cc_start: 0.9115 (t0) cc_final: 0.8708 (t0) REVERT: D 269 ASN cc_start: 0.9114 (t0) cc_final: 0.8707 (t0) REVERT: E 19 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8678 (tptt) REVERT: E 46 GLU cc_start: 0.8417 (tt0) cc_final: 0.8144 (tt0) REVERT: E 71 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8518 (ptm-80) REVERT: E 72 ASP cc_start: 0.8348 (t0) cc_final: 0.7941 (OUTLIER) REVERT: F 19 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8676 (tptt) REVERT: F 46 GLU cc_start: 0.8439 (tt0) cc_final: 0.8167 (tt0) REVERT: F 71 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8517 (ptm-80) REVERT: F 72 ASP cc_start: 0.8347 (t0) cc_final: 0.7940 (OUTLIER) REVERT: G 19 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8679 (tptt) REVERT: G 46 GLU cc_start: 0.8443 (tt0) cc_final: 0.8176 (tt0) REVERT: G 71 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8517 (ptm-80) REVERT: G 72 ASP cc_start: 0.8344 (t0) cc_final: 0.7938 (OUTLIER) REVERT: H 19 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8679 (tptt) REVERT: H 46 GLU cc_start: 0.8428 (tt0) cc_final: 0.8156 (tt0) REVERT: H 71 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8522 (ptm-80) REVERT: H 72 ASP cc_start: 0.8348 (t0) cc_final: 0.7941 (OUTLIER) REVERT: I 3 VAL cc_start: 0.9333 (t) cc_final: 0.9115 (m) REVERT: I 100 GLN cc_start: 0.8870 (pt0) cc_final: 0.8381 (pm20) REVERT: J 3 VAL cc_start: 0.9334 (t) cc_final: 0.9116 (m) REVERT: J 100 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8401 (pm20) REVERT: K 3 VAL cc_start: 0.9334 (t) cc_final: 0.9113 (m) REVERT: K 100 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8410 (pm20) REVERT: L 3 VAL cc_start: 0.9333 (t) cc_final: 0.9115 (m) REVERT: L 100 GLN cc_start: 0.8875 (pt0) cc_final: 0.8388 (pm20) outliers start: 62 outliers final: 16 residues processed: 316 average time/residue: 0.6335 time to fit residues: 223.3139 Evaluate side-chains 262 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 240 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 19 LYS Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 100 GLN Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 148 optimal weight: 0.9980 chunk 172 optimal weight: 7.9990 chunk 184 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 ASN A 435 ASN B 401 ASN B 435 ASN C 401 ASN C 435 ASN D 401 ASN D 435 ASN E 3 GLN E 105 GLN F 3 GLN F 105 GLN G 3 GLN G 105 GLN H 3 GLN H 105 GLN I 100 GLN L 100 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.091504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.071789 restraints weight = 35654.415| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.50 r_work: 0.2811 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 20116 Z= 0.241 Angle : 0.639 12.005 27408 Z= 0.330 Chirality : 0.048 0.168 2960 Planarity : 0.005 0.043 3512 Dihedral : 5.800 52.475 3144 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.73 % Allowed : 12.50 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.17), residues: 2476 helix: -0.92 (0.64), residues: 24 sheet: 0.19 (0.16), residues: 1008 loop : -0.29 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 38 TYR 0.020 0.002 TYR C 252 PHE 0.017 0.002 PHE B 410 TRP 0.016 0.002 TRP C 178 HIS 0.006 0.002 HIS C 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.24 (20056) covalent geometry : angle 0.63526 / 0.33 (27268) SS BOND : bond 0.00274 / 0.17 ( 40) SS BOND : angle 0.65407 / 0.42 ( 80) hydrogen bonds : bond 0.03832 / 2.63 ( 664) hydrogen bonds : angle 6.29150 / 4.42 ( 1872) link_BETA1-4 : bond 0.00421 / 0.21 ( 4) link_BETA1-4 : angle 1.24617 / 0.68 ( 12) link_BETA1-6 : bond 0.00213 / 0.10 ( 4) link_BETA1-6 : angle 1.35345 / 0.75 ( 12) link_NAG-ASN : bond 0.00326 / 0.23 ( 12) link_NAG-ASN : angle 1.85410 / 1.11 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 240 time to evaluate : 0.764 Fit side-chains REVERT: A 402 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8432 (mm-30) REVERT: A 445 SER cc_start: 0.9175 (t) cc_final: 0.8945 (m) REVERT: B 402 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8434 (mm-30) REVERT: B 445 SER cc_start: 0.9170 (t) cc_final: 0.8936 (m) REVERT: C 402 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8419 (mm-30) REVERT: C 445 SER cc_start: 0.9172 (t) cc_final: 0.8943 (m) REVERT: D 402 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8418 (mm-30) REVERT: D 445 SER cc_start: 0.9169 (t) cc_final: 0.8941 (m) REVERT: E 19 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8597 (tptt) REVERT: E 71 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8525 (ptm-80) REVERT: E 72 ASP cc_start: 0.8387 (t0) cc_final: 0.7986 (OUTLIER) REVERT: F 19 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8593 (tptt) REVERT: F 71 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8527 (ptm-80) REVERT: F 72 ASP cc_start: 0.8387 (t0) cc_final: 0.7987 (OUTLIER) REVERT: G 19 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8594 (tptt) REVERT: G 71 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8528 (ptm-80) REVERT: G 72 ASP cc_start: 0.8390 (t0) cc_final: 0.7990 (OUTLIER) REVERT: H 19 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8595 (tptt) REVERT: H 71 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8529 (ptm-80) REVERT: H 72 ASP cc_start: 0.8384 (t0) cc_final: 0.7984 (OUTLIER) REVERT: I 3 VAL cc_start: 0.9362 (t) cc_final: 0.9131 (m) REVERT: I 100 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8368 (pm20) REVERT: J 3 VAL cc_start: 0.9361 (t) cc_final: 0.9130 (m) REVERT: J 100 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8316 (pm20) REVERT: K 3 VAL cc_start: 0.9361 (t) cc_final: 0.9129 (m) REVERT: K 100 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8319 (pm20) REVERT: L 3 VAL cc_start: 0.9361 (t) cc_final: 0.9131 (m) REVERT: L 100 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8367 (pm20) outliers start: 80 outliers final: 24 residues processed: 284 average time/residue: 0.6147 time to fit residues: 194.7221 Evaluate side-chains 264 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 19 LYS Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 100 GLN Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 100 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 168 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 204 optimal weight: 0.4980 chunk 227 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 87 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 55 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 ASN A 435 ASN B 401 ASN B 435 ASN C 401 ASN C 435 ASN D 401 ASN D 435 ASN E 3 GLN F 3 GLN G 3 GLN H 3 GLN I 100 GLN J 100 GLN K 100 GLN L 100 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.094143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.074491 restraints weight = 35225.040| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.53 r_work: 0.2862 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20116 Z= 0.123 Angle : 0.582 9.654 27408 Z= 0.302 Chirality : 0.045 0.149 2960 Planarity : 0.004 0.036 3512 Dihedral : 5.532 50.142 3144 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 3.17 % Allowed : 13.06 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.17), residues: 2476 helix: -1.12 (0.64), residues: 24 sheet: 0.23 (0.16), residues: 1032 loop : -0.20 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 38 TYR 0.015 0.001 TYR C 252 PHE 0.013 0.001 PHE D 410 TRP 0.017 0.001 TRP C 178 HIS 0.004 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (20056) covalent geometry : angle 0.57830 / 0.30 (27268) SS BOND : bond 0.00224 / 0.14 ( 40) SS BOND : angle 0.63852 / 0.42 ( 80) hydrogen bonds : bond 0.03376 / 2.28 ( 664) hydrogen bonds : angle 6.10247 / 4.29 ( 1872) link_BETA1-4 : bond 0.00362 / 0.18 ( 4) link_BETA1-4 : angle 1.19381 / 0.64 ( 12) link_BETA1-6 : bond 0.00237 / 0.11 ( 4) link_BETA1-6 : angle 1.30994 / 0.72 ( 12) link_NAG-ASN : bond 0.00234 / 0.16 ( 12) link_NAG-ASN : angle 1.64069 / 0.98 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 236 time to evaluate : 0.603 Fit side-chains REVERT: A 402 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8372 (mm-30) REVERT: B 402 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8373 (mm-30) REVERT: C 402 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8367 (mm-30) REVERT: D 402 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8366 (mm-30) REVERT: E 71 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8600 (ptm-80) REVERT: E 72 ASP cc_start: 0.8378 (t0) cc_final: 0.7974 (t0) REVERT: F 71 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8601 (ptm-80) REVERT: F 72 ASP cc_start: 0.8377 (t0) cc_final: 0.7974 (t0) REVERT: G 71 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8606 (ptm-80) REVERT: G 72 ASP cc_start: 0.8370 (t0) cc_final: 0.7966 (t0) REVERT: H 71 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8604 (ptm-80) REVERT: H 72 ASP cc_start: 0.8366 (t0) cc_final: 0.7963 (t0) REVERT: I 3 VAL cc_start: 0.9367 (t) cc_final: 0.9153 (m) REVERT: I 27 GLN cc_start: 0.8787 (pt0) cc_final: 0.8549 (pm20) REVERT: I 100 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8394 (pm20) REVERT: J 3 VAL cc_start: 0.9366 (t) cc_final: 0.9151 (m) REVERT: J 27 GLN cc_start: 0.8796 (pt0) cc_final: 0.8557 (pm20) REVERT: J 100 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8331 (pm20) REVERT: K 3 VAL cc_start: 0.9368 (t) cc_final: 0.9153 (m) REVERT: K 27 GLN cc_start: 0.8801 (pt0) cc_final: 0.8561 (pm20) REVERT: K 100 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8326 (pm20) REVERT: L 3 VAL cc_start: 0.9365 (t) cc_final: 0.9150 (m) REVERT: L 27 GLN cc_start: 0.8786 (pt0) cc_final: 0.8546 (pm20) REVERT: L 100 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8398 (pm20) outliers start: 68 outliers final: 16 residues processed: 276 average time/residue: 0.6025 time to fit residues: 186.0730 Evaluate side-chains 248 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 100 GLN Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 100 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 112 optimal weight: 2.9990 chunk 228 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 210 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 93 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 ASN A 435 ASN B 401 ASN B 435 ASN C 401 ASN C 435 ASN D 401 ASN D 435 ASN E 3 GLN F 3 GLN G 3 GLN H 3 GLN I 100 GLN J 100 GLN K 100 GLN L 100 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.094070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.074457 restraints weight = 35224.137| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.52 r_work: 0.2860 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20116 Z= 0.143 Angle : 0.586 9.861 27408 Z= 0.302 Chirality : 0.045 0.152 2960 Planarity : 0.004 0.037 3512 Dihedral : 5.380 46.930 3144 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.33 % Allowed : 14.09 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.17), residues: 2476 helix: -1.05 (0.66), residues: 24 sheet: 0.14 (0.16), residues: 1028 loop : -0.08 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 96 TYR 0.015 0.001 TYR C 252 PHE 0.013 0.002 PHE C 410 TRP 0.015 0.001 TRP D 178 HIS 0.004 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (20056) covalent geometry : angle 0.58154 / 0.30 (27268) SS BOND : bond 0.00207 / 0.13 ( 40) SS BOND : angle 0.72993 / 0.47 ( 80) hydrogen bonds : bond 0.03361 / 2.28 ( 664) hydrogen bonds : angle 6.01447 / 4.23 ( 1872) link_BETA1-4 : bond 0.00408 / 0.19 ( 4) link_BETA1-4 : angle 1.15502 / 0.62 ( 12) link_BETA1-6 : bond 0.00255 / 0.12 ( 4) link_BETA1-6 : angle 1.30585 / 0.72 ( 12) link_NAG-ASN : bond 0.00247 / 0.17 ( 12) link_NAG-ASN : angle 1.62881 / 0.97 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 234 time to evaluate : 0.679 Fit side-chains REVERT: E 46 GLU cc_start: 0.8430 (tt0) cc_final: 0.8131 (pt0) REVERT: E 71 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8693 (ptm-80) REVERT: E 72 ASP cc_start: 0.8447 (t0) cc_final: 0.8050 (t0) REVERT: E 83 ARG cc_start: 0.8353 (mpt-90) cc_final: 0.8012 (mpt-90) REVERT: F 46 GLU cc_start: 0.8438 (tt0) cc_final: 0.8143 (pt0) REVERT: F 71 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8693 (ptm-80) REVERT: F 72 ASP cc_start: 0.8441 (t0) cc_final: 0.8043 (t0) REVERT: F 83 ARG cc_start: 0.8362 (mpt-90) cc_final: 0.8020 (mpt-90) REVERT: G 46 GLU cc_start: 0.8438 (tt0) cc_final: 0.8139 (pt0) REVERT: G 71 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8698 (ptm-80) REVERT: G 72 ASP cc_start: 0.8438 (t0) cc_final: 0.8041 (t0) REVERT: G 83 ARG cc_start: 0.8368 (mpt-90) cc_final: 0.8027 (mpt-90) REVERT: H 46 GLU cc_start: 0.8429 (tt0) cc_final: 0.8128 (pt0) REVERT: H 71 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8700 (ptm-80) REVERT: H 72 ASP cc_start: 0.8440 (t0) cc_final: 0.8043 (t0) REVERT: H 83 ARG cc_start: 0.8354 (mpt-90) cc_final: 0.8013 (mpt-90) REVERT: I 3 VAL cc_start: 0.9381 (t) cc_final: 0.9164 (m) REVERT: I 27 GLN cc_start: 0.8815 (pt0) cc_final: 0.8607 (pm20) REVERT: I 100 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8498 (pm20) REVERT: J 3 VAL cc_start: 0.9378 (t) cc_final: 0.9161 (m) REVERT: J 27 GLN cc_start: 0.8812 (pt0) cc_final: 0.8606 (pm20) REVERT: J 100 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8290 (pm20) REVERT: K 3 VAL cc_start: 0.9380 (t) cc_final: 0.9161 (m) REVERT: K 27 GLN cc_start: 0.8813 (pt0) cc_final: 0.8605 (pm20) REVERT: K 100 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8281 (pm20) REVERT: L 3 VAL cc_start: 0.9378 (t) cc_final: 0.9161 (m) REVERT: L 27 GLN cc_start: 0.8812 (pt0) cc_final: 0.8603 (pm20) REVERT: L 100 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8502 (pm20) outliers start: 50 outliers final: 22 residues processed: 256 average time/residue: 0.6347 time to fit residues: 181.1564 Evaluate side-chains 248 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 435 ASN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 435 ASN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 100 GLN Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 100 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 183 optimal weight: 0.4980 chunk 123 optimal weight: 0.2980 chunk 227 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 ASN B 401 ASN C 401 ASN D 401 ASN E 3 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN G 3 GLN H 3 GLN 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 = 0.094631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.074978 restraints weight = 35478.120| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.56 r_work: 0.2866 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20116 Z= 0.135 Angle : 0.583 9.614 27408 Z= 0.300 Chirality : 0.045 0.149 2960 Planarity : 0.004 0.037 3512 Dihedral : 5.229 42.649 3144 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.05 % Allowed : 14.65 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.17), residues: 2476 helix: -1.03 (0.66), residues: 24 sheet: 0.11 (0.16), residues: 1004 loop : 0.00 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 96 TYR 0.014 0.001 TYR D 252 PHE 0.013 0.001 PHE C 410 TRP 0.015 0.001 TRP D 178 HIS 0.004 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (20056) covalent geometry : angle 0.57933 / 0.30 (27268) SS BOND : bond 0.00190 / 0.12 ( 40) SS BOND : angle 0.55946 / 0.36 ( 80) hydrogen bonds : bond 0.03311 / 2.23 ( 664) hydrogen bonds : angle 5.94190 / 4.18 ( 1872) link_BETA1-4 : bond 0.00384 / 0.18 ( 4) link_BETA1-4 : angle 1.13452 / 0.61 ( 12) link_BETA1-6 : bond 0.00249 / 0.12 ( 4) link_BETA1-6 : angle 1.28917 / 0.71 ( 12) link_NAG-ASN : bond 0.00235 / 0.16 ( 12) link_NAG-ASN : angle 1.60009 / 0.95 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 230 time to evaluate : 0.575 Fit side-chains REVERT: E 46 GLU cc_start: 0.8429 (tt0) cc_final: 0.8123 (pt0) REVERT: E 72 ASP cc_start: 0.8426 (t0) cc_final: 0.8029 (t0) REVERT: E 83 ARG cc_start: 0.8329 (mpt-90) cc_final: 0.7969 (mpt-90) REVERT: F 46 GLU cc_start: 0.8432 (tt0) cc_final: 0.8131 (pt0) REVERT: F 72 ASP cc_start: 0.8421 (t0) cc_final: 0.8023 (t0) REVERT: F 83 ARG cc_start: 0.8330 (mpt-90) cc_final: 0.7969 (mpt-90) REVERT: G 46 GLU cc_start: 0.8427 (tt0) cc_final: 0.8123 (pt0) REVERT: G 72 ASP cc_start: 0.8414 (t0) cc_final: 0.8017 (t0) REVERT: G 83 ARG cc_start: 0.8334 (mpt-90) cc_final: 0.7975 (mpt-90) REVERT: H 46 GLU cc_start: 0.8424 (tt0) cc_final: 0.8121 (pt0) REVERT: H 72 ASP cc_start: 0.8415 (t0) cc_final: 0.8020 (t0) REVERT: H 83 ARG cc_start: 0.8328 (mpt-90) cc_final: 0.7968 (mpt-90) REVERT: I 3 VAL cc_start: 0.9398 (t) cc_final: 0.9169 (m) REVERT: I 27 GLN cc_start: 0.8818 (pt0) cc_final: 0.8611 (pm20) REVERT: I 100 GLN cc_start: 0.9053 (pt0) cc_final: 0.8646 (pm20) REVERT: J 3 VAL cc_start: 0.9395 (t) cc_final: 0.9167 (m) REVERT: J 27 GLN cc_start: 0.8813 (pt0) cc_final: 0.8605 (pm20) REVERT: K 3 VAL cc_start: 0.9396 (t) cc_final: 0.9166 (m) REVERT: K 27 GLN cc_start: 0.8815 (pt0) cc_final: 0.8605 (pm20) REVERT: L 3 VAL cc_start: 0.9396 (t) cc_final: 0.9166 (m) REVERT: L 27 GLN cc_start: 0.8812 (pt0) cc_final: 0.8602 (pm20) REVERT: L 100 GLN cc_start: 0.9058 (pt0) cc_final: 0.8653 (pm20) outliers start: 44 outliers final: 24 residues processed: 254 average time/residue: 0.6123 time to fit residues: 173.7564 Evaluate side-chains 250 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 93 optimal weight: 0.5980 chunk 142 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 195 optimal weight: 7.9990 chunk 37 optimal weight: 0.1980 chunk 73 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 180 optimal weight: 0.4980 chunk 148 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 ASN A 435 ASN B 401 ASN B 435 ASN C 401 ASN D 401 ASN D 435 ASN E 3 GLN F 3 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN H 3 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.095507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.075849 restraints weight = 35196.944| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.56 r_work: 0.2881 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20116 Z= 0.117 Angle : 0.578 9.023 27408 Z= 0.297 Chirality : 0.045 0.145 2960 Planarity : 0.004 0.037 3512 Dihedral : 4.738 20.967 3128 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.47 % Allowed : 14.13 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.17), residues: 2476 helix: -1.01 (0.68), residues: 24 sheet: 0.14 (0.16), residues: 1004 loop : 0.04 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 24 TYR 0.013 0.001 TYR D 252 PHE 0.012 0.001 PHE D 410 TRP 0.015 0.001 TRP D 178 HIS 0.004 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (20056) covalent geometry : angle 0.57392 / 0.30 (27268) SS BOND : bond 0.00247 / 0.16 ( 40) SS BOND : angle 0.84506 / 0.55 ( 80) hydrogen bonds : bond 0.03237 / 2.17 ( 664) hydrogen bonds : angle 5.86948 / 4.12 ( 1872) link_BETA1-4 : bond 0.00420 / 0.20 ( 4) link_BETA1-4 : angle 1.11698 / 0.60 ( 12) link_BETA1-6 : bond 0.00236 / 0.11 ( 4) link_BETA1-6 : angle 1.27505 / 0.70 ( 12) link_NAG-ASN : bond 0.00218 / 0.15 ( 12) link_NAG-ASN : angle 1.54334 / 0.92 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 238 time to evaluate : 0.819 Fit side-chains REVERT: E 19 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8425 (tptm) REVERT: E 46 GLU cc_start: 0.8392 (tt0) cc_final: 0.8102 (pt0) REVERT: E 71 ARG cc_start: 0.9063 (ppt90) cc_final: 0.8617 (ptm-80) REVERT: E 72 ASP cc_start: 0.8355 (t0) cc_final: 0.7978 (t0) REVERT: E 83 ARG cc_start: 0.8243 (mpt-90) cc_final: 0.7875 (mpt-90) REVERT: F 19 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8420 (tptm) REVERT: F 46 GLU cc_start: 0.8393 (tt0) cc_final: 0.8105 (pt0) REVERT: F 71 ARG cc_start: 0.9061 (ppt90) cc_final: 0.8614 (ptm-80) REVERT: F 72 ASP cc_start: 0.8351 (t0) cc_final: 0.7976 (t0) REVERT: F 83 ARG cc_start: 0.8251 (mpt-90) cc_final: 0.7883 (mpt-90) REVERT: G 19 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8425 (tptm) REVERT: G 46 GLU cc_start: 0.8392 (tt0) cc_final: 0.8100 (pt0) REVERT: G 71 ARG cc_start: 0.9063 (ppt90) cc_final: 0.8616 (ptm-80) REVERT: G 72 ASP cc_start: 0.8346 (t0) cc_final: 0.7970 (t0) REVERT: G 83 ARG cc_start: 0.8250 (mpt-90) cc_final: 0.7883 (mpt-90) REVERT: H 19 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8425 (tptm) REVERT: H 46 GLU cc_start: 0.8381 (tt0) cc_final: 0.8089 (pt0) REVERT: H 71 ARG cc_start: 0.9062 (ppt90) cc_final: 0.8614 (ptm-80) REVERT: H 72 ASP cc_start: 0.8345 (t0) cc_final: 0.7970 (t0) REVERT: H 83 ARG cc_start: 0.8251 (mpt-90) cc_final: 0.7885 (mpt-90) REVERT: I 3 VAL cc_start: 0.9398 (t) cc_final: 0.9176 (m) REVERT: I 27 GLN cc_start: 0.8807 (pt0) cc_final: 0.8599 (pm20) REVERT: J 3 VAL cc_start: 0.9395 (t) cc_final: 0.9171 (m) REVERT: J 27 GLN cc_start: 0.8805 (pt0) cc_final: 0.8595 (pm20) REVERT: K 3 VAL cc_start: 0.9395 (t) cc_final: 0.9171 (m) REVERT: K 27 GLN cc_start: 0.8806 (pt0) cc_final: 0.8595 (pm20) REVERT: L 3 VAL cc_start: 0.9396 (t) cc_final: 0.9174 (m) REVERT: L 27 GLN cc_start: 0.8803 (pt0) cc_final: 0.8595 (pm20) outliers start: 53 outliers final: 34 residues processed: 268 average time/residue: 0.6209 time to fit residues: 186.4245 Evaluate side-chains 268 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 230 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 19 LYS Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 89 MET Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 89 MET Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 192 optimal weight: 0.5980 chunk 223 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 226 optimal weight: 0.9980 chunk 37 optimal weight: 0.0970 chunk 119 optimal weight: 0.9990 chunk 103 optimal weight: 0.0970 chunk 190 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 ASN A 435 ASN B 401 ASN B 435 ASN C 401 ASN C 435 ASN D 401 ASN D 435 ASN E 3 GLN F 3 GLN G 3 GLN H 3 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.096022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.076574 restraints weight = 35083.262| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.50 r_work: 0.2898 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20116 Z= 0.114 Angle : 0.584 8.780 27408 Z= 0.300 Chirality : 0.045 0.141 2960 Planarity : 0.004 0.037 3512 Dihedral : 4.666 20.110 3128 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.05 % Allowed : 14.93 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.17), residues: 2476 helix: -0.96 (0.69), residues: 24 sheet: 0.16 (0.16), residues: 1004 loop : 0.08 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 24 TYR 0.013 0.001 TYR D 252 PHE 0.011 0.001 PHE D 410 TRP 0.014 0.001 TRP A 178 HIS 0.003 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (20056) covalent geometry : angle 0.58057 / 0.30 (27268) SS BOND : bond 0.00195 / 0.13 ( 40) SS BOND : angle 0.75394 / 0.49 ( 80) hydrogen bonds : bond 0.03135 / 2.10 ( 664) hydrogen bonds : angle 5.79467 / 4.07 ( 1872) link_BETA1-4 : bond 0.00422 / 0.20 ( 4) link_BETA1-4 : angle 1.10051 / 0.59 ( 12) link_BETA1-6 : bond 0.00300 / 0.14 ( 4) link_BETA1-6 : angle 1.27735 / 0.70 ( 12) link_NAG-ASN : bond 0.00201 / 0.13 ( 12) link_NAG-ASN : angle 1.50389 / 0.89 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 236 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 SER cc_start: 0.9154 (t) cc_final: 0.8925 (m) REVERT: B 445 SER cc_start: 0.9154 (t) cc_final: 0.8924 (m) REVERT: C 445 SER cc_start: 0.9151 (t) cc_final: 0.8924 (m) REVERT: D 445 SER cc_start: 0.9140 (t) cc_final: 0.8916 (m) REVERT: E 46 GLU cc_start: 0.8407 (tt0) cc_final: 0.8120 (pt0) REVERT: E 71 ARG cc_start: 0.9082 (ppt90) cc_final: 0.8683 (ptm-80) REVERT: E 72 ASP cc_start: 0.8408 (t0) cc_final: 0.8029 (t0) REVERT: E 80 MET cc_start: 0.7533 (ttp) cc_final: 0.7144 (ttt) REVERT: E 83 ARG cc_start: 0.8262 (mpt-90) cc_final: 0.8058 (mpt-90) REVERT: F 46 GLU cc_start: 0.8411 (tt0) cc_final: 0.8128 (pt0) REVERT: F 71 ARG cc_start: 0.9077 (ppt90) cc_final: 0.8676 (ptm-80) REVERT: F 72 ASP cc_start: 0.8402 (t0) cc_final: 0.8023 (t0) REVERT: F 80 MET cc_start: 0.7531 (ttp) cc_final: 0.7145 (ttt) REVERT: F 83 ARG cc_start: 0.8270 (mpt-90) cc_final: 0.8067 (mpt-90) REVERT: G 46 GLU cc_start: 0.8400 (tt0) cc_final: 0.8112 (pt0) REVERT: G 71 ARG cc_start: 0.9079 (ppt90) cc_final: 0.8681 (ptm-80) REVERT: G 72 ASP cc_start: 0.8393 (t0) cc_final: 0.8014 (t0) REVERT: G 80 MET cc_start: 0.7550 (ttp) cc_final: 0.7157 (ttt) REVERT: G 83 ARG cc_start: 0.8280 (mpt-90) cc_final: 0.8076 (mpt-90) REVERT: H 46 GLU cc_start: 0.8402 (tt0) cc_final: 0.8113 (pt0) REVERT: H 71 ARG cc_start: 0.9078 (ppt90) cc_final: 0.8677 (ptm-80) REVERT: H 72 ASP cc_start: 0.8389 (t0) cc_final: 0.8010 (t0) REVERT: H 80 MET cc_start: 0.7554 (ttp) cc_final: 0.7160 (ttt) REVERT: H 83 ARG cc_start: 0.8270 (mpt-90) cc_final: 0.8065 (mpt-90) REVERT: I 3 VAL cc_start: 0.9431 (t) cc_final: 0.9200 (m) REVERT: I 27 GLN cc_start: 0.8817 (pt0) cc_final: 0.8567 (pm20) REVERT: J 3 VAL cc_start: 0.9428 (t) cc_final: 0.9200 (m) REVERT: J 27 GLN cc_start: 0.8815 (pt0) cc_final: 0.8565 (pm20) REVERT: K 3 VAL cc_start: 0.9428 (t) cc_final: 0.9196 (m) REVERT: K 27 GLN cc_start: 0.8814 (pt0) cc_final: 0.8561 (pm20) REVERT: L 3 VAL cc_start: 0.9428 (t) cc_final: 0.9198 (m) REVERT: L 27 GLN cc_start: 0.8817 (pt0) cc_final: 0.8567 (pm20) outliers start: 44 outliers final: 24 residues processed: 260 average time/residue: 0.6061 time to fit residues: 176.4031 Evaluate side-chains 256 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 232 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 435 ASN Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 435 ASN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 25 optimal weight: 0.0370 chunk 134 optimal weight: 0.2980 chunk 243 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 240 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 ASN B 401 ASN C 401 ASN D 401 ASN E 3 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN G 3 GLN H 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.095867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.076129 restraints weight = 35339.017| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.57 r_work: 0.2885 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20116 Z= 0.130 Angle : 0.592 9.158 27408 Z= 0.304 Chirality : 0.045 0.143 2960 Planarity : 0.004 0.037 3512 Dihedral : 4.653 20.100 3128 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.68 % Allowed : 15.49 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.17), residues: 2476 helix: -0.83 (0.73), residues: 24 sheet: 0.17 (0.16), residues: 1004 loop : 0.10 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 24 TYR 0.014 0.001 TYR C 252 PHE 0.012 0.001 PHE D 410 TRP 0.013 0.001 TRP C 178 HIS 0.004 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (20056) covalent geometry : angle 0.58873 / 0.30 (27268) SS BOND : bond 0.00200 / 0.13 ( 40) SS BOND : angle 0.72891 / 0.47 ( 80) hydrogen bonds : bond 0.03198 / 2.13 ( 664) hydrogen bonds : angle 5.78500 / 4.07 ( 1872) link_BETA1-4 : bond 0.00519 / 0.24 ( 4) link_BETA1-4 : angle 1.11617 / 0.59 ( 12) link_BETA1-6 : bond 0.00311 / 0.15 ( 4) link_BETA1-6 : angle 1.30292 / 0.72 ( 12) link_NAG-ASN : bond 0.00211 / 0.14 ( 12) link_NAG-ASN : angle 1.52593 / 0.90 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 0.691 Fit side-chains REVERT: A 445 SER cc_start: 0.9149 (t) cc_final: 0.8912 (m) REVERT: B 445 SER cc_start: 0.9143 (t) cc_final: 0.8905 (m) REVERT: C 445 SER cc_start: 0.9144 (t) cc_final: 0.8906 (m) REVERT: D 445 SER cc_start: 0.9134 (t) cc_final: 0.8900 (m) REVERT: E 46 GLU cc_start: 0.8364 (tt0) cc_final: 0.8078 (pt0) REVERT: E 71 ARG cc_start: 0.9062 (ppt90) cc_final: 0.8662 (ptm-80) REVERT: E 72 ASP cc_start: 0.8325 (t0) cc_final: 0.7952 (t0) REVERT: E 83 ARG cc_start: 0.8211 (mpt-90) cc_final: 0.7997 (mpt-90) REVERT: F 46 GLU cc_start: 0.8368 (tt0) cc_final: 0.8089 (pt0) REVERT: F 71 ARG cc_start: 0.9059 (ppt90) cc_final: 0.8654 (ptm-80) REVERT: F 72 ASP cc_start: 0.8320 (t0) cc_final: 0.7946 (t0) REVERT: F 83 ARG cc_start: 0.8218 (mpt-90) cc_final: 0.8004 (mpt-90) REVERT: G 46 GLU cc_start: 0.8358 (tt0) cc_final: 0.8070 (pt0) REVERT: G 71 ARG cc_start: 0.9060 (ppt90) cc_final: 0.8656 (ptm-80) REVERT: G 72 ASP cc_start: 0.8313 (t0) cc_final: 0.7939 (t0) REVERT: G 83 ARG cc_start: 0.8220 (mpt-90) cc_final: 0.8006 (mpt-90) REVERT: H 46 GLU cc_start: 0.8361 (tt0) cc_final: 0.8077 (pt0) REVERT: H 71 ARG cc_start: 0.9058 (ppt90) cc_final: 0.8654 (ptm-80) REVERT: H 72 ASP cc_start: 0.8315 (t0) cc_final: 0.7941 (t0) REVERT: H 83 ARG cc_start: 0.8214 (mpt-90) cc_final: 0.7999 (mpt-90) REVERT: I 3 VAL cc_start: 0.9418 (t) cc_final: 0.9181 (m) REVERT: I 27 GLN cc_start: 0.8809 (pt0) cc_final: 0.8596 (pm20) REVERT: J 3 VAL cc_start: 0.9416 (t) cc_final: 0.9182 (m) REVERT: J 27 GLN cc_start: 0.8809 (pt0) cc_final: 0.8595 (pm20) REVERT: K 3 VAL cc_start: 0.9417 (t) cc_final: 0.9179 (m) REVERT: K 27 GLN cc_start: 0.8808 (pt0) cc_final: 0.8592 (pm20) REVERT: L 3 VAL cc_start: 0.9417 (t) cc_final: 0.9181 (m) REVERT: L 27 GLN cc_start: 0.8808 (pt0) cc_final: 0.8595 (pm20) outliers start: 36 outliers final: 24 residues processed: 246 average time/residue: 0.6722 time to fit residues: 184.7688 Evaluate side-chains 254 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 230 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 142 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 147 optimal weight: 0.7980 chunk 170 optimal weight: 0.2980 chunk 165 optimal weight: 0.4980 chunk 208 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 ASN B 401 ASN C 401 ASN D 401 ASN E 3 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN H 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.095189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.075067 restraints weight = 33916.677| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.52 r_work: 0.2897 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20116 Z= 0.133 Angle : 0.606 11.332 27408 Z= 0.310 Chirality : 0.045 0.144 2960 Planarity : 0.004 0.037 3512 Dihedral : 4.647 20.036 3128 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.45 % Allowed : 15.67 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.17), residues: 2476 helix: -0.79 (0.73), residues: 24 sheet: 0.10 (0.16), residues: 1004 loop : 0.10 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 24 TYR 0.013 0.001 TYR D 252 PHE 0.012 0.001 PHE C 410 TRP 0.012 0.001 TRP D 178 HIS 0.004 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 (20056) covalent geometry : angle 0.60307 / 0.31 (27268) SS BOND : bond 0.00194 / 0.12 ( 40) SS BOND : angle 0.74412 / 0.48 ( 80) hydrogen bonds : bond 0.03200 / 2.15 ( 664) hydrogen bonds : angle 5.75404 / 4.05 ( 1872) link_BETA1-4 : bond 0.00351 / 0.17 ( 4) link_BETA1-4 : angle 1.07220 / 0.57 ( 12) link_BETA1-6 : bond 0.00272 / 0.13 ( 4) link_BETA1-6 : angle 1.28377 / 0.70 ( 12) link_NAG-ASN : bond 0.00218 / 0.15 ( 12) link_NAG-ASN : angle 1.53041 / 0.91 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6275.21 seconds wall clock time: 107 minutes 53.92 seconds (6473.92 seconds total)