Starting phenix.real_space_refine on Thu Feb 5 20:36:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o4q_70111/02_2026/9o4q_70111.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o4q_70111/02_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_70111/02_2026/9o4q_70111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o4q_70111/02_2026/9o4q_70111.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o4q_70111/02_2026/9o4q_70111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o4q_70111/02_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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, 31 Unusual residues: {' CA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.86, per 1000 atoms: 0.25 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: 1.89 Conformation dependent library (CDL) restraints added in 864.3 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: 0.87 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: 4.08 Time building geometry restraints manager: 2.51 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 2.510 nonbonded pdb=" O GLY C 345 " pdb="CA CA C 503 " model vdw 2.181 2.510 nonbonded pdb=" O GLY A 345 " pdb="CA CA A 503 " model vdw 2.181 2.510 nonbonded pdb=" O GLY D 345 " pdb="CA CA D 503 " model vdw 2.181 2.510 nonbonded pdb=" OD2 ASP C 324 " pdb="CA CA C 503 " model vdw 2.188 2.510 ... (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: 11.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.500 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 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 covalent geometry : bond 0.00534 (20056) covalent geometry : angle 0.85462 (27268) SS BOND : bond 0.00298 ( 40) SS BOND : angle 1.72102 ( 80) hydrogen bonds : bond 0.13008 ( 664) hydrogen bonds : angle 8.86519 ( 1872) link_BETA1-4 : bond 0.00596 ( 4) link_BETA1-4 : angle 0.90577 ( 12) link_BETA1-6 : bond 0.00350 ( 4) link_BETA1-6 : angle 1.14530 ( 12) link_NAG-ASN : bond 0.00280 ( 12) link_NAG-ASN : angle 2.55058 ( 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 : 0.851 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: 0.7156 time to fit residues: 302.0519 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 : 0.816 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3257 r_free = 0.3257 target = 0.089324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.069431 restraints weight = 35825.254| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.55 r_work: 0.2761 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.067 20116 Z= 0.371 Angle : 0.754 13.524 27408 Z= 0.392 Chirality : 0.053 0.171 2960 Planarity : 0.006 0.041 3512 Dihedral : 6.968 55.487 3160 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.36 % Allowed : 10.45 % Favored : 86.19 % 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: -0.30 (0.17), residues: 2476 helix: -1.11 (0.55), residues: 24 sheet: 0.30 (0.17), residues: 972 loop : -0.49 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 61 TYR 0.029 0.002 TYR B 252 PHE 0.021 0.003 PHE B 410 TRP 0.023 0.003 TRP C 178 HIS 0.010 0.003 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00882 (20056) covalent geometry : angle 0.74922 (27268) SS BOND : bond 0.00376 ( 40) SS BOND : angle 0.90326 ( 80) hydrogen bonds : bond 0.04864 ( 664) hydrogen bonds : angle 6.86102 ( 1872) link_BETA1-4 : bond 0.00409 ( 4) link_BETA1-4 : angle 1.44952 ( 12) link_BETA1-6 : bond 0.00004 ( 4) link_BETA1-6 : angle 1.50056 ( 12) link_NAG-ASN : bond 0.00493 ( 12) link_NAG-ASN : angle 2.14389 ( 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 312 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 240 time to evaluate : 1.076 Fit side-chains REVERT: A 402 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8492 (mm-30) REVERT: B 402 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8496 (mm-30) REVERT: C 402 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8482 (mm-30) REVERT: D 402 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8498 (mm-30) REVERT: E 13 LYS cc_start: 0.9017 (mmmt) cc_final: 0.8805 (mmmt) REVERT: E 71 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8574 (ptm-80) REVERT: E 72 ASP cc_start: 0.8458 (t0) cc_final: 0.8079 (t0) REVERT: E 83 ARG cc_start: 0.8271 (ptp90) cc_final: 0.7877 (ptp90) REVERT: F 13 LYS cc_start: 0.9017 (mmmt) cc_final: 0.8804 (mmmt) REVERT: F 71 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8569 (ptm-80) REVERT: F 72 ASP cc_start: 0.8460 (t0) cc_final: 0.8082 (t0) REVERT: F 83 ARG cc_start: 0.8272 (ptp90) cc_final: 0.7879 (ptp90) REVERT: G 13 LYS cc_start: 0.9018 (mmmt) cc_final: 0.8807 (mmmt) REVERT: G 71 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8571 (ptm-80) REVERT: G 72 ASP cc_start: 0.8461 (t0) cc_final: 0.8084 (t0) REVERT: G 83 ARG cc_start: 0.8281 (ptp90) cc_final: 0.7887 (ptp90) REVERT: H 13 LYS cc_start: 0.9020 (mmmt) cc_final: 0.8808 (mmmt) REVERT: H 71 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8577 (ptm-80) REVERT: H 72 ASP cc_start: 0.8458 (t0) cc_final: 0.8080 (t0) REVERT: H 83 ARG cc_start: 0.8279 (ptp90) cc_final: 0.7884 (ptp90) REVERT: I 100 GLN cc_start: 0.9001 (pt0) cc_final: 0.8470 (pm20) REVERT: J 100 GLN cc_start: 0.8997 (pt0) cc_final: 0.8463 (pm20) REVERT: K 100 GLN cc_start: 0.8996 (pt0) cc_final: 0.8461 (pm20) REVERT: L 100 GLN cc_start: 0.9002 (pt0) cc_final: 0.8473 (pm20) outliers start: 72 outliers final: 24 residues processed: 276 average time/residue: 0.7723 time to fit residues: 235.6606 Evaluate side-chains 256 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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: 1.9990 chunk 118 optimal weight: 0.9990 chunk 223 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 208 optimal weight: 9.9990 chunk 110 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412AHIS A 435 ASN ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412AHIS C 412AHIS C 435 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412AHIS 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 J 100 GLN K 100 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.092978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.073206 restraints weight = 35416.721| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.54 r_work: 0.2832 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20116 Z= 0.147 Angle : 0.606 9.802 27408 Z= 0.316 Chirality : 0.046 0.152 2960 Planarity : 0.004 0.036 3512 Dihedral : 5.926 52.729 3144 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.26 % Allowed : 10.31 % Favored : 86.43 % 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: -0.16 (0.17), residues: 2476 helix: -1.27 (0.55), residues: 24 sheet: 0.25 (0.17), residues: 1000 loop : -0.28 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 24 TYR 0.018 0.001 TYR C 252 PHE 0.015 0.002 PHE B 410 TRP 0.019 0.001 TRP C 178 HIS 0.005 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00341 (20056) covalent geometry : angle 0.60247 (27268) SS BOND : bond 0.00310 ( 40) SS BOND : angle 0.54054 ( 80) hydrogen bonds : bond 0.03745 ( 664) hydrogen bonds : angle 6.44203 ( 1872) link_BETA1-4 : bond 0.00470 ( 4) link_BETA1-4 : angle 1.25615 ( 12) link_BETA1-6 : bond 0.00213 ( 4) link_BETA1-6 : angle 1.32160 ( 12) link_NAG-ASN : bond 0.00281 ( 12) link_NAG-ASN : angle 1.78549 ( 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 338 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 268 time to evaluate : 0.890 Fit side-chains REVERT: A 402 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8466 (mm-30) REVERT: B 402 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8464 (mm-30) REVERT: C 402 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8450 (mm-30) REVERT: D 402 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8457 (mm-30) REVERT: E 13 LYS cc_start: 0.9014 (mmmt) cc_final: 0.8771 (mmmm) REVERT: E 19 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8751 (tptm) REVERT: E 71 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8513 (ptm-80) REVERT: E 72 ASP cc_start: 0.8366 (t0) cc_final: 0.7962 (OUTLIER) REVERT: F 13 LYS cc_start: 0.9012 (mmmt) cc_final: 0.8769 (mmmm) REVERT: F 19 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8749 (tptm) REVERT: F 71 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8504 (ptm-80) REVERT: F 72 ASP cc_start: 0.8363 (t0) cc_final: 0.7958 (OUTLIER) REVERT: G 13 LYS cc_start: 0.9016 (mmmt) cc_final: 0.8771 (mmmm) REVERT: G 19 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8752 (tptm) REVERT: G 71 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8505 (ptm-80) REVERT: G 72 ASP cc_start: 0.8354 (t0) cc_final: 0.7950 (OUTLIER) REVERT: H 13 LYS cc_start: 0.9015 (mmmt) cc_final: 0.8770 (mmmm) REVERT: H 19 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8747 (tptm) REVERT: H 71 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8513 (ptm-80) REVERT: H 72 ASP cc_start: 0.8368 (t0) cc_final: 0.7964 (OUTLIER) REVERT: I 3 VAL cc_start: 0.9339 (t) cc_final: 0.9114 (m) REVERT: I 100 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8461 (pm20) REVERT: J 3 VAL cc_start: 0.9342 (t) cc_final: 0.9114 (m) REVERT: J 100 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8469 (pm20) REVERT: K 3 VAL cc_start: 0.9343 (t) cc_final: 0.9116 (m) REVERT: K 100 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8468 (pm20) REVERT: L 3 VAL cc_start: 0.9336 (t) cc_final: 0.9111 (m) REVERT: L 100 GLN cc_start: 0.8919 (pt0) cc_final: 0.8434 (pm20) outliers start: 70 outliers final: 12 residues processed: 304 average time/residue: 0.8166 time to fit residues: 274.3141 Evaluate side-chains 251 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 232 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 148 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 201 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 241 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 J 100 GLN K 100 GLN L 100 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.092239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.072898 restraints weight = 35840.795| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.52 r_work: 0.2826 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20116 Z= 0.184 Angle : 0.604 10.888 27408 Z= 0.312 Chirality : 0.047 0.159 2960 Planarity : 0.004 0.040 3512 Dihedral : 5.694 51.768 3144 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.92 % Allowed : 13.25 % 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: -0.19 (0.17), residues: 2476 helix: -1.12 (0.60), residues: 24 sheet: 0.17 (0.16), residues: 1008 loop : -0.24 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 61 TYR 0.018 0.001 TYR C 252 PHE 0.016 0.002 PHE D 410 TRP 0.016 0.001 TRP B 178 HIS 0.005 0.001 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00436 (20056) covalent geometry : angle 0.59965 (27268) SS BOND : bond 0.00266 ( 40) SS BOND : angle 0.59611 ( 80) hydrogen bonds : bond 0.03614 ( 664) hydrogen bonds : angle 6.21715 ( 1872) link_BETA1-4 : bond 0.00450 ( 4) link_BETA1-4 : angle 1.22854 ( 12) link_BETA1-6 : bond 0.00180 ( 4) link_BETA1-6 : angle 1.31601 ( 12) link_NAG-ASN : bond 0.00286 ( 12) link_NAG-ASN : angle 1.76406 ( 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: 84 poor density : 236 time to evaluate : 0.878 Fit side-chains REVERT: A 402 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8512 (mm-30) REVERT: B 402 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8507 (mm-30) REVERT: C 402 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8498 (mm-30) REVERT: D 402 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8503 (mm-30) REVERT: E 13 LYS cc_start: 0.9022 (mmmt) cc_final: 0.8813 (mmmt) REVERT: E 19 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8630 (tptt) REVERT: E 71 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.8546 (ptm-80) REVERT: E 72 ASP cc_start: 0.8391 (t0) cc_final: 0.7991 (t0) REVERT: F 13 LYS cc_start: 0.9021 (mmmt) cc_final: 0.8812 (mmmt) REVERT: F 19 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8627 (tptt) REVERT: F 71 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8536 (ptm-80) REVERT: F 72 ASP cc_start: 0.8390 (t0) cc_final: 0.7990 (t0) REVERT: G 13 LYS cc_start: 0.9019 (mmmt) cc_final: 0.8809 (mmmt) REVERT: G 19 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8630 (tptt) REVERT: G 71 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8538 (ptm-80) REVERT: G 72 ASP cc_start: 0.8384 (t0) cc_final: 0.7984 (t0) REVERT: H 13 LYS cc_start: 0.9020 (mmmt) cc_final: 0.8811 (mmmt) REVERT: H 19 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8626 (tptt) REVERT: H 71 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8547 (ptm-80) REVERT: H 72 ASP cc_start: 0.8386 (t0) cc_final: 0.7989 (t0) REVERT: I 3 VAL cc_start: 0.9358 (t) cc_final: 0.9124 (m) REVERT: I 100 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8376 (pm20) REVERT: J 3 VAL cc_start: 0.9356 (t) cc_final: 0.9123 (m) REVERT: J 100 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8375 (pm20) REVERT: K 3 VAL cc_start: 0.9359 (t) cc_final: 0.9124 (m) REVERT: K 100 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8384 (pm20) REVERT: L 3 VAL cc_start: 0.9356 (t) cc_final: 0.9122 (m) REVERT: L 100 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8406 (pm20) outliers start: 84 outliers final: 20 residues processed: 288 average time/residue: 0.7525 time to fit residues: 241.1259 Evaluate side-chains 260 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 19 LYS Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 105 GLN 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 19 LYS Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 105 GLN 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 168 optimal weight: 0.4980 chunk 123 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 204 optimal weight: 0.4980 chunk 227 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.093489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.073924 restraints weight = 35179.821| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.52 r_work: 0.2851 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2344 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= 0.130 Angle : 0.579 9.484 27408 Z= 0.300 Chirality : 0.045 0.148 2960 Planarity : 0.004 0.036 3512 Dihedral : 5.449 49.579 3144 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.99 % Allowed : 14.18 % 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: -0.14 (0.17), residues: 2476 helix: -1.11 (0.65), residues: 24 sheet: 0.17 (0.16), residues: 1008 loop : -0.19 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 24 TYR 0.015 0.001 TYR C 252 PHE 0.013 0.002 PHE C 410 TRP 0.016 0.001 TRP B 178 HIS 0.004 0.001 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00306 (20056) covalent geometry : angle 0.57498 (27268) SS BOND : bond 0.00151 ( 40) SS BOND : angle 0.66631 ( 80) hydrogen bonds : bond 0.03366 ( 664) hydrogen bonds : angle 6.04829 ( 1872) link_BETA1-4 : bond 0.00383 ( 4) link_BETA1-4 : angle 1.18569 ( 12) link_BETA1-6 : bond 0.00234 ( 4) link_BETA1-6 : angle 1.30989 ( 12) link_NAG-ASN : bond 0.00236 ( 12) link_NAG-ASN : angle 1.64097 ( 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 303 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 239 time to evaluate : 0.846 Fit side-chains REVERT: A 402 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8433 (mm-30) REVERT: B 402 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8425 (mm-30) REVERT: C 402 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8423 (mm-30) REVERT: D 402 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8425 (mm-30) REVERT: E 13 LYS cc_start: 0.9020 (mmmt) cc_final: 0.8737 (mmmm) REVERT: E 71 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8607 (ptm-80) REVERT: E 72 ASP cc_start: 0.8365 (t0) cc_final: 0.7966 (t0) REVERT: F 13 LYS cc_start: 0.9017 (mmmt) cc_final: 0.8732 (mmmm) REVERT: F 71 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8603 (ptm-80) REVERT: F 72 ASP cc_start: 0.8361 (t0) cc_final: 0.7962 (t0) REVERT: G 13 LYS cc_start: 0.9021 (mmmt) cc_final: 0.8737 (mmmm) REVERT: G 71 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8599 (ptm-80) REVERT: G 72 ASP cc_start: 0.8345 (t0) cc_final: 0.7947 (t0) REVERT: H 13 LYS cc_start: 0.9020 (mmmt) cc_final: 0.8736 (mmmm) REVERT: H 71 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8603 (ptm-80) REVERT: H 72 ASP cc_start: 0.8340 (t0) cc_final: 0.7943 (t0) REVERT: I 3 VAL cc_start: 0.9363 (t) cc_final: 0.9146 (m) REVERT: I 27 GLN cc_start: 0.8807 (pt0) cc_final: 0.8562 (pm20) REVERT: I 100 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8271 (pm20) REVERT: J 3 VAL cc_start: 0.9361 (t) cc_final: 0.9144 (m) REVERT: J 27 GLN cc_start: 0.8805 (pt0) cc_final: 0.8559 (pm20) REVERT: J 100 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8266 (pm20) REVERT: K 3 VAL cc_start: 0.9361 (t) cc_final: 0.9143 (m) REVERT: K 27 GLN cc_start: 0.8806 (pt0) cc_final: 0.8559 (pm20) REVERT: K 100 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8264 (pm20) REVERT: L 3 VAL cc_start: 0.9354 (t) cc_final: 0.9132 (m) REVERT: L 27 GLN cc_start: 0.8802 (pt0) cc_final: 0.8557 (pm20) REVERT: L 100 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8369 (pm20) outliers start: 64 outliers final: 24 residues processed: 275 average time/residue: 0.7105 time to fit residues: 218.3332 Evaluate side-chains 255 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 10 GLU Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 10 GLU 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: 0.9990 chunk 228 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 210 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3313 r_free = 0.3313 target = 0.092945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.073437 restraints weight = 35096.797| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.49 r_work: 0.2841 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20116 Z= 0.156 Angle : 0.582 10.119 27408 Z= 0.301 Chirality : 0.046 0.153 2960 Planarity : 0.004 0.036 3512 Dihedral : 5.324 45.928 3144 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.24 % Allowed : 14.93 % 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: -0.11 (0.17), residues: 2476 helix: -1.01 (0.66), residues: 24 sheet: 0.13 (0.16), residues: 1028 loop : -0.11 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 24 TYR 0.015 0.001 TYR C 252 PHE 0.014 0.002 PHE B 410 TRP 0.014 0.001 TRP C 178 HIS 0.005 0.001 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00368 (20056) covalent geometry : angle 0.57766 (27268) SS BOND : bond 0.00258 ( 40) SS BOND : angle 0.71565 ( 80) hydrogen bonds : bond 0.03377 ( 664) hydrogen bonds : angle 5.99916 ( 1872) link_BETA1-4 : bond 0.00414 ( 4) link_BETA1-4 : angle 1.17140 ( 12) link_BETA1-6 : bond 0.00231 ( 4) link_BETA1-6 : angle 1.30212 ( 12) link_NAG-ASN : bond 0.00254 ( 12) link_NAG-ASN : angle 1.65010 ( 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 273 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 225 time to evaluate : 0.871 Fit side-chains REVERT: A 402 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8469 (mm-30) REVERT: B 402 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8468 (mm-30) REVERT: C 402 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8462 (mm-30) REVERT: D 402 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8461 (mm-30) REVERT: E 13 LYS cc_start: 0.9051 (mmmt) cc_final: 0.8753 (mmmm) REVERT: E 46 GLU cc_start: 0.8457 (tt0) cc_final: 0.8224 (pt0) REVERT: E 71 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8686 (ptm-80) REVERT: E 72 ASP cc_start: 0.8437 (t0) cc_final: 0.8020 (t0) REVERT: F 13 LYS cc_start: 0.9050 (mmmt) cc_final: 0.8751 (mmmm) REVERT: F 46 GLU cc_start: 0.8468 (tt0) cc_final: 0.8236 (pt0) REVERT: F 71 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8682 (ptm-80) REVERT: F 72 ASP cc_start: 0.8435 (t0) cc_final: 0.8018 (t0) REVERT: G 13 LYS cc_start: 0.9049 (mmmt) cc_final: 0.8750 (mmmm) REVERT: G 46 GLU cc_start: 0.8470 (tt0) cc_final: 0.8239 (pt0) REVERT: G 71 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8681 (ptm-80) REVERT: G 72 ASP cc_start: 0.8419 (t0) cc_final: 0.8002 (t0) REVERT: H 13 LYS cc_start: 0.9050 (mmmt) cc_final: 0.8751 (mmmm) REVERT: H 46 GLU cc_start: 0.8459 (tt0) cc_final: 0.8226 (pt0) REVERT: H 71 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8684 (ptm-80) REVERT: H 72 ASP cc_start: 0.8419 (t0) cc_final: 0.8003 (t0) REVERT: I 3 VAL cc_start: 0.9388 (t) cc_final: 0.9163 (m) REVERT: I 27 GLN cc_start: 0.8826 (pt0) cc_final: 0.8621 (pm20) REVERT: I 100 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8478 (pm20) REVERT: J 3 VAL cc_start: 0.9387 (t) cc_final: 0.9161 (m) REVERT: J 27 GLN cc_start: 0.8821 (pt0) cc_final: 0.8617 (pm20) REVERT: J 100 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8476 (pm20) REVERT: K 3 VAL cc_start: 0.9388 (t) cc_final: 0.9161 (m) REVERT: K 27 GLN cc_start: 0.8825 (pt0) cc_final: 0.8617 (pm20) REVERT: K 100 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8475 (pm20) REVERT: L 3 VAL cc_start: 0.9381 (t) cc_final: 0.9151 (m) REVERT: L 27 GLN cc_start: 0.8823 (pt0) cc_final: 0.8615 (pm20) REVERT: L 100 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8370 (pm20) outliers start: 48 outliers final: 32 residues processed: 252 average time/residue: 0.7757 time to fit residues: 217.0239 Evaluate side-chains 262 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 222 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 3 GLN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 51 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 150 optimal weight: 0.0770 chunk 23 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 123 optimal weight: 0.7980 chunk 227 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN B 401 ASN C 401 ASN D 401 ASN E 3 GLN F 3 GLN G 3 GLN H 3 GLN L 100 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.093743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.074248 restraints weight = 35332.504| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.51 r_work: 0.2853 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20116 Z= 0.134 Angle : 0.576 9.666 27408 Z= 0.299 Chirality : 0.045 0.149 2960 Planarity : 0.004 0.036 3512 Dihedral : 5.182 41.285 3144 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.91 % Allowed : 15.25 % 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: -0.05 (0.17), residues: 2476 helix: -1.01 (0.67), residues: 24 sheet: 0.17 (0.16), residues: 1028 loop : -0.07 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 24 TYR 0.014 0.001 TYR D 252 PHE 0.013 0.002 PHE D 410 TRP 0.015 0.001 TRP C 178 HIS 0.004 0.001 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00314 (20056) covalent geometry : angle 0.57240 (27268) SS BOND : bond 0.00187 ( 40) SS BOND : angle 0.56622 ( 80) hydrogen bonds : bond 0.03285 ( 664) hydrogen bonds : angle 5.92066 ( 1872) link_BETA1-4 : bond 0.00327 ( 4) link_BETA1-4 : angle 1.13528 ( 12) link_BETA1-6 : bond 0.00255 ( 4) link_BETA1-6 : angle 1.29369 ( 12) link_NAG-ASN : bond 0.00248 ( 12) link_NAG-ASN : angle 1.59952 ( 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 270 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 229 time to evaluate : 0.814 Fit side-chains REVERT: A 402 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8414 (mm-30) REVERT: B 402 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8410 (mm-30) REVERT: C 402 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8409 (mm-30) REVERT: D 402 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8406 (mm-30) REVERT: E 12 LYS cc_start: 0.9230 (mmmm) cc_final: 0.8976 (mmmm) REVERT: E 13 LYS cc_start: 0.9044 (mmmt) cc_final: 0.8783 (mmmm) REVERT: E 46 GLU cc_start: 0.8371 (tt0) cc_final: 0.8099 (pt0) REVERT: E 72 ASP cc_start: 0.8383 (t0) cc_final: 0.7984 (t0) REVERT: E 82 LEU cc_start: 0.8870 (mt) cc_final: 0.8573 (mm) REVERT: F 12 LYS cc_start: 0.9232 (mmmm) cc_final: 0.8978 (mmmm) REVERT: F 13 LYS cc_start: 0.9044 (mmmt) cc_final: 0.8781 (mmmm) REVERT: F 46 GLU cc_start: 0.8383 (tt0) cc_final: 0.8114 (pt0) REVERT: F 72 ASP cc_start: 0.8383 (t0) cc_final: 0.7984 (t0) REVERT: F 82 LEU cc_start: 0.8868 (mt) cc_final: 0.8569 (mm) REVERT: G 12 LYS cc_start: 0.9228 (mmmm) cc_final: 0.8973 (mmmm) REVERT: G 13 LYS cc_start: 0.9047 (mmmt) cc_final: 0.8785 (mmmm) REVERT: G 46 GLU cc_start: 0.8383 (tt0) cc_final: 0.8114 (pt0) REVERT: G 72 ASP cc_start: 0.8366 (t0) cc_final: 0.7968 (t0) REVERT: G 82 LEU cc_start: 0.8863 (mt) cc_final: 0.8567 (mm) REVERT: H 12 LYS cc_start: 0.9231 (mmmm) cc_final: 0.8976 (mmmm) REVERT: H 13 LYS cc_start: 0.9046 (mmmt) cc_final: 0.8783 (mmmm) REVERT: H 46 GLU cc_start: 0.8382 (tt0) cc_final: 0.8109 (pt0) REVERT: H 72 ASP cc_start: 0.8374 (t0) cc_final: 0.7977 (t0) REVERT: H 82 LEU cc_start: 0.8867 (mt) cc_final: 0.8571 (mm) REVERT: I 3 VAL cc_start: 0.9386 (t) cc_final: 0.9148 (m) REVERT: I 27 GLN cc_start: 0.8810 (pt0) cc_final: 0.8600 (pm20) REVERT: J 3 VAL cc_start: 0.9386 (t) cc_final: 0.9148 (m) REVERT: J 27 GLN cc_start: 0.8806 (pt0) cc_final: 0.8596 (pm20) REVERT: K 3 VAL cc_start: 0.9386 (t) cc_final: 0.9146 (m) REVERT: K 27 GLN cc_start: 0.8807 (pt0) cc_final: 0.8596 (pm20) REVERT: L 3 VAL cc_start: 0.9377 (t) cc_final: 0.9141 (m) REVERT: L 27 GLN cc_start: 0.8808 (pt0) cc_final: 0.8596 (pm20) REVERT: L 100 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8525 (pm20) outliers start: 41 outliers final: 16 residues processed: 253 average time/residue: 0.7640 time to fit residues: 214.8531 Evaluate side-chains 246 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 229 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 3 GLN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 51 ILE 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 Chi-restraints excluded: chain L residue 100 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 93 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 25 optimal weight: 0.0000 chunk 117 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 195 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 180 optimal weight: 0.9990 chunk 148 optimal weight: 0.5980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN B 401 ASN C 401 ASN D 401 ASN E 3 GLN 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 = 0.3335 r_free = 0.3335 target = 0.094159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.074693 restraints weight = 35223.502| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.53 r_work: 0.2863 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20116 Z= 0.122 Angle : 0.567 9.245 27408 Z= 0.294 Chirality : 0.045 0.146 2960 Planarity : 0.004 0.037 3512 Dihedral : 4.709 20.852 3128 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.93 % Allowed : 15.67 % 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: 0.00 (0.17), residues: 2476 helix: -0.97 (0.68), residues: 24 sheet: 0.22 (0.16), residues: 1052 loop : -0.05 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 24 TYR 0.013 0.001 TYR D 252 PHE 0.012 0.001 PHE B 410 TRP 0.014 0.001 TRP B 178 HIS 0.004 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00285 (20056) covalent geometry : angle 0.56247 (27268) SS BOND : bond 0.00209 ( 40) SS BOND : angle 0.79480 ( 80) hydrogen bonds : bond 0.03214 ( 664) hydrogen bonds : angle 5.84740 ( 1872) link_BETA1-4 : bond 0.00366 ( 4) link_BETA1-4 : angle 1.11425 ( 12) link_BETA1-6 : bond 0.00272 ( 4) link_BETA1-6 : angle 1.28711 ( 12) link_NAG-ASN : bond 0.00223 ( 12) link_NAG-ASN : angle 1.54522 ( 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 256 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 236 time to evaluate : 0.717 Fit side-chains REVERT: A 402 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8407 (mm-30) REVERT: A 435 ASN cc_start: 0.9032 (t0) cc_final: 0.8747 (t0) REVERT: A 445 SER cc_start: 0.9154 (t) cc_final: 0.8912 (m) REVERT: B 402 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8406 (mm-30) REVERT: B 435 ASN cc_start: 0.9027 (t0) cc_final: 0.8740 (t0) REVERT: B 445 SER cc_start: 0.9151 (t) cc_final: 0.8911 (m) REVERT: C 402 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8397 (mm-30) REVERT: C 435 ASN cc_start: 0.9025 (t0) cc_final: 0.8738 (t0) REVERT: C 445 SER cc_start: 0.9152 (t) cc_final: 0.8912 (m) REVERT: D 402 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8401 (mm-30) REVERT: D 435 ASN cc_start: 0.9028 (t0) cc_final: 0.8742 (t0) REVERT: D 445 SER cc_start: 0.9142 (t) cc_final: 0.8903 (m) REVERT: E 12 LYS cc_start: 0.9228 (mmmm) cc_final: 0.8982 (mmmm) REVERT: E 13 LYS cc_start: 0.9048 (mmmt) cc_final: 0.8780 (mmmm) REVERT: E 46 GLU cc_start: 0.8356 (tt0) cc_final: 0.8115 (pt0) REVERT: E 72 ASP cc_start: 0.8386 (t0) cc_final: 0.8016 (t0) REVERT: E 80 MET cc_start: 0.7491 (ttp) cc_final: 0.7187 (ttt) REVERT: E 82 LEU cc_start: 0.8866 (mt) cc_final: 0.8572 (mm) REVERT: F 12 LYS cc_start: 0.9236 (mmmm) cc_final: 0.8991 (mmmm) REVERT: F 13 LYS cc_start: 0.9049 (mmmt) cc_final: 0.8778 (mmmm) REVERT: F 46 GLU cc_start: 0.8360 (tt0) cc_final: 0.8118 (pt0) REVERT: F 72 ASP cc_start: 0.8378 (t0) cc_final: 0.8008 (t0) REVERT: F 80 MET cc_start: 0.7487 (ttp) cc_final: 0.7188 (ttt) REVERT: F 82 LEU cc_start: 0.8865 (mt) cc_final: 0.8566 (mm) REVERT: G 12 LYS cc_start: 0.9231 (mmmm) cc_final: 0.8984 (mmmm) REVERT: G 13 LYS cc_start: 0.9049 (mmmt) cc_final: 0.8776 (mmmm) REVERT: G 46 GLU cc_start: 0.8366 (tt0) cc_final: 0.8124 (pt0) REVERT: G 72 ASP cc_start: 0.8366 (t0) cc_final: 0.7997 (t0) REVERT: G 80 MET cc_start: 0.7513 (ttp) cc_final: 0.7203 (ttt) REVERT: G 82 LEU cc_start: 0.8862 (mt) cc_final: 0.8569 (mm) REVERT: H 12 LYS cc_start: 0.9228 (mmmm) cc_final: 0.8979 (mmmm) REVERT: H 13 LYS cc_start: 0.9051 (mmmt) cc_final: 0.8780 (mmmm) REVERT: H 46 GLU cc_start: 0.8354 (tt0) cc_final: 0.8111 (pt0) REVERT: H 72 ASP cc_start: 0.8365 (t0) cc_final: 0.7996 (t0) REVERT: H 80 MET cc_start: 0.7492 (ttp) cc_final: 0.7195 (ttt) REVERT: H 82 LEU cc_start: 0.8861 (mt) cc_final: 0.8566 (mm) REVERT: I 3 VAL cc_start: 0.9398 (t) cc_final: 0.9154 (m) REVERT: I 27 GLN cc_start: 0.8816 (pt0) cc_final: 0.8607 (pm20) REVERT: J 3 VAL cc_start: 0.9395 (t) cc_final: 0.9151 (m) REVERT: J 27 GLN cc_start: 0.8812 (pt0) cc_final: 0.8603 (pm20) REVERT: K 3 VAL cc_start: 0.9397 (t) cc_final: 0.9152 (m) REVERT: K 27 GLN cc_start: 0.8812 (pt0) cc_final: 0.8601 (pm20) REVERT: L 3 VAL cc_start: 0.9384 (t) cc_final: 0.9145 (m) REVERT: L 27 GLN cc_start: 0.8811 (pt0) cc_final: 0.8601 (pm20) outliers start: 20 outliers final: 20 residues processed: 252 average time/residue: 0.7128 time to fit residues: 200.5868 Evaluate side-chains 256 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 236 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 3 GLN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 3 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 192 optimal weight: 0.9980 chunk 223 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 226 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 190 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 131 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN B 401 ASN C 401 ASN D 401 ASN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.093612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.074026 restraints weight = 35090.313| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.52 r_work: 0.2854 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2594 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= 0.146 Angle : 0.579 9.780 27408 Z= 0.299 Chirality : 0.045 0.148 2960 Planarity : 0.004 0.037 3512 Dihedral : 4.706 20.810 3128 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.87 % Allowed : 15.30 % 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: -0.00 (0.17), residues: 2476 helix: -0.89 (0.68), residues: 24 sheet: 0.21 (0.16), residues: 1052 loop : -0.05 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 24 TYR 0.014 0.001 TYR B 252 PHE 0.013 0.002 PHE D 410 TRP 0.013 0.001 TRP C 178 HIS 0.004 0.001 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00346 (20056) covalent geometry : angle 0.57547 (27268) SS BOND : bond 0.00226 ( 40) SS BOND : angle 0.76060 ( 80) hydrogen bonds : bond 0.03269 ( 664) hydrogen bonds : angle 5.84847 ( 1872) link_BETA1-4 : bond 0.00419 ( 4) link_BETA1-4 : angle 1.10687 ( 12) link_BETA1-6 : bond 0.00247 ( 4) link_BETA1-6 : angle 1.28657 ( 12) link_NAG-ASN : bond 0.00234 ( 12) link_NAG-ASN : angle 1.57447 ( 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 272 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 0.815 Fit side-chains REVERT: A 402 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8376 (mm-30) REVERT: A 435 ASN cc_start: 0.9050 (t0) cc_final: 0.8769 (t0) REVERT: A 445 SER cc_start: 0.9163 (t) cc_final: 0.8926 (m) REVERT: B 402 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8380 (mm-30) REVERT: B 435 ASN cc_start: 0.9050 (t0) cc_final: 0.8768 (t0) REVERT: B 445 SER cc_start: 0.9162 (t) cc_final: 0.8924 (m) REVERT: C 402 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8371 (mm-30) REVERT: C 435 ASN cc_start: 0.9047 (t0) cc_final: 0.8765 (t0) REVERT: C 445 SER cc_start: 0.9163 (t) cc_final: 0.8926 (m) REVERT: D 402 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8372 (mm-30) REVERT: D 435 ASN cc_start: 0.9050 (t0) cc_final: 0.8769 (t0) REVERT: D 445 SER cc_start: 0.9154 (t) cc_final: 0.8918 (m) REVERT: E 12 LYS cc_start: 0.9222 (mmmm) cc_final: 0.8982 (mmmm) REVERT: E 13 LYS cc_start: 0.9053 (mmmt) cc_final: 0.8752 (mmmm) REVERT: E 46 GLU cc_start: 0.8341 (tt0) cc_final: 0.8082 (pt0) REVERT: E 71 ARG cc_start: 0.9077 (ppt90) cc_final: 0.8646 (ptm-80) REVERT: E 72 ASP cc_start: 0.8383 (t0) cc_final: 0.8001 (t0) REVERT: E 80 MET cc_start: 0.7446 (ttp) cc_final: 0.7149 (ttt) REVERT: F 12 LYS cc_start: 0.9235 (mmmm) cc_final: 0.8995 (mmmm) REVERT: F 13 LYS cc_start: 0.9057 (mmmt) cc_final: 0.8755 (mmmm) REVERT: F 46 GLU cc_start: 0.8341 (tt0) cc_final: 0.8082 (pt0) REVERT: F 71 ARG cc_start: 0.9074 (ppt90) cc_final: 0.8642 (ptm-80) REVERT: F 72 ASP cc_start: 0.8370 (t0) cc_final: 0.7989 (t0) REVERT: F 80 MET cc_start: 0.7440 (ttp) cc_final: 0.7147 (ttt) REVERT: G 12 LYS cc_start: 0.9227 (mmmm) cc_final: 0.8987 (mmmm) REVERT: G 13 LYS cc_start: 0.9056 (mmmt) cc_final: 0.8753 (mmmm) REVERT: G 46 GLU cc_start: 0.8350 (tt0) cc_final: 0.8089 (pt0) REVERT: G 71 ARG cc_start: 0.9072 (ppt90) cc_final: 0.8635 (ptm-80) REVERT: G 72 ASP cc_start: 0.8356 (t0) cc_final: 0.7974 (t0) REVERT: G 80 MET cc_start: 0.7459 (ttp) cc_final: 0.7158 (ttt) REVERT: H 12 LYS cc_start: 0.9224 (mmmm) cc_final: 0.8982 (mmmm) REVERT: H 13 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8751 (mmmm) REVERT: H 46 GLU cc_start: 0.8343 (tt0) cc_final: 0.8082 (pt0) REVERT: H 71 ARG cc_start: 0.9071 (ppt90) cc_final: 0.8637 (ptm-80) REVERT: H 72 ASP cc_start: 0.8364 (t0) cc_final: 0.7983 (t0) REVERT: H 80 MET cc_start: 0.7438 (ttp) cc_final: 0.7135 (ttt) REVERT: I 3 VAL cc_start: 0.9406 (t) cc_final: 0.9152 (m) REVERT: I 27 GLN cc_start: 0.8813 (pt0) cc_final: 0.8593 (pm20) REVERT: J 3 VAL cc_start: 0.9403 (t) cc_final: 0.9148 (m) REVERT: J 27 GLN cc_start: 0.8810 (pt0) cc_final: 0.8590 (pm20) REVERT: K 3 VAL cc_start: 0.9405 (t) cc_final: 0.9148 (m) REVERT: K 27 GLN cc_start: 0.8812 (pt0) cc_final: 0.8589 (pm20) REVERT: L 3 VAL cc_start: 0.9388 (t) cc_final: 0.9139 (m) REVERT: L 27 GLN cc_start: 0.8811 (pt0) cc_final: 0.8591 (pm20) REVERT: L 100 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8534 (pm20) outliers start: 40 outliers final: 27 residues processed: 256 average time/residue: 0.7274 time to fit residues: 207.2676 Evaluate side-chains 256 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain D residue 127 LEU 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 33 LEU Chi-restraints excluded: chain L residue 100 GLN 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: 0.0470 chunk 134 optimal weight: 0.4980 chunk 243 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 240 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN B 401 ASN C 401 ASN D 401 ASN E 3 GLN F 3 GLN G 3 GLN H 3 GLN L 100 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.093652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.073920 restraints weight = 35429.287| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.58 r_work: 0.2843 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20116 Z= 0.150 Angle : 0.582 9.943 27408 Z= 0.300 Chirality : 0.045 0.148 2960 Planarity : 0.004 0.037 3512 Dihedral : 4.734 20.810 3128 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.54 % Allowed : 15.44 % 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: 0.00 (0.17), residues: 2476 helix: -0.89 (0.67), residues: 24 sheet: 0.23 (0.16), residues: 1028 loop : -0.06 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 24 TYR 0.014 0.001 TYR D 252 PHE 0.013 0.002 PHE B 410 TRP 0.013 0.001 TRP C 178 HIS 0.005 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00355 (20056) covalent geometry : angle 0.57777 (27268) SS BOND : bond 0.00220 ( 40) SS BOND : angle 0.72844 ( 80) hydrogen bonds : bond 0.03365 ( 664) hydrogen bonds : angle 5.88046 ( 1872) link_BETA1-4 : bond 0.00387 ( 4) link_BETA1-4 : angle 1.10117 ( 12) link_BETA1-6 : bond 0.00248 ( 4) link_BETA1-6 : angle 1.28764 ( 12) link_NAG-ASN : bond 0.00237 ( 12) link_NAG-ASN : angle 1.57773 ( 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 264 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 0.740 Fit side-chains REVERT: A 402 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8393 (mm-30) REVERT: A 435 ASN cc_start: 0.9072 (t0) cc_final: 0.8800 (t0) REVERT: A 445 SER cc_start: 0.9181 (t) cc_final: 0.8942 (m) REVERT: B 402 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8401 (mm-30) REVERT: B 435 ASN cc_start: 0.9068 (t0) cc_final: 0.8795 (t0) REVERT: B 445 SER cc_start: 0.9176 (t) cc_final: 0.8938 (m) REVERT: C 402 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8383 (mm-30) REVERT: C 435 ASN cc_start: 0.9068 (t0) cc_final: 0.8795 (t0) REVERT: C 445 SER cc_start: 0.9182 (t) cc_final: 0.8943 (m) REVERT: D 402 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8384 (mm-30) REVERT: D 435 ASN cc_start: 0.9069 (t0) cc_final: 0.8797 (t0) REVERT: D 445 SER cc_start: 0.9174 (t) cc_final: 0.8935 (m) REVERT: E 12 LYS cc_start: 0.9244 (mmmm) cc_final: 0.9012 (mmmm) REVERT: E 13 LYS cc_start: 0.9087 (mmmt) cc_final: 0.8780 (mmmm) REVERT: E 46 GLU cc_start: 0.8343 (tt0) cc_final: 0.8083 (pt0) REVERT: E 71 ARG cc_start: 0.9077 (ppt90) cc_final: 0.8660 (ptm-80) REVERT: E 72 ASP cc_start: 0.8343 (t0) cc_final: 0.7960 (t0) REVERT: E 80 MET cc_start: 0.7425 (ttp) cc_final: 0.7076 (ttt) REVERT: F 12 LYS cc_start: 0.9253 (mmmm) cc_final: 0.9021 (mmmm) REVERT: F 13 LYS cc_start: 0.9094 (mmmt) cc_final: 0.8786 (mmmm) REVERT: F 46 GLU cc_start: 0.8345 (tt0) cc_final: 0.8088 (pt0) REVERT: F 71 ARG cc_start: 0.9075 (ppt90) cc_final: 0.8655 (ptm-80) REVERT: F 72 ASP cc_start: 0.8338 (t0) cc_final: 0.7956 (t0) REVERT: F 80 MET cc_start: 0.7448 (ttp) cc_final: 0.7095 (ttt) REVERT: G 12 LYS cc_start: 0.9247 (mmmm) cc_final: 0.9014 (mmmm) REVERT: G 13 LYS cc_start: 0.9089 (mmmt) cc_final: 0.8779 (mmmm) REVERT: G 46 GLU cc_start: 0.8348 (tt0) cc_final: 0.8087 (pt0) REVERT: G 71 ARG cc_start: 0.9075 (ppt90) cc_final: 0.8653 (ptm-80) REVERT: G 72 ASP cc_start: 0.8322 (t0) cc_final: 0.7940 (t0) REVERT: G 80 MET cc_start: 0.7460 (ttp) cc_final: 0.7099 (ttt) REVERT: H 12 LYS cc_start: 0.9244 (mmmm) cc_final: 0.9011 (mmmm) REVERT: H 13 LYS cc_start: 0.9087 (mmmt) cc_final: 0.8775 (mmmm) REVERT: H 46 GLU cc_start: 0.8345 (tt0) cc_final: 0.8083 (pt0) REVERT: H 71 ARG cc_start: 0.9073 (ppt90) cc_final: 0.8656 (ptm-80) REVERT: H 72 ASP cc_start: 0.8329 (t0) cc_final: 0.7947 (t0) REVERT: H 80 MET cc_start: 0.7431 (ttp) cc_final: 0.7080 (ttt) REVERT: I 3 VAL cc_start: 0.9425 (t) cc_final: 0.9176 (m) REVERT: I 27 GLN cc_start: 0.8812 (pt0) cc_final: 0.8591 (pm20) REVERT: J 3 VAL cc_start: 0.9423 (t) cc_final: 0.9173 (m) REVERT: J 27 GLN cc_start: 0.8811 (pt0) cc_final: 0.8590 (pm20) REVERT: K 3 VAL cc_start: 0.9422 (t) cc_final: 0.9172 (m) REVERT: K 27 GLN cc_start: 0.8812 (pt0) cc_final: 0.8589 (pm20) REVERT: L 3 VAL cc_start: 0.9394 (t) cc_final: 0.9139 (m) REVERT: L 27 GLN cc_start: 0.8813 (pt0) cc_final: 0.8592 (pm20) REVERT: L 100 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8596 (pm20) outliers start: 33 outliers final: 24 residues processed: 250 average time/residue: 0.7345 time to fit residues: 204.4695 Evaluate side-chains 252 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 100 GLN 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: 0.7980 chunk 146 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 170 optimal weight: 0.4980 chunk 165 optimal weight: 0.7980 chunk 208 optimal weight: 0.0870 chunk 211 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN B 401 ASN C 401 ASN D 401 ASN E 3 GLN F 3 GLN G 3 GLN H 3 GLN L 100 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.094464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.074840 restraints weight = 35245.597| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.56 r_work: 0.2863 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20116 Z= 0.125 Angle : 0.576 9.341 27408 Z= 0.298 Chirality : 0.045 0.149 2960 Planarity : 0.004 0.037 3512 Dihedral : 4.670 20.061 3128 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.35 % Allowed : 15.67 % Favored : 82.98 % 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: -0.00 (0.17), residues: 2476 helix: -0.93 (0.67), residues: 24 sheet: 0.19 (0.16), residues: 1028 loop : -0.03 (0.17), residues: 1424 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 B 410 TRP 0.015 0.001 TRP C 178 HIS 0.004 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00294 (20056) covalent geometry : angle 0.57256 (27268) SS BOND : bond 0.00191 ( 40) SS BOND : angle 0.68517 ( 80) hydrogen bonds : bond 0.03299 ( 664) hydrogen bonds : angle 5.83179 ( 1872) link_BETA1-4 : bond 0.00375 ( 4) link_BETA1-4 : angle 1.07890 ( 12) link_BETA1-6 : bond 0.00284 ( 4) link_BETA1-6 : angle 1.27614 ( 12) link_NAG-ASN : bond 0.00221 ( 12) link_NAG-ASN : angle 1.52402 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7380.72 seconds wall clock time: 126 minutes 51.06 seconds (7611.06 seconds total)